US00787 1991 B2

(12) United States Patent (10) Patent No.: US 7,871,991 B2 Boojamra et al. (45) Date of Patent: Jan. 18, 2011

(54) PHOSPHONATE ANALOGS OF HIV EP O 632 048 3, 2001 INHIBITOR COMPOUNDS RU 21.06353 3, 1998 RU 21882O3 8, 2002 (75) Inventors: Constantine G. Boojamra, San WO WO91, 19721 12/1991 Francisco, CA (US); Kuei-Ying Lin, WO WO-92fOO988 1, 1992 Fremont, CA (US); Richard Mackman, WO WO92, 13869 8, 1992 Millbrae, CA (US); David Y. WO WO-93/24510 12/1993 Markevitch, Los Angeles, CA (US); WO WO94,21604 9, 1994 Oleg V. Petrakovsky, San Mateo, CA WO WO 3.O792O 1995 (US); Adrian S. Ray, San Mateo, CA W WOCS: A * g.. (US); Lijun Zhang, Palo Alto, CA (US) WO WOO3,O90690 11, 2003 WO WOO3,091,264 11, 2003 (73) Assignee: stad Sciences, Inc., Foster City, CA WO WO 2004/096,233 1, 2004 (US) WO WO 2004/096,235 1, 2004 WO WO 2004/096286 1, 2004 (*) Notice: Subject to any disclaimer, the term of this WO WO 2005/O12324 2, 2005 patent is extended or adjusted under 35 WO WO 2005/063751 7/2005 U.S.C. 154(b) by 506 days. WO WO 2006/O15262 2, 2006

(21) Appl.ppl. No.: 11/190,2259 WO WO-2006/11 O157 10, 2006 (22) Filed: Jul. 26, 2005 OTHER PUBLICATIONS (65) Prior Publication Dat Lee, Journal of Medicinal Chemistry (1999), 42(7), 1320-1328.* O DO Moon, Journal of the Chemical Society, Perkin Transactions 1 US 2007/OO497.54 A1 Mar. 1, 2007 (2002), (15), 1800-1804.* Chong J. Med. Chem. 45 (22), 4888-4898, 2002.* Related U.S. Application Data Jeong, J. Med. Chem., 46 (2), 201-203, 2003.* Anan Eva et al. "(2-Iodoethyl)Phosphonic Derivatives.” 53(3):480 (60) Provisional application No. 60/591,811, filed on Jul. 483; J. Gen. Chem. USSR, 1983. 27, 2004. Anderson et al. “2-Chloro-4(R),5(R)-dimethyl-2-oxo-1,3,2- dioxaphospholane, a New Chiral Derivatizing Agent.” 49: 1304 (51) Int. C. 1305; J Org Chem, 1984. C7F 9/656 (2006.01) Asante-Appiah et al.'HIV-1 Integrase: Structural Organization, A6 IK3I/675 (2006.01) Conformational Changes, and Catalysis,” 52:351-369:Advances in A6IP3 L/18 (2006.01) Virus Research, 1999. CO7D 473/40 (2006.01) Alexander et al. "Investigation of (Oxodioxolenyl)methyl Carbam ates as Nonchiral Bioreversible Prodrug Moieties for Chiral Amines.” CO7D 473/34 (2006.01) 39:480-486;J Med Chem, 1996. CO7D 473/30 (2006.01) Balsigeretal."Synthesis of Potential Anticancer Agents. XVIII. Ana (52) U.S. Cl...... 514/81: 544/244; 544/276; logs of Carbamoyl Phosphate.” 24:434-436:JOrg Chem, 1959. 544/264; 54.4/265 Balthazor et al."Nickel-Catalyzed Arbuzov Reaction: Mechanistic (58) Field of Classification Search ...... 544/277, Observations.”45:5425-5426:J Org Chem, 1980. 544/244: 514/81, 263.4 Beusen et al. “Solid-State Nuclear Magnetic Resonance Anlysis of See application file for complete search history. the Conformation of an Inhibitor Bound to Thermolysin' 38: 2742 2747:J Med Chem, 1995. (56) References Cited Bundgaard et al."Design and Application of Prodrugs.” pp. 113 191:Textbook of Drug Design and Development, 1991. U.S. PATENT DOCUMENTS Burger et al. "Monoesters and Ester-amidates of Aromatic 4,816,570 A 3/1989 Farquhar Phosphonic Acids” 79:3575-3579;J Am ChemSoc. 1957. 4,968,788 A 1 1/1990 Farquhar Barre-Sinoussi, Francoise. “HIV as the cause of AIDS.” 348:31-35; 5,663,159 A 9/1997 Starrett, Jr. et al. Lancet, 1996. 5,792,756 A 8/1998 Starrett, Jr. et al. 6,018,049 A 1/2000 Hajima et al. (Continued) 6,312,662 B1 1 1/2001 Erion et al. Primary Examiner Mark L. Berch 7.358,261 B2 * 4/2008 Carson et al...... 514,311 2002/0103378 A1 8, 2002 Ellis (74) Attorney, Agent, or Firm Allan Kutzenco 2002/01 19443 A1 8, 2002 Becker et al. 2005/0037925 A1 2/2005 Tsukamoto et al...... 504.238 (57) ABSTRACT 2007/0225249 A1* 9, 2007 Shi ...... 514,49 2008/0207620 A1* 8, 2008 Desai et al...... 514,238.2 The invention is related to phosphorus substituted anti-viral 2009/0012037 A1* 1/2009 Boojamra et al...... 514.48 inhibitory compounds, compositions containing Such com 2009/0202470 A1* 8/2009 Boojamra et al...... 424/85.2 pounds, and therapeutic methods that include the administra 2010/0093667 A1* 4/2010 Graetz et al...... 514/81 tion of such compounds, as well as to processes and interme diates useful for preparing Such compounds. FOREIGN PATENT DOCUMENTS EP 347852 A2 * 12/1989 18 Claims, No Drawings US 7,871.991 B2 Page 2

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(1999) “The Presence of Substituents on the Aryl Sun et al.''A General Synthesis of Dioxolenone Prodrug Moi Moiety of the Aryl Phosphoramidate Derivative of D4T Enhances eties'43:1 161-1164:Tet Lett.2002. Anti-HIV Efficacy in Cell Culture: A Structure-Activity Relation Szabo et al. “Solid Phase Synthesis of 5-Methylenephosphonate ship” Journal of Medicinal Chemistry 42(3):393-399. DNA” 14(3-5):871-874;Nucls & Nuclt, 1995. * cited by examiner US 7,871,991 B2 1. 2 PHOSPHONATE ANALOGS OF HIV Drugs approved in the United States for AIDS therapy INHIBITOR COMPOUNDS include nucleoside inhibitors of RT (Smith et al (1994) Clini cal Investigator; 17:226-243), protease inhibitors and non This non-provisional application claims the benefit of Pro nucleoside RT inhibitors (NNRTI), (Johnson et al (2000) visional Application No. 60/591,811, filed Jul. 27, 2004, and 5 Advances in Internal Medicine, 45 (1-40; Porche DJ (1999) all of which are incorporated herein by reference. Nursing Clinics of North America, 34:95-112). Inhibitors of HIV protease are useful to limit the establish FIELD OF THE INVENTION ment and progression of infection by therapeutic administra tion as well as in diagnostic assays for HIV. Protease inhibitor The invention relates generally to compounds with antivi 10 drugs approved by the FDA include: ral activity and more specifically with anti-HIV properties. saquinavir (Invirase(R). Fortovase(R), Hoffman-La Roche, EP-00432695 and EP-00432694) BACKGROUND OF THE INVENTION ritonavir (Norvir R, Abbott Laboratories) indinavir (Crixivan(R), Merck & Co.) AIDS is a major public health problem worldwide. 15 nelfinavir (Viracept R, Pfizer) Although drugs targeting HIV viruses are in wide use and amprenavir (Agenerase(R), GlaxoSmithKline, Vertex Phar have shown effectiveness, toxicity and development of resis maceuticals) tant Strains have limited their usefulness. Assay methods lopinavir/ritonavir (Kaletra R, Abbott Laboratories) capable of determining the presence, absence or amounts of Experimental protease inhibitor drugs include: HIV viruses are of practical utility in the search for inhibitors fosamprenavir (GlaxoSmithKline, Vertex Pharmaceuti as well as for diagnosing the presence of HIV. cals) Human immunodeficiency virus (HIV) infection and tipranavir (Boehringer Ingelheim) related disease is a major public health problem worldwide. atazanavir (Bristol-Myers Squibb). The retrovirus human immunodeficiency virus type 1 (HIV There is a need for anti-HIV therapeutic agents, i.e. drugs 1), a member of the primate lentivirus family (DeClercq E 25 having improved antiviral and pharmacokinetic properties (1994) Annals of the New York Academy of Sciences, 724: with enhanced activity against development of HIV resis 438-456; Barre-Sinoussi F (1996) Lancet, 348:31-35), is gen tance, improved oral bioavailability, greater potency and erally accepted to be the causative agent of acquired immu extended effective half-life in vivo. New HIV antivirals nodeficiency syndrome (AIDS) Tarrago et al. FASEB Journal should be active against mutant HIV strains, have distinct 1994, 8:497-503). AIDS is the result of repeated replication 30 resistance profiles, fewer side effects, less complicated dos of HIV-1 and a decrease in immune capacity, most promi ing schedules, and orally active. In particular, there is a need nently a fall in the number of CD4+ lymphocytes. The mature for a less onerous dosage regimen, Such as one pill, once per virus has a single stranded RNA genome that encodes 15 day. Although drugs targeting HIV RT are in wide use and proteins (Frankel et al. (1998) Annual Review of Biochemis have shown effectiveness, particularly when employed in try, 67:1-25; Katz et al. (1994) Annual Review of Biochemis 35 combination, toxicity and development of resistant strains try, 63:133-173), including three key enzymes: (i) protease have limited their usefulness. (Prt) (von der Helm K(1996) Biological Chemistry, 377:765 Combination therapy of HIV antivirals has proven to be 774); (ii) reverse transcriptase (RT) (Hottiger et al. (1996) highly effective in Suppressing viral replication to unduanti Biological Chemistry Hoppe-Seyler; 377: 97-120), an enzyme fiable levels for a sustained period of time. Also, combination unique to retroviruses; and (iii) integrase (Asante et al. (1999) 40 therapy with RT and other HIV inhibitors have shown syner Advances in Virus Research 52:351–369; Wlodawer A (1999) gistic effects in Suppressing HIV replication. Unfortunately, Advances in Virus Research 52:335-350; Esposito et al. many patients currently fail combination therapy due to the (1999) Advances in Virus Research 52:319-333). Protease is development of drug resistance, non-compliance with com responsible for processing the viral precursor polyproteins, plicated dosing regimens, pharmacokinetic interactions, tox integrase is responsible for the integration of the double 45 icity, and lack of potency. Therefore, there is a need for new stranded DNA form of the viral genome into host DNA and HIV RT inhibitors that are synergistic in combination with RT is the key enzyme in the replication of the viral genome. In other HIV inhibitors. viral replication, RT acts as both an RNA- and a DNA-depen Improving the delivery of drugs and other agents to target dent DNA polymerase, to convert the single stranded RNA cells and tissues has been the focus of considerable research genome into double stranded DNA. Since virally encoded 50 for many years. Though many attempts have been made to Reverse Transcriptase (RT) mediates specific reactions dur develop effective methods for importing biologically active ing the natural reproduction of the virus, inhibition of HIV RT molecules into cells, both in vivo and in vitro, none has is an important therapeutic target for treatment of HIV infec proved to be entirely satisfactory. Optimizing the association tion and related disease. of the inhibitory drug with its intracellular target, while mini Sequence analysis of the complete genomes from several 55 mizing intercellular redistribution of the drug, e.g. to neigh infective and non-infective HIV-isolates has shed consider boring cells, is often difficult or inefficient. able light on the make-up of the virus and the types of mol Most agents currently administered to a patient parenter ecules that are essential for its replication and maturation to ally are not targeted, resulting in systemic delivery of the an infective species. The HIV protease is essential for the agent to cells and tissues of the body where it is unnecessary, processing of the viral gag and gag-pol polypeptides into 60 and often undesirable. This may result in adverse drug side mature virion proteins. L. Ratner, et al., Nature, 313:277-284 effects, and often limits the dose of a drug (e.g., cytotoxic (1985); L. H. Pearl and W. R. Taylor, Nature, 329:351 (1987). agents and other anti-cancer or anti-viral drugs) that can be HIV exhibits the same gag?pol/env organization seen in other administered. By comparison, although oral administration retroviruses. L. Ratner, et al., above; S. Wain-Hobson, et al., of drugs is generally recognized as a convenient and eco Cell, 40:9-17 (1985): R. Sanchez-Pescador, et al., Science, 65 nomical method of administration, oral administration can 227:484-492 (1985); and M. A. Muesing, et al., Nature, 313: result in either (a) uptake of the drug through the cellular and 450-458 (1985). tissue barriers, e.g. blood/brain, epithelial, cell membrane, US 7,871,991 B2 3 resulting in undesirable systemic distribution, or (b) tempo rary residence of the drug within the gastrointestinal tract. -continued Accordingly, a major goal has been to develop methods for A is specifically targeting agents to cells and tissues. Benefits of Y2 Such treatment includes avoiding the general physiological 5 Y2 Yw3. effects of inappropriate delivery of such agents to other cells 2 2 and tissues, such as uninfected cells. Intracellular targeting R R af2. 2. may be achieved by methods and compositions which allow A is: accumulation or retention of biologically active agents inside 10 cells. Yl Yl SUMMARY OF THE INVENTION

The present invention provides novel compounds with HIV 15 activity, i.e. novel human retroviral RT inhibitors. Therefore, the compounds of the invention may inhibit retroviral RT and thus inhibit the replication of the virus. They are useful for Y' is independently O, S, N(R), N(O)(R), N(OR), N(O) treating human patients infected with a human retrovirus, (OR), or N(N(R)(R)); such as human immunodeficiency virus (strains of HIV-1 or Y is independently a bond,Y, N(R), N(O)(R), N(OR), HIV-2) or human T-cell leukemia viruses (HTLV-I or HTLV N(O)(OR), N(N(R)(R)). —S(O)—, or —S(O)—S II) which results in acquired immunodeficiency syndrome (O) ; (AIDS) and/or related diseases. The present invention Y is O, S(O), S, or C(R): includes novel phosphonate HIV RT inhibitor compounds 25 R’ is independently H, R', R. W., a protecting group, or and phosphonate analogs of known approved and experimen the formula: tal protease inhibitors. The compounds of the invention optionally provide cellular accumulation as set forth below. Yl R. R. Yl The present invention relates generally to the accumulation 30 or retention of therapeutic compounds inside cells. The inven R’s tion is more particularly related to attaining high concentra Y2 Y2 Y2 tions of phosphonate-containing molecules in HIV infected M1C M1 cells. Intracellular targeting may be achieved by methods and compositions which allow accumulation or retention of bio 35 wherein: logically active agents inside cells. Such effective targeting R’ is independently H. W., R or a protecting group: may be applicable to a variety of therapeutic formulations and R" is independently H or alkyl of 1 to 18 carbon atoms: procedures. RandR'' are independently H, R', R, or R' wherein each Compositions of the invention include new RT compounds R" is independently substituted with 0 to 3 R groups or, when having at least one phosphonate group. The invention 40 taken together at a carbon atom, two R groups form a ring of includes all known approved and experimental protease 3 to 8 and the ring may be substituted with 0 to 3 R groups; inhibitors with at least one phosphonate group. R is R. R. R. R., or R, provided that when R is In one aspect, the invention includes compounds, including bound to a heteroatom, then R is R or R': enantiomers thereof, of Formula 1A, or a pharmaceutically R is R, CN, N or NO; acceptable salt or solvate thereof, 45 R is (—Y'); R is R, N(R)(R), SR, S(O)R', S(O),R, S(O)(OR), S(O)(OR), OC(Y)R’, OC(Y)OR, 1A OC(Y)(N(R)(R)), SC(Y)R', SC(Y)OR', SC A9 Y3 Base (Y)(N(R')(R)), N(R)C(Y)R’, N(R)C(Y)OR, or 50 N(R)C(Y)(N(R)(R)); R2 R2 Riis C(Y)R’, C(Y)OR or C(Y)(N(R)(R)); R is F, Cl, Br or I; R2a R3a R" is an alkyl of 1 to 18 carbon atoms, alkenyl of 2 to 18 55 carbon atoms, or alkynyl of 2 to 18 carbon atoms; wherein: R is Hor R, wherein each R is substituted with 0 to 3 R' groups: A is A, A, or A: W is W or W5; W is R., C(Y)R, C(Y)W, SOR, or 60 —SOW: A is W is carbocycle or heterocycle wherein W is indepen Y2 dently substituted with 0 to 3 R' groups; Y2 Yw6. W is W independently substituted with 1, 2, or 3 A groups: 2 2 R R af2. 65 M2 is 0, 1 or 2: 2. M12a is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; M12b is 0, 1, 2, 3, 4, 5,s 6, 7, 8, 9, 10, 11 or 12; US 7,871,991 B2 5 M1a, M1 c, and M1d are independently 0 or 1; and M12c is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; provided that the compound of Formula 1A is not of the Structure 556-E.6

556-E.6 NH2 N O 2 N 10 HON P O O N / N Ho1'N1 N 2/ wherein

15 R’ is halo, NH, R or H: F R2 is —(R), (X), (R), (X), (R), (N(R)), X independently is O or S; or its ethyl diester. M1-m3 independently are 0-1; M4-m3 independently are 0-1 n is 0-2: 556-E.6 NH2 R’ independently is unsubstituted C-Cls alkyl, Ca-C1s N alkenyl, C-C arylalkenyl, C-Cs arylalkynyl, C-Cls O 2 N 25 alkynyl, C-C-alkylamino-C-C alkyl, Cs-Cs aralkyl, HON P O O N W N C-Cls heteroaralkyl, Cs-Caryl or C-C heterocycloalkyl, Ho1 N1 -/ or said groups optionally substituted with 1 to 3 of halo, N alkoxy, alkylthio, nitro, OH. =O, haloalkyl, CN, R' or N: R' independently is selected from the group consisting of F 30 H, C-C alkyl, C-C alkenyl, C-Cs arylalkenyl, C-Cls arylalkynyl, C-C alkynyl, C-C-alkylamino-C-C, DETAILED DESCRIPTION OF EXEMPLARY alkyl, Cs-Cs aralkyl, C-Cls heteroaralkyl, Cs-Caryl, EMBODIMENTS 35 —C(O)R. —C(O)OR and C-C heterocycloalkyl, optionally both R' of N(R') are joined together with N Reference will now be made in detail to certain embodi to form a saturated or unsaturated Cs-C heterocycle ments of the invention, examples of which are illustrated in containing one or two N heteroatoms and optionally an the accompanying structures and formulas. While the inven 40 additional O or Sheteroatom, tion will be described in conjunction with the enumerated and the foregoing R'groups which are substituted with 1 embodiments, it will be understood that they are not intended to 3 of halo, alkoxy, alkythio, nitro, OH, =O, haloalkyl, to limit the invention to those embodiments. On the contrary, CN or N.; and the invention is intended to cover all alternatives, modifica Z is N or C(R3), provided that the heterocyclic nucleus tions, and equivalents, which may be included within the 45 scope of the present invention as defined by the embodiments. varies from purine by no more than two Z. Alkyl, alkynyl and alkenyl groups in the formula (1) groups Definitions are normal, secondary, tertiary or cyclic. Unless stated otherwise, the following terms and phrases as Ordinarily, n is 1, m1 is 0 or 1, R is C1-C3 alkyl, R is H, used herein are intended to have the following meanings: 50 m2-ms are all 0; one or two R' groups are not H; R' is C-C, alkyl (including C-C cycloalkyl, particularly cyclopropyl); When tradenames are used herein, applicants intend to inde and one R' is H. IfZ is C(R3) at the 5 and/or 7 positions, R pendently include the tradename product and the active phar is halo, usually fluoro. maceutical ingredient(s) of the tradename product. 55 The compounds of this invention are noteworthy in their “Base' is a term of art in the nucleoside and nucleotide ability to act effectively against HIV which bears resistance fields. It is frequently abbreviated as “B” Within the context mutations in the polymerase gene, in particular, HIV which is of the present invention, “Base' or “B” mean, without limi resistant to tenofovir, FTC and other established anti-HIV tation, at least those bases know to the ordinary artisan or agents. taught in the art. Exemplary definitions 1) to 10) below are 60 illustrative. Preferable “Bases” or “Bs' include purines, more 1) B is a heterocyclic amine base. preferably purines of 1) to 10) below. More preferably yet, In the specification “Heterocyclic amine base' is defined as “Base” or “B” means the purines of 4) to 10) below. Most a monocyclic, bicyclic, or polycyclic ring system comprising preferably “Base” or “B” means 10) below. 65 one or more nitrogens. For example, B includes the naturally In embodiments of this invention, Base or B is a group occurring heterocycles found in nucleic acids, nucleotides having structure (1) below and nucleosides, and analogs thereof. US 7,871,991 B2 7 2) B is selected from the group consisting of -continued O O

N HN y and HN e T16 N N sx S. 10

wherein: To is H, OH, F, Cl, Br, I, OT, SH, ST, NH, or NHTs: 15 T is N, CF, CC1, CBr, CI, CT, CST, or COT: T is N or CH: T is N, CH, CCN, CCF, CC=CH or CC(O)NH; Ta is H, OH, NH, SH, SCH SCHCH SCHC=CH, SCH-CH=CH, SCH7, NH(CH), N(CH), NH(CHCH), N(CHCH), NH(CHC=CH), NH(CH, CH=CH-), NH(CH) or halogen (F, Cl, Br or I): T is H, OH, F, Cl, Br, I, SCH SCHCH SCHC=CH, SCH-CH=CH SCH, OT, NH, or NHTs; and T is O.S or Se. 25 T, is Calkyl (including CH, CHCH, CHC=CH, CH-CH=CH, and CHz); Ts is Calkyl (including CH, CHCH, CHC=CH, wherein: CH-CH=CH, and CHz); U, G, and Jare each independently CH or N: To is H. Coalkyl, Coalkenyl, Coalkynyl or C7 aryl D is N, CH, C CN, C NO, C-C alkyl, C. NH 30 alkyl unsubstituted or substituted by OH, O, N, F, Cl, Br or I CONH, C CONTT, C CSNTT C COOT, (including CH, CHCH, CH=CH, CH=CHBr, C-C(—NH)NH, C-hydroxy, C–C alkoxy, C-amino, CHCHCl, CHCHF, CHC=CH, CH-CH=CH, CH, C Calkylamino, C-di(Calkyl)amino, C-halogen, C-(1, CHOH, CHOCH, CHOCH, CHOC=CH, 3-oxazol-2-yl), C-(1,3 thiazol-2-yl), or C-(imidazol-2-yl); CHOCH-CH=CH, CHCH, CHCH-OH, wherein alkyl is unsubstituted or substituted with one to three 35 CHCHOCH, CHCHOCH, CHCHOC=CH, groups independently selected from halogen, amino, CHCHOCH-CH=CH, CHCHOCH: hydroxy, carboxy, and C alkoxy; 4) B is adenine, guanine, cytosine, uracil, thymine, 7-dea E is N or CTs: Zaadenine, 7-deazaguanine, 7-deaza-8-azaguanine, 7-deaza W is O or S; 8-azaadenine, inosine, nebularine, nitropyrrole, nitroindole, T is H. Calkyl, Calkenyl, C-alkynyl, Calky 40 2-aminopurine, 2-amino-6-chloropurine, 2,6-diaminopurine, lamino, CF, or halogen; hypoxanthine, pseudouridine, pseudocytosine, pseudoisocy T is H, OH, SH, NH, Calkylamino, di(Calkyl) tosine, 5-propynylcytosine, isocytosine, isoguanine, 7-deaza amino, C. cycloalkylamino, halo, Calkyl, Calkoxy, or guanine, 2-thiopyrimidine, 6-thioguanine, 4-thiothymine, CF: 4-thiouracil, O'-methylguanine, N'-methyladenine, O-me T is H. amino, Calkylamino, C. cycloalkylamino, or 45 thylthymine, 5,6-dihydrothymine, 5,6-dihydrouracil, 4-me di(Calkyl)amino; thylindole, or pyrazolo 3,4-dipyrimidine; T is H. halo, CN, carboxy, Calkyloxycarbonyl, N. 5) B is amino, Calkylamino, di(Calkyl)amino, hydroxy, hypoxanthine, Calkoxy, Calkylthio, Calkylsulfonyl, or (C. inosine, alkyl)o aminomethyl; 50 thymine, Ts is independently H or Calkyl; and uracil, T is H. CF, Calkyl, amino, Calkylamino, Cecy Xanthine, cloalkylamino, or di(Calkyl)amino; an 8-aza derivative of 2-aminopurine, 2,6-diaminopurine, 55 2-amino-6-chloropurine, hypoxanthine, inosine or Xanthine; 3) B is selected from a 7-deaza-8-aza derivative of adenine, guanine, 2-ami nopurine, 2,6-diaminopurine, 2-amino-6-chloropurine, hypoxanthine, inosine or Xanthine; a 1-deaza derivative of 2-aminopurine, 2,6-diaminopurine, 60 2-amino-6-chloropurine, hypoxanthine, inosine or Xanthine; a 7-deaza derivative of 2-aminopurine, 2,6-diaminopurine, 2-amino-6-chloropurine, hypoxanthine, inosine or Xanthine; a 3-deaza derivatives of 2-aminopurine, 2,6-diaminopu rine, 2-amino-6-chloropurine, hypoxanthine, inosine or Xan 65 thine; 6-azacytosine; 5-fluorocytosine; US 7,871,991 B2 10 5-chlorocytosine; as functional groups or moieties that comprise a prodrug 5-iodocytosine; moiety that can separate from a compound so that the com 5-bromocytosine; pound retains a phosphorous having Such characteristics. In 5-methylcytosine; another specific embodiment of the invention, the terms 5-bromovinyluracil; “phosphonate' and “phosphonate group' include functional 5-fluorouracil; groups or moieties within a molecule that comprises a phos 5-chlorouracil; phorous that is 1) single-bonded to a carbon, 2) double 5-iodouracil; bonded to an oxygen, 3) single-bonded to an oxygen or nitro 5-bromouracil; gen, and 4) single-bonded to another oxygen or nitrogen, as 5-trifluoromethyluracil; 10 well as functional groups or moieties that comprise a prodrug 5-methoxymethyluracil; moiety that can separate from a compound so that the com 5-ethynyluracil; or pound retains a phosphorous having such characteristics. 5-propynyluracil The term “prodrug as used herein refers to any compound 6) Bisaguanyl, 3-deazaguanyl, 1-deazaguanyl, 8-azaguanyl. that when administered to a biological system generates the 7-deazaguanyl, adenyl, 3-deazaadenyl, 1-deZazadenyl, 15 drug Substance, i.e. active ingredient, as a result of spontane 8-azaadenyl, 7-deaZaadenyl, 2,6-diaminopurinyl, 2-ami ous chemical reaction(s), enzyme catalyzed chemical reac tion(s), photolysis, and/or metabolic chemical reaction(s). A nopurinyl, 6-chloro-2-aminopurinyl 6-thio-2-aminopurinyl, prodrug is thus a covalently modified analog or latent form of cytosinyl, 5-halocytosinyl, or 5-(C-C alkyl)cytosinyl. a therapeutically-active compound. 7) B is “Prodrug moiety” refers to a labile functional group which separates from the active inhibitory compound during metabolism, systemically, inside a cell, by hydrolysis, enzy T8 matic cleavage, or by some other process (Bundgaard, Hans, “Design and Application of Prodrugs' in A Textbook of Drug S N 25 Design and Development (1991), P. Krogsgaard-Larsen and T7= H. Bundgaard, Eds. Harwood Academic Publishers, pp. 113 2 191). Enzymes which are capable of an enzymatic activation N N T9 mechanism with the phosphonate prodrug compounds of the invention include, but are not limited to, amidases, esterases, 30 microbial enzymes, phospholipases, cholinesterases, and phosphases. Prodrug moieties can serve to enhance solubility, wherein T7 and T are each independently O or S and T is H. absorption and lipophilicity to optimize drug delivery, bio amino, hydroxy, Cl, or Br. availability and efficacy. A prodrug moiety may include an 8) B is thymine, adenine, uracil, a 5-halouracil, a 5-alkylu active metabolite or drug itself. racil, guanine, cytosine, a 5-halocytosine, a 5-alkylcytosine, 35 Exemplary prodrug moieties include the hydrolytically or 2,6-diaminopurine. sensitive or labile acyloxymethylesters —CHC(=O)R and acyloxymethyl carbonates —CHC(=O)CR where R is 9) B is guanine, cytosine, uracil, or thymine. C-C alkyl, C-C substituted alkyl, Co-Co aryl or Co-Co 10) B is adenine. substituted aryl. The acyloxyalkyl ester was first used as a “Bioavailability” is the degree to which the pharmaceuti 40 prodrug strategy for carboxylic acids and then applied to cally active agent becomes available to the target tissue after phosphates and phosphonates by Farquhar et al. (1983) J. the agents introduction into the body. Enhancement of the Pharm. Sci. 72: 324; also U.S. Pat. Nos. 4,816,570, 4,968, bioavailability of a pharmaceutically active agent can provide 788, 5,663,159 and 5,792,756. Subsequently, the acyloxy a more efficient and effective treatment for patients because, alkyl ester was used to deliver phosphonic acids across cell for a given dose, more of the pharmaceutically active agent 45 membranes and to enhance oral bioavailability. A close vari will be available at the targeted tissue sites. ant of the acyloxyalkyl ester, the alkoxycarbonyloxyalkyl The terms “phosphonate' and “phosphonate group' ester (carbonate), may also enhance oral bioavailability as a include functional groups or moieties within a molecule that prodrug moiety in the compounds of the combinations of the comprises a phosphorous that is 1) single-bonded to a carbon, invention. An exemplary acyloxymethyl ester is pivaloy 2) double-bonded to a heteroatom, 3) single-bonded to a 50 loxymethoxy, (POM) —CHOC(=O)C(CH). An exem heteroatom, and 4) single-bonded to another heteroatom, plary acyloxymethyl carbonate prodrug moiety is pivaloy wherein each heteroatom can be the same or different. The loxymethylcarbonate (POC) —CHC(=O)CC(CH). terms “phosphonate' and “phosphonate group' also include The phosphonate group may be a phosphonate prodrug functional groups or moieties that comprise a phosphorous in moiety. The prodrug moiety may be sensitive to hydrolysis, the same oxidation state as the phosphorous described above, 55 Such as, but not limited to a pivaloyloxymethyl carbonate as well as functional groups or moieties that comprise a (POC) or POM group. Alternatively, the prodrug moiety may prodrug moiety that can separate from a compound so that the be sensitive to enzymatic potentiated cleavage, such as a compound retains a phosphorous having the characteristics lactate ester or a phosphonamidate-ester group. described above. For example, the terms “phosphonate” and Aryl esters of phosphorus groups, especially phenyl esters, “phosphonate group' include phosphonic acid, phosphonic 60 are reported to enhance oral bioavailability (De Lombaert et monoester, phosphonic diester, phosphonamidate, and phos al. (1994).J. Med. Chem. 37: 498). Phenyl esters containing a phonthioate functional groups. In one specific embodiment of carboxylic ester ortho to the phosphate have also been the invention, the terms “phosphonate' and “phosphonate described (Khamnei and Torrence, (1996) J. Med. Chem. group' include functional groups or moieties within a mol 39:4109-4115). Benzyl esters are reported to generate the ecule that comprises a phosphorous that is 1) single-bonded 65 parent phosphonic acid. In some cases, Substituents at the to a carbon, 2) double-bonded to an oxygen, 3) single-bonded ortho- or para-position may accelerate the hydrolysis. Benzyl to an oxygen, and 4) single-bonded to another oxygen, as well analogs with an acylated phenol or an alkylated phenol may US 7,871,991 B2 11 12 generate the phenolic compound through the action of Physiologically acceptable salts of a compound of an enzymes, e.g., esterases, oxidases, etc., which in turn under hydroxy group include the anion of said compound in com goes cleavage at the benzylic C-O bond to generate the bination with a suitable cation such as Na" and NX phosphoric acid and the quinone methide intermediate. (wherein X is independently selected from Hora C-C alkyl Examples of this class of prodrugs are described by Mitchell group). et al. (1992).J. Chem. Soc. Perkin Trans. II 2345; Glazier WO For therapeutic use, salts of active ingredients of the com 91/19721. Still other benzylic prodrugs have been described pounds of the invention will be physiologically acceptable, containing a carboxylic ester-containing group attached to i.e. they will be salts derived from a physiologically accept the benzylic methylene (Glazier WO 91/19721). Thio-con able acid or base. However, salts of acids or bases which are taining prodrugs are reported to be useful for the intracellular 10 not physiologically acceptable may also find use, for delivery of phosphonate drugs. These proesters contain an example, in the preparation or purification of a physiologi ethylthio group in which the thiol group is either esterified cally acceptable compound. All salts, whether or not derived with an acyl group or combined with another thiol group to form a physiologically acceptable acid or base, are within the form a disulfide. Deesterification or reduction of the disulfide Scope of the present invention. generates the free thio intermediate which Subsequently 15 Alkyl is C-Cs hydrocarbon containing normal, second breaks down to the phosphoric acid and episulfide (Puechet ary, tertiary or cyclic carbon atoms. Examples are methyl al. (1993) Antiviral Res., 22: 155-174; Benzaria et al. (1996) (Me, —CH), ethyl (Et, —CHCH), 1-propyl (n-Pr, n-pro J. Med. Chem. 39: 4958). Cyclic phosphonate esters have also pyl, —CH2CH2CH), 2-propyl (i-Pr. i-propyl, -CH(CH)), been described as prodrugs of phosphorus-containing com 1-butyl (n-Bu, n-butyl, —CH2CH2CHCH), 2-methyl-1- pounds (Erion et al., U.S. Pat. No. 6.312,662). propyl (i-Bu, i-butyl, —CH2CHCCH)), 2-butyl (s-Bu, s-bu “Protecting group' refers to a moiety of a compound that tyl, -CH(CH)CHCH), 2-methyl-2-propyl (t-Bu, t-butyl, masks or alters the properties of a functional group or the —C(CH)), 1-pentyl (n-pentyl, —CH2CH2CH2CHCH). properties of the compound as a whole. Chemical protecting 2-pentyl ( CH(CH)CHCHCH), 3-pentyl ( CH groups and strategies for protection/deprotection are well (CHCH)), 2-methyl-2-butyl ( C(CH),CHCH), 3-me known in the art. See e.g., Protective Groups in Organic 25 thyl-2-butyl ( CH(CH)CH(CH)), 3-methyl-1-butyl Chemistry, Theodora W. Greene, John Wiley & Sons, Inc., (—CH2CHCHCCH)), 2-methyl-1-butyl ( CHCH(CH) New York, 1991. Protecting groups are often utilized to mask CHCH), 1-hexyl ( CHCH2CH2CH2CHCH), 2-hexyl the reactivity of certain functional groups, to assist in the (-CH(CH)CHCHCHCH), 3-hexyl ( CH(CHCH.) efficiency of desired chemical reactions, e.g., making and (CHCHCH)), 2-methyl-2-pentyl (—C(CH) breaking chemical bonds in an ordered and planned fashion. 30 CHCHCH), 3-methyl-2-pentyl ( CH(CH)CH(CH) Protection of functional groups of a compound alters other CHCH), 4-methyl-2-pentyl ( CH(CH)CHCH(CH)), physical properties besides the reactivity of the protected 3-methyl-3-pentyl ( C(CH)(CHCH)), 2-methyl-3-pen functional group, Such as the polarity, lipophilicity (hydro tyl ( CH(CHCH)CH(CH)), 2,3-dimethyl-2-butyl ( C phobicity), and other properties which can be measured by (CH)-CH(CH)), 3.3-dimethyl-2-butyl ( CH(CH)C common analytical tools. Chemically protected intermedi 35 (CH). ates may themselves be biologically active or inactive. Alkenyl is C-Cs hydrocarbon containing normal, sec Protected compounds may also exhibit altered, and in some ondary, tertiary or cyclic carbonatoms with at least one site of cases, optimized properties in vitro and in vivo, Such as pas unsaturation, i.e. a carbon-carbon, sp' double bond. sage through cellular membranes and resistance to enzymatic Examples include, but are not limited to, ethylene or vinyl degradation or sequestration. In this role, protected com 40 pounds with intended therapeutic effects may be referred to as (—CH=CH-), allyl ( CH-CH=CH), cyclopentenyl prodrugs. Another function of a protecting group is to convert (—CH), and 5-hexenyl ( CHCHCHCH-CH=CH-). the parental drug into a prodrug, whereby the parental drug is Alkynyl is C-Cs hydrocarbon containing normal, sec released upon conversion of the prodrug in vivo. Because ondary, tertiary or cyclic carbonatoms with at least one site of active prodrugs may be absorbed more effectively than the 45 unsaturation, i.e. a carbon-carbon, sp triple bond. Examples parental drug, prodrugs may possess greater potency in vivo include, but are not limited to, acetylenic ( C=CH) and than the parental drug. Protecting groups are removed either propargyl ( CH-C=CH), in vitro, in the instance of chemical intermediates, or in vivo, Alkylene' refers to a saturated, branched or straight chain in the case of prodrugs. With chemical intermediates, it is not or cyclic hydrocarbon radical of 1-18 carbon atoms, and particularly important that the resulting products after depro 50 having two monovalent radical centers derived by the tection, e.g., alcohols, be physiologically acceptable, removal of two hydrogen atoms from the same or two differ although in general it is more desirable if the products are ent carbonatoms of a parent alkane. Typical alkylene radicals pharmacologically innocuous. include, but are not limited to, methylene (-CH ) 1.2- Any reference to any of the compounds of the invention ethyl (-CH2CH2—), 1,3-propyl (-CH2CH2CH2—), 1,4- also includes a reference to a physiologically acceptable salt 55 butyl ( CHCHCHCH ), and the like. thereof. Examples of physiologically acceptable salts of the Alkenylene' refers to an unsaturated, branched or straight compounds of the invention include salts derived from an chain or cyclic hydrocarbon radical of 2-18 carbonatoms, and appropriate base. Such as an alkali metal (for example, having two monovalent radical centers derived by the Sodium), an alkaline earth (for example, magnesium), ammo removal of two hydrogen atoms from the same or two differ nium and NX (wherein X is C-C alkyl). Physiologically 60 ent carbonatoms of a parent alkene. Typical alkenylene radi acceptable salts of an hydrogen atom or an amino group cals include, but are not limited to, 1.2-ethylene include salts of organic carboxylic acids such as acetic, ben (-CH=CH-). Zoic, lactic, fumaric, tartaric, maleic, malonic, malic, Alkynylene' refers to an unsaturated, branched or straight isethionic, lactobionic and Succinic acids; organic Sulfonic chain or cyclic hydrocarbon radical of 2-18 carbonatoms, and acids, such as methanesulfonic, ethanesulfonic, benzene 65 having two monovalent radical centers derived by the Sulfonic and p-toluenesulfonic acids; and inorganic acids, removal of two hydrogen atoms from the same or two differ Such as hydrochloric, Sulfuric, phosphoric and Sulfamic acids. ent carbonatoms of a parent alkyne. Typical alkynylene radi US 7,871,991 B2 13 14 cals include, but are not limited to, acetylene ( -C=C- ), isoindolinyl, quinuclidinyl, morpholinyl, oxazolidinyl, ben propargyl (—CH2C=C ), and 4-pentynyl Zotriazolyl, benzisoxazolyl, OXindolyl, benzoxazolinyl, isati ( CHCHCH-C=CH-). noyl, and bis-tetrahydrofuranyl: Aryl means a monovalent aromatic hydrocarbon radical of6-20 carbonatoms derived by the removal of one hydrogen 5 atom from a single carbon atom of a parent aromatic ring system. Typical aryl groups include, but are not limited to, radicals derived from benzene, substituted benzene, naphtha lene, anthracene, biphenyl, and the like. Arylalkyl refers to an acyclic alkyl radical in which one 10 of the hydrogen atoms bonded to a carbon atom, typically a terminal or sp carbon atom, is replaced with an aryl radical. Typical arylalkyl groups include, but are not limited to, ben By way of example and not limitation, carbon bonded Zyl. 2-phenylethan-1-yl, naphthylmethyl 2-naphthylethan-1- heterocycles are bonded at position 2, 3, 4, 5, or 6 of a yl, naphthobenzyl, 2-naphthophenylethan-1-yl and the like. 15 pyridine, position 3, 4, 5, or 6 of a pyridazine, position 2, 4, 5, The arylalkyl group comprises 6 to 20 carbonatoms, e.g., the or 6 of a pyrimidine, position 2, 3, 5, or 6 of a pyrazine, alkyl moiety, including alkanyl, alkenyl or alkynyl groups, of position 2, 3, 4, or 5 of a furan, tetrahydrofuran, thiofuran, the arylalkyl group is 1 to 6 carbon atoms and the aryl moiety thiophene, pyrrole or tetrahydropyrrole, position 2, 4, or 5 of is 5 to 14 carbon atoms. an oxazole, imidazole or thiazole, position 3, 4, or 5 of an “Substituted alkyl, “substituted aryl', and “substituted isoxazole, pyrazole, or isothiazole, position 2 or 3 of an arylalkyl mean alkyl, aryl, and arylalkyl respectively, in aziridine, position 2, 3, or 4 of anaZetidine, position 2, 3, 4, 5, which one or more hydrogen atoms are each independently 6, 7, or 8 of a quinoline or position 1, 3, 4, 5, 6, 7, or 8 of an replaced with a non-hydrogen Substituent. Typical Substitu isoquinoline. Still more typically; carbon bonded hetero ents include, but are not limited to, —X, —R, —O, —OR, cycles include 2-pyridyl, 3-pyridyl, 4-pyridyl, 5-pyridyl, —SR, S, NR = NR, —NR, CX-CN, OCN, 25 6-pyridyl, 3-pyridazinyl, 4-pyridaZinyl, 5-pyridazinyl, 6-py —SCN, N=C=O, NCS, NO, NO. —N - N. ridazinyl, 2-pyrimidinyl, 4-pyrimidinyl, 5-pyrimidinyl, 6-py NC(=O)R, C(=O)R, C(=O)NRR - S(=O),O, rimidinyl, 2-pyrazinyl, 3-pyrazinyl, 5-pyrazinyl, 6-pyrazinyl, —S(=O).OH, -S(=O),R, —OS(=O),OR, -S(-O), 2-thiazolyl, 4-thiazolyl, or 5-thiazolyl. NR, S(=O)R, OP(=O)CRR, P(=O)CRR By way of example and not limitation, nitrogen bonded —P(=O)(O), -P(=O)(OH), C(=O)R, —C(=O)x, 30 heterocycles are bonded at position 1 of an aziridine, aZeti —C(S)R, —C(O)OR, C(O)O, C(S)OR, C(O)SR, dine, pyrrole, pyrrolidine, 2-pyrroline, 3-pyrroline, imida C(S)SR, C(O)NRR, C(S)NRR, C(NR)NRR, where Zole, imidazolidine, 2-imidazoline, 3-imidazoline, pyrazole, each X is independently a halogen: F, Cl, Br, or I; and each R pyrazoline, 2-pyrazoline, 3-pyrazoline, piperidine, pipera is independently —H, alkyl, aryl, heterocycle, protecting Zine, indole, indoline, 1H-indazole, position 2 of a isoindole, group or prodrug moiety. Alkylene, alkenylene, and alky 35 or isoindoline, position 4 of a morpholine, and position 9 of a nylene groups may also be similarly Substituted. carbazole, or 3-carboline. Still more typically, nitrogen “Heterocycle” as used herein includes by way of example bonded heterocycles include 1-aziridyl, 1-azetedyl, 1-pyrro and not limitation these heterocycles described in Paquette, lyl, 1-imidazolyl, 1-pyrazolyl, and 1-piperidinyl. Leo A.; Principles of Modern Heterocyclic Chemistry (W. A. “Carbocycle” refers to a saturated, unsaturated or aromatic Benjamin, New York, 1968), particularly Chapters 1, 3, 4, 6, 40 ring having 3 to 7 carbon atoms as a monocycle, 7 to 12 7, and 9. The Chemistry of Heterocyclic Compounds, A Series carbonatoms as a bicycle, and up to about 20 carbonatoms as of Monographs” (John Wiley & Sons, New York, 1950 to a polycycle. Monocyclic carbocycles have 3 to 6 ring atoms, present), in particular Volumes 13, 14, 16, 19, and 28; and J. still more typically 5 or 6 ring atoms. Bicyclic carbocycles Am. Chem. Soc. (1960) 82:5566. In one specific embodiment have 7 to 12 ring atoms, e.g., arranged as a bicyclo4.5, 5.5, of the invention "heterocycle” includes a “carbocycle” as 45 5.6 or 6.6 system, or 9 or 10 ring atoms arranged as a defined herein, wherein one or more (e.g. 1, 2, 3, or 4) carbon bicyclo 5.6 or 6.6 system. Examples of monocyclic car atoms have been replaced with a heteroatom (e.g. O, N, or S). bocycles include cyclopropyl, cyclobutyl, cyclopentyl, 1-cy Examples of heterocycles include by way of example and clopent-1-enyl, 1-cyclopent-2-enyl, 1-cyclopent-3-enyl, not limitation pyridyl, dihydroypyridyl, tetrahydropyridyl cyclohexyl, 1-cyclohex-1-enyl, 1-cyclohex-2-enyl, 1-cyclo (piperidyl), thiazolyl, tetrahydrothiophenyl, sulfur oxidized 50 tetrahydrothiophenyl, pyrimidinyl, furanyl, thienyl, pyrrolyl, hex-3-enyl, phenyl, spiryland naphthyl. pyrazolyl, imidazolyl, tetrazolyl, benzofuranyl, thianaphtha “Linker' or “link” refers to a chemical moiety comprising lenyl, indolyl, indolenyl, quinolinyl, isoquinolinyl, benzimi a covalent bond or a chain or group of atoms that covalently dazolyl, piperidinyl, 4-piperidonyl, pyrrolidinyl, 2-pyrrolido attaches a phosphonate group to a drug. Linkers include por nyl, pyrrolinyl, tetrahydrofuranyl, tetrahydroquinolinyl, 55 tions of substituents A" and A, which include moieties such tetrahydroisoquinolinyl, decahydroquinolinyl, octahydroiso as: repeating units of alkyloxy (e.g., polyethylenoxy, PEG, quinolinyl, azocinyl, triazinyl, 6H-1,2,5-thiadiazinyl, polymethyleneoxy) and alkylamino (e.g., polyethylene 2H,6H-1.5.2-dithiazinyl, thienyl, thianthrenyl, pyranyl, amino, JeffamineTM); and diacid ester and amides including isobenzofuranyl, chromenyl, Xanthenyl, phenoxathinyl, Succinate. Succinamide, diglycolate, malonate, and caproam ide. 2H-pyrrolyl, isothiazolyl, isoxazolyl pyrazinyl, pyridazinyl, 60 indolizinyl, isoindolyl, 3H-indolyl, 1H-indazoly, purinyl, The term "chiral refers to molecules which have the prop 4H-quinolizinyl, phthalazinyl, naphthyridinyl, quinoxalinyl, erty of non-Superimposability of the mirror image partner, quinazolinyl, cinnolinyl, pteridinyl, 4aH-carbazolyl, carba while the term “achiral” refers to molecules which are super Zolyl, B-carbolinyl, phenanthridinyl, acridinyl, pyrimidinyl, imposable on their mirror image partner. phenanthrolinyl, phenazinyl, phenothiazinyl, furazanyl, phe 65 The term “stereoisomers' refers to compounds which have noxazinyl, isochromanyl, chromanyl, imidazolidinyl, imida identical chemical constitution, but differ with regard to the Zolinyl, pyrazolidinyl, pyrazolinyl, piperazinyl, indolinyl, arrangement of the atoms or groups in space. US 7,871,991 B2 15 16 “Diastereomer' refers to a stereoisomer with two or more protecting groups are neither ether-norester-forming groups, centers of chirality and whose molecules are not mirror as will be understood by those skilled in the art, and are images of one another. Diastereomers have different physical included with amides, discussed below. properties, e.g., melting points, boiling points, spectral prop A very large number of hydroxyl protecting groups and erties, and reactivities. Mixtures of diastereomers may sepa- 5 amide-forming groups and corresponding chemical cleavage rate under high resolution analytical procedures such as elec trophoresis and chromatography. reactions are described in Protective Groups in Organic Syn "Enantiomers' refer to two stereoisomers of a compound thesis, Theodora W. Greene (John Wiley & Sons, Inc., New which are non-Superimposable mirror images of one another. York, 1991, ISBN 0-471-62301-6) (“Greene'). See also The term “treatment” or “treating to the extent it relates to 10 Kocienski, Philip J.; Protecting Groups (Georg Thieme Ver a disease or condition includes preventing the disease or lag Stuttgart, New York, 1994), which is incorporated by condition from occurring, inhibiting the disease or condition, reference in its entirety herein. In particular Chapter 1, Pro eliminating the disease or condition, and/or relieving one or tecting Groups: An Overview, pages 1-20, Chapter 2, more symptoms of the disease or condition. Hydroxyl Protecting Groups, pages 21-94, Chapter 3, Diol Stereochemical definitions and conventions used herein 15 Protecting Groups, pages 95-117, Chapter 4, Carboxyl Pro generally follow S.P. Parker, Ed., McGraw-Hill Dictionary of tecting Groups, pages 118-154, Chapter 5, Carbonyl Protect Chemical Terms (1984) McGraw-Hill Book Company, New ing Groups, pages 155-184. For protecting groups for car York; and Eliel, E. and Wilen, S., Stereochemistry of Organic boxylic acid, phosphonic acid, phosphonate, Sulfonic acid Compounds (1994) John Wiley & Sons, Inc., New York. and other protecting groups for acids see Greene as set forth Many organic compounds exist in optically active forms, i.e., 20 below. Such groups include by way of example and not limi they have the ability to rotate the plane of plane-polarized tation, esters, amides, hydrazides, and the like. light. In describing an optically active compound, the prefixes D and L or R and S are used to denote the absolute configu Ether- and Ester-Forming Protecting Groups ration of the molecule about its chiral center(s). The prefixes Ester-forming groups include: (1) phosphonate ester-form d and 1 or (+) and (-) are employed to designate the sign of 25 ing groups, such as phosphonamidate esters, phosphorothio rotation of plane-polarized light by the compound, with (-) or ate esters, phosphonate esters, and phosphon-bis-amidates; 1 meaning that the compound is levorotatory. A compound (2) carboxyl ester-forming groups, and (3) Sulphur ester prefixed with (+) or d is dextrorotatory. For a given chemical forming groups, such as Sulphonate, Sulfate, and Sulfinate. structure, these stereoisomers are identical except that they The optional phosphonate moieties of the compounds of are mirror images of one another. A specific stereoisomer may 30 the invention may or may not be prodrug moieties, i.e. they also be referred to as an enantiomer, and a mixture of Such may or may be susceptible to hydrolytic or enzymatic cleav isomers is often called an enantiomeric mixture. A 50:50 age or modification. Certain phosphonate moieties are stable mixture of enantiomers is referred to as a racemic mixture or under most or nearly all metabolic conditions. For example, a a racemate, which may occur where there has been no stereo dialkylphosphonate, where the alkyl groups are two or more selection or stereospecificity in a chemical reaction or pro- 35 carbons, may have appreciable stability in vivo due to a slow cess. The terms “racemic mixture' and “racemate” refer to an rate of hydrolysis. equimolar mixture of two enantiomeric species, devoid of Within the context of phosphonate prodrug moieties, a optical activity. large number of structurally-diverse prodrugs have been Protecting Groups 40 described for phosphonic acids (Freeman and Ross in Progress in Medicinal Chemistry 34:112-147 (1997) and are In the context of the present invention, protecting groups included within the scope of the present invention. An exem include prodrug moieties and chemical protecting groups. plary phosphonate ester-forming group is the phenyl car Protecting groups are available, commonly known and used, and are optionally used to prevent side reactions with bocycle in substructure A having the formula: the protected group during synthetic procedures, i.e. routes or 45 methods to prepare the compounds of the invention. For the most part the decision as to which groups to protect, when to N do so, and the nature of the chemical protecting group “PG” HR, will be dependent upon the chemistry of the reaction to be 2 protected against (e.g., acidic, basic, oxidative, reductive or 50 O other conditions) and the intended direction of the synthesis. \ -O R The PG groups do not need to be, and generally are not, the O 1 same if the compound is substituted with multiple PG. In general, PG will be used to protect functional groups such as 4x1R. R. \, OR carboxyl, hydroxyl, thio, or amino groups and to thus prevent 55 O side reactions or to otherwise facilitate the synthetic effi ciency. The order of deprotection to yield free, deprotected groups is dependent upon the intended direction of the Syn wherein R' may be H or C-C alkyl: m1 is 1,2,3,4, 5, 6, thesis and the reaction conditions to be encountered, and may 7 or 8, and the phenyl carbocycle is substituted with 0 to 3 R occur in any order as determined by the artisan. 60 groups. Where Y is O, a lactate ester is formed, and where Y Various functional groups of the compounds of the inven is N(R), N(OR) or N(N(R), a phosphonamidate ester tion may be protected. For example, protecting groups for results. —OH groups (whether hydroxyl, carboxylic acid, phospho In its ester-forming role, a protecting group typically is nic acid, or other functions) include “ether- or ester-forming bound to any acidic group Such as, by way of example and not groups”. Ether- or ester-forming groups are capable of func- 65 limitation, a COH or —C(S)OH group, thereby resulting tioning as chemical protecting groups in the synthetic in —COR where R is defined herein. Also, R for example schemes set forth herein. However, some hydroxyl and thio includes the enumerated ester groups of WO95/07920. US 7,871,991 B2 17 18 Examples of protecting groups include: (including —CH, —CH(CH), —C(CH), —CH2CH, C-C heterocycle (described above) or aryl. These aro —(CH2)CH, —(CH2)CH, —(CH2)CH, —(CH2)CH, matic groups optionally are polycyclic or monocyclic. —CHCHF, —CHCHCl, —CHCF, and —CHCCl); Examples include phenyl, spiryl, 2- and 3-pyrrolyl, 2- and 3-thienyl, 2- and 4-imidazolyl, 2-, 4- and 5-oxazolyl, 3- and 5 4-isoxazolyl, 2-, 4- and 5-thiazolyl, 3-, 4- and 5-isothiazolyl, 3- and 4-pyrazolyl, 1-, 2-, 3- and 4-pyridinyl, and 1-, 2-, 4- and N-1a/ Y. 5-pyrimidinyl, C-C heterocycle or aryl substituted with halo, R', R"—O C-C alkylene, C-C alkoxy, CN, NO,OH, car 10 boxy, carboxyester, thiol, thioester, C-C haloalkyl (1-6 —N-2-propylmorpholino, 2,3-dihydro-6-hydroxyindene, halogen atoms), C-C alkenyl or C-C alkynyl. Such sesamol, catechol monoester, —CH2—C(O)—N(R'), groups include 2-, 3- and 4-alkoxyphenyl (C-C alkyl), 2-, —CH S(O)(R'), —CH-S(O) (R'), —CH-CH(OC 3- and 4-methoxyphenyl, 2-, 3- and 4-ethoxyphenyl, 2.3-, (O)CHR)-CH(OC(O)CHR), cholesteryl, enolpyruvate 2.4-, 2.5-, 2,6-, 3.4- and 3.5-diethoxyphenyl, 2- and 3-car 15 (HOOC C(=CH-)—), glycerol: boethoxy-4-hydroxyphenyl, 2- and 3-ethoxy-4-hydroxyphe a 5 or 6 carbon monosaccharide, disaccharide or oligosac nyl, 2- and 3-ethoxy-5-hydroxyphenyl, 2- and 3-ethoxy-6- charide (3 to 9 monosaccharide residues); hydroxyphenyl, 2-, 3- and 4-O-acetylphenyl, 2-, 3- and triglycerides such as C-D-B-diglycerides (wherein the fatty 4-dimethylaminophenyl, 2-, 3- and 4-methylmercaptophe acids composing glyceride lipids generally are naturally nyl, 2-, 3- and 4-halophenyl (including 2-, 3- and 4-fluo occurring saturated or unsaturated C-2, C-1s or Coo fatty rophenyl and 2-, 3- and 4-chlorophenyl), 2.3-, 2,4-, 2.5-, 2,6-, acids such as linoleic, lauric, myristic, palmitic, Stearic, oleic, 3,4- and 3.5-dimethylphenyl, 2.3-, 2,4-, 2.5-, 2,6-, 3.4- and palmitoleic, linolenic and the like fatty acids) linked to acyl of 3,5-biscarboxyethylphenyl, 2.3-, 2,4-, 2.5-, 2,6-, 3,4- and 3.5- the parental compounds herein through a glyceryl oxygen of dimethoxyphenyl, 2.3-, 2,4-, 2.5-, 2,6-, 3,4- and 3,5-dih the triglyceride; alophenyl (including 2,4-difluorophenyl and 3,5-difluo 25 phospholipids linked to the carboxyl group through the rophenyl), 2-, 3- and 4-haloalkylphenyl (1 to 5 halogenatoms, phosphate of the phospholipid; C-C alkyl including 4-trifluoromethylphenyl), 2-, 3- and phthalidyl (shown in FIG. 1 of Clayton et al., Antimicrob, 4-cyanophenyl, 2-, 3- and 4-nitrophenyl, 2-, 3- and 4-ha Agents Chemo. (1974)5(6):670-671): loalkylbenzyl (1 to 5 halogen atoms, C-C alkyl including cyclic carbonates Such as (5-R-2-oxo-1,3-dioxolen-4-yl) 4-trifluoromethylbenzyl and 2-, 3- and 4-trichloromethylphe 30 methyl esters (Sakamoto et al., Chem. Pharm. Bull. (1984) nyl and 2-, 3- and 4-trichloromethylphenyl), 4-N-methylpip 32(6)2241-2248) where R is R. R. or aryl; and eridinyl, 3-N-methylpiperidinyl, 1-ethylpiperazinyl, benzyl, alkylsalicylphenyl (C-C alkyl, including 2-, 3- and 4-ethyl salicylphenyl), 2-3- and 4-acetylphenyl, 1,8-dihydroxynaph thyl ( CoH OH) and aryloxyethyl Co-Co aryl (includ 35 ing phenoxyethyl), 2,2'-dihydroxybiphenyl, 2-, 3- and 4-N. N-dialkylaminophenol, —CHCH N(CH), trimethoxybenzyl, triethoxybenzyl, 2-alkyl pyridinyl (Ca The hydroxyl groups of the compounds of this invention alkyl); optionally are substituted with one of groups III, IV or V 40 disclosed in WO94/21604, or with isopropyl. Table A lists examples of protecting group ester moieties that for example can be bonded via oxygen to —C(O)C)—and —P(O)(O—) groups. Several amidates also are shown, -CH-O-C(O) which are bound directly to —C(O) or - P(O). Esters of 45 structures 1-5, 8-10 and 16, 17, 19-22 are synthesized by N reacting the compound herein having a free hydroxyl with the corresponding halide (chloride or acyl chloride and the like) and N,N-dicyclohexyl-N-morpholine carboxamidine (or another base such as DBU, triethylamine, CsCO, N,N-dim 50 ethylaniline and the like) in DMF (or other solvent such as acetonitrile or N-methylpyrrolidone). When the compound to be protected is a phosphonate, the esters of structures 5-7, 11, 12, 21, and 23-26 are synthesized by reaction of the alcohol or C-C esters of 2-carboxyphenyl; and C-C alkylene-C-C, 55 alkoxide Salt (or the corresponding amines in the case of aryl (including benzyl, —CH-pyrrolyl, -CH2-thienyl, compounds such as 13, 14 and 15) with the monochlorophos —CH-imidazolyl, -CH2-oxazolyl, -CH2-isoxazolyl, phonate or dichlorophosphonate (or another activated phos —CH2-thiazolyl, —CH2-isothiazolyl, -CH2-pyrazolyl, phonate). —CH2-pyridinyl and —CH-pyrimidinyl) substituted in the aryl moiety by 3 to 5 halogenatoms or 1 to 2 atoms or groups 60 TABLE A selected from halogen, C-C alkoxy (including methoxy and ethoxy), cyano, nitro, OH, C-Chaloalkyl (1 to 6 halo gen atoms; including —CHCCl), C-C alkyl (including methyl and ethyl), C-C alkenyl or C-C alkynyl; alkoxy ethyl C-C alkyl including —CH2—CH-O-CH (meth 65 oxy ethyl); alkyl substituted by any of the groups set forth N-ethylmorpholino above for aryl, in particular OH or by 1 to 3 halo atoms US 7,871,991 B2 19 20

TABLE A-continued

O -CHSCOCH,

10 —CHOCON(CH), or alkyl- or aryl-acyloxyalkyl groups of the structure CH(R' or W)O((CO)R7) or CH(R' or W)(CO)OR) (linked to oxygen of the acidic group) wherein R7 and Rare alkyl, aryl, or alkylaryl groups (see 15 U.S. Pat. No. 4,968,788). Frequently R7 and Rare bulky groups such as branched alkyl, ortho-substituted aryl, meta 19. Substituted aryl, or combinations thereof, including normal, secondary, iso- and tertiary alkyls of 1-6 carbon atoms. An -CHC(O)N O example is the pivaloyloxymethyl group. These are of par ticular use with prodrugs for oral administration. Examples of Such useful protecting groups are alkylacyloxymethyl esters and their derivatives, including —CH(CHCHOCH)OC (O)C(CH), N H 25 O

21. HO O OH HO 30

HO —CHOC(O)CHs —CHOC(O)C(CH), —CH 22. N (CHOCH)OC(O)C(CH), —CH(CH(CH))OC(O)C (CH), —CHOC(O)CH-CH(CH), —CHOC(O)CH, -CH-O-C(O) / \ —CHOC(O)CHs —CHOC(O)CHs —CHOC(O) CHCH, -CHOC(O)CH(CH), —CHOC(O)C(CH), and —CHOC(O)CHCHs. 23. N In Some embodiments the protected acidic group is an ester of the acidic group and is the residue of a hydroxyl-containing -CHCH -() 40 functionality. In other embodiments, an amino compound is used to protect the acid functionality. The residues of suitable 24. CHO(O)C hydroxyl or amino-containing functionalities are set forth above or are found in WO95/07920. Of particular interest are the residues of amino acids, amino acid esters, polypeptides, 45 or aryl alcohols. Typical amino acid, polypeptide and car boxyl-esterified amino acid residues are described on pages 11-18 and related text of WO95/07920 as groups L1 or L2. 25. CHCHO(O)C WO95/07920 expressly teaches the amidates of phosphonic 50 acids, but it will be understood that such amidates are formed with any of the acid groups set forth herein and the amino acid residues set forth in WO95/07920. Typical esters for protecting acidic functionalities are also described in WO95/07920, again understanding that the 26. OCH3 55 same esters can be formed with the acidic groups herein as with the phosphonate of the 920 publication. Typical ester groups are defined at least on WO95/07920 pages 89-93 (under R' or R), the table on page 105, and pages 21-23 (as R). Of particular interest are esters of unsubstituted aryl such 60 as phenyl or arylalkyl such benzyl, or hydroxy-, halo ---OCH alkoxy-, carboxy- and/or alkylestercarboxy-Substituted aryl or alkylaryl, especially phenyl, ortho-ethoxyphenyl, or C-C, alkylestercarboxyphenyl (Salicylate C-C alkylesters). Otheresters that are suitable for use herein are described in The protected acidic groups, particularly when using the EP 632O48. 65 esters or amides of WO95/07920, are useful as prodrugs for Protecting groups also includes “double ester forming oral administration. However, it is not essential that the acidic profunctionalities such as —CHOC(O)OCH, group be protected in order for the compounds of this inven US 7,871,991 B2 21 22 tion to be effectively administered by the oral route. When the Adamantoate, Crotonate, 4-Methoxycrotonate, Ben compounds of the invention having protected groups, in par Zoate, p-Phenylbenzoate, 2.4.6-Trimethylbenzoate ticular amino acid amidates or Substituted and unsubstituted (Mesitoate)); aryl esters are administered systemically or orally they are Carbonates (Methyl, 9-Fluorenylmethyl, Ethyl, 2.2.2- capable of hydrolytic cleavage in vivo to yield the free acid. Trichloroethyl 2-(Trimethylsilyl)ethyl 2-(Phenylsulfo One or more of the acidic hydroxyls are protected. If more nyl)ethyl, 2-(Triphenylphosphonio)ethyl, Isobutyl, than one acidic hydroxyl is protected then the same or a Vinyl, Allyl, p-Nitrophenyl, Benzyl, p-Methoxybenzyl, different protecting group is employed, e.g., the esters may be 3,4-Dimethoxybenzyl, o-Nitrobenzyl, p-Nitrobenzyl, different or the same, or a mixed amidate and ester may be S-Benzyl Thiocarbonate, 4-Ethoxy-1-naphthyl, Methyl used. 10 Dithiocarbonate); Typical hydroxy protecting groups described in Greene Groups With Assisted Cleavage (2-Iodobenzoate, 4-Azi (pages 14-118) include substituted methyl and alkyl ethers, dobutyrate, 4-Nitro-4-methylpentanoate, o-(Dibro substituted benzyl ethers, silyl ethers, esters including sul momethyl)benzoate, 2-Formylbenzenesulfonate, fonic acid esters, and carbonates. For example: 2-(Methylthiomethoxy)ethyl Carbonate, 4-(Methylthi Ethers (methyl, t-butyl, allyl); 15 omethoxy)butyrate, 2-(Methylthiomethoxymethyl)ben Substituted Methyl Ethers (Methoxymethyl, Methylthi Zoate); Miscellaneous Esters (2,6-Dichloro-4-meth omethyl, t-Butylthiomethyl, (Phenyldimethylsilyl) ylphenoxyacetate, 2,6-Dichloro-4-(1,1.3.3 methoxymethyl, Benzyloxymethyl, p-Methoxybenzy tetramethylbutyl)phenoxyacetate, 2,4-Bis(1,1-dimeth loxymethyl, (4-Methoxyphenoxy)methyl, ylpropyl)phenoxyacetate, Chlorodiphenylacetate, Guaiacolmethyl, t-Butoxymethyl, 4-Pentenyloxym Isobutyrate, Monosuccinate, (E)-2-Methyl-2-butenoate ethyl, Siloxymethyl, 2-Methoxyethoxymethyl, 2.2.2- (Tigloate), o-(Methoxycarbonyl)benzoate, p-poly-Ben Trichloroethoxymethyl, Bis(2-chloroethoxy)methyl, Zoate, C.-Naphthoate, Nitrate, Alkyl N,N,N',N'-Tetram 2-(Trimethylsilyl)ethoxymethyl, Tetrahydropyranyl, ethylphosphorodiamidate, N-Phenylcarbamate, Borate, 3-Bromotetrahydropyranyl, Tetrahydropthiopyranyl, Dimethylphosphinothioyl, 2,4-Dinitrophenyl 1-Methoxycyclohexyl, 4-Methoxytetrahydropyranyl, 25 Sulfenate); and 4-Methoxytetrahydrothiopyranyl, 4-Methoxytetrahy Sulfonates (Sulfate, Methanesulfonate (Mesylate), Ben dropthiopyranyl SS-Dioxido, 1-(2-Chloro-4-methyl) Zylsulfonate, Tosylate). phenyl-4-methoxypiperidin-4-yl, 1,4-Dioxan-2-yl, Typical 1.2-diol protecting groups (thus, generally where Tetrahydrofuranyl, Tetrahydrothiofuranyl, 2.3.3a,4,5,6, two OH groups are taken together with the protecting func 7.7a-Octahydro-7,8,8-trimethyl-4,7-methanobenzofu 30 tionality) are described in Greene at pages 118-142 and ran-2-yl)); include Cyclic Acetals and Ketals (Methylene, Ethylidene, Substituted Ethyl Ethers (1-Ethoxyethyl, 1-(2-Chloroet 1-t-Butylethylidene, 1-Phenylethylidene, (4-Methoxyphe hoxy)ethyl, 1-Methyl-1-methoxyethyl, 1-Methyl-1- nyl)ethylidene, 2.2.2-Trichloroethylidene, Acetonide (Iso benzyloxyethyl, 1-Methyl-1-benzyloxy-2-fluoroethyl, propylidene), Cyclopentylidene, Cyclohexylidene, Cyclo 2.2.2-Trichloroethyl, 2-Trimethylsilylethyl, 2-(Phe 35 heptylidene, Benzylidene, p-Methoxybenzylidene, 2,4- nylselenyl)ethyl, Dimethoxybenzylidene, 3,4-Dimethoxybenzylidene, p-Chlorophenyl, p-Methoxyphenyl, 2,4-Dinitrophenyl, 2-Nitrobenzylidene); Cyclic Ortho Esters (Methoxymethyl Benzyl); ene, Ethoxymethylene, Dimethoxymethylene, 1-Methoxy Substituted Benzyl Ethers (p-Methoxybenzyl, 3,4- ethylidene, 1-Ethoxyethylidine, 1,2-Dimethoxyethylidene, Dimethoxybenzyl, o-Nitrobenzyl, p-Nitrobenzyl, p-Ha 40 C.-Methoxybenzylidene, 1-(N,N-Dimethylamino)ethylidene lobenzyl, 2,6-Dichlorobenzyl, p-Cyanobenzyl, p-Phe Derivative, C.-(N,N-Dimethylamino)benzylidene Derivative, nylbenzyl, 2- and 4-Picolyl. 3-Methyl-2-picolyl 2-Oxacyclopentylidene); Silyl Derivatives (Di-t-butylsi N-Oxido, Diphenylmethyl, p.p'-Dinitrobenzhydryl, lylene Group, 1,3-(1,1,3,3-Tetraisopropyldisiloxanylidene), 5-Dibenzosuberyl, Triphenylmethyl, C-Naphthyldiphe and Tetra-t-butoxydisiloxane-1,3-diylidene), Cyclic Carbon nylmethyl, p-methoxyphenyldiphenylmethyl, Di(p- 45 ates, Cyclic Boronates, Ethyl Boronate and Phenyl Boronate. methoxyphenyl)phenylmethyl, Tri(p-methoxyphenyl) More typically, 1,2-diol protecting groups include those methyl, 4-(4-Bromophenacyloxy) shown in Table B, still more typically, epoxides, acetonides, phenyldiphenylmethyl, 44'4"-Tris(4,5- cyclic ketals and aryl acetals. dichlorophthalimidophenyl)methyl, 44'4"-Tris (levulinoyloxyphenyl)methyl, 44'4"-Tris 50 (benzoyloxyphenyl)methyl, 3-(Imidazol-1-ylmethyl) TABLE B bis(4,4'-dimethoxyphenyl)methyl, 1,1-Bis(4- methoxyphenyl)-1-pyrenylmethyl, 9-Anthryl, 9-(9- Phenyl)xanthenyl, 9-(9-Phenyl-10-oxo)anthryl, 1,3- JS-> Benzodithiolan-2-yl, Benzisothiazolyl SS-Dioxido); 55 Silyl Ethers (Trimethylsilyl, Triethylsilyl, Triisopropylsi lyl, Dimethylisopropylsilyl, Diethylisopropylsilyl, O Dimethylthexylsilyl, t-Butyldimethylsilyl, t-Butyl diphenylsilyl, Tribenzylsilyl, Tri-p-xylylsilyl, Triph X enylsilyl, Diphenylmethylsilyl, t-Butylmethoxyphenyl 60 silyl); Esters (Formate, Benzoylformate, Acetate, Choroacetate, Dichloroacetate, Trichloroacetate, Trifluoroacetate, O O Methoxyacetate, Triphenylmethoxyacetate, Phenoxy acetate, p-Chlorophenoxyacetate, p-poly-Phenylac 65 etate, 3-Phenylpropionate, 4-Oxopentanoate (Levuli nate), 4.4-(Ethylenedithio)pentanoate, Pivaloate,

US 7,871,991 B2 25 26 Imine Derivatives: (N-1,1-dimethylthiomethylene, N-ben CHCH-CH CH, —CH2—CHs —CH2CH2—S— Zylidene, N-p-methoxybenylidene, N-diphenylmethyl CH, -CHOH, -CH(OH) CH, CH, SH, -CH ene, N-(2-pyridyl)mesitylmethylene, N.(N',N'-dim CHOH, -CH CO. NH, —CH2—CH CO. NH2, ethylaminomethylene, N,N'-isopropylidene, N-p- CH-COOH, -CH CH-COOH, -(CH), NH, nitrobenzylidene, N-salicylidene, N-5- and —(CH2). NH CONH2) NH. R'' also includes chlorosalicylidene, N-(5-chloro-2-hydroxyphenyl) 1-guanidinoprop-3-yl, benzyl, 4-hydroxybenzyl, imidazol-4- phenylmethylene, N-cyclohexylidene); yl, indol-3-yl, methoxyphenyl and ethoxyphenyl. Enamine Derivatives: (N-(5,5-dimethyl-3-oxo-1-cyclo Another set of protecting groups include the residue of an hexenyl)); amino-containing compound, in particular an amino acid, a N-Metal Derivatives (N-borane derivatives, N-diphenyl 10 polypeptide, a protecting group, —NHSOR, NHC(O)R. borinic acid derivatives, N-phenyl (pentacarbonylchro —N(R), NH or NH(R)(H), whereby for example a car mium- or-tungsten) carbenyl, N-copper or N-Zinc che boxylic acid is reacted, i.e. coupled, with the amine to forman late); amide, as in C(O)NR2. A phosphonic acid may be reacted N N Derivatives: (N-nitro, N-nitroso, N-oxide); with the amine to form a phosphonamidate, as in —P(O)(OR) N P Derivatives: (N-diphenylphosphinyl, N-dimethylth 15 (NR). iophosphinyl, N-diphenylthiophosphinyl, N-dialkyl In general, amino acids have the structure RC(O)CH phosphoryl, N-dibenzyl phosphoryl, N-diphenyl phos (R')NH , where R'7 is -OH, -OR, an amino acid or a phoryl); polypeptide residue. Amino acids are low molecular weight N-Si Derivatives, N-S Derivatives, and N-Sulfenyl compounds, on the order of less than about 1000 MW and Derivatives: (N-benzenesulfenyl, N-o-nitrobenzene which contain at least one amino or imino group and at least Sulfenyl, N-2,4-dinitrobenzenesulfenyl, N-pentachlo one carboxyl group. Generally the amino acids will be found robenzenesulfenyl, N-2-nitro-4-methoxybenzenesulfe in nature, i.e., can be detected in biological material Such as nyl, N-triphenylmethylsulfenyl, N-3- bacteria or other microbes, plants, animals or man. Suitable nitropyridinesulfenyl); and N-sulfonyl Derivatives amino acids typically are alpha amino acids, i.e. compounds (N-p-toluenesulfonyl, N-benzenesulfonyl, N-2,3,6-tri 25 characterized by one amino or imino nitrogenatom separated methyl-4-methoxybenzenesulfonyl, N-2,4,6-tri from the carbon atom of one carboxyl group by a single methoxybenzenesulfonyl, N-2,6-dimethyl-4-methoxy substituted or unsubstituted alpha carbonatom. Of particular benzenesulfonyl, N-pentamethylbenzenesulfonyl, N-2, interest are hydrophobic residues such as mono- or di-alkyl or 3,5,6,-tetramethyl-4-methoxybenzenesulfonyl, N-4- arylamino acids, cycloalkylamino acids and the like. These methoxybenzenesulfonyl, N-2,4,6- 30 residues contribute to cell permeability by increasing the trimethylbenzenesulfonyl, N-2,6-dimethoxy-4- partition coefficient of the parental drug. Typically, the resi methylbenzenesulfonyl, N-2,2,5,7,8- due does not contain a sulfhydryl or guanidino substituent. pentamethylchroman-6-sulfonyl, N-methanesulfonyl, Naturally-occurring amino acid residues are those residues N-B-trimethylsilyethanesulfonyl, N-9-anthracenesulfo found naturally in plants, animals or microbes, especially nyl, N-4-(4,8-dimethoxynaphthylmethyl)benzene 35 proteins thereof. Polypeptides most typically will be substan sulfonyl, N-benzylsulfonyl, N-trifluoromethylsulfonyl, tially composed of Such naturally-occurring amino acid resi N-phenacylsulfonyl). dues. These amino acids are glycine, alanine, Valine, leucine, More typically, protected amino groups include carbam isoleucine, serine, threonine, cysteine, methionine, glutamic ates and amides, still more typically, NHC(O)R' or acid, aspartic acid, lysine, hydroxylysine, arginine, histidine, —N=CR'N(R'). Another protecting group, also useful as a 40 phenylalanine, tyrosine, tryptophan, proline, asparagine, prodrug for amino or -NH(R), is: glutamine and hydroxyproline. Additionally, unnatural amino acids, for example, Valanine, phenylglycine and homoarginine are also included. Commonly encountered amino acids that are not gene-encoded may also be used in the 45 present invention. All of the amino acids used in the present invention may be either the D- or L-optical isomer. In addi - tion, other peptidomimetics are also useful in the present invention. For a general review, see Spatola, A. F., in Chem istry and Biochemistry of Amino Acids, Peptides and Pro 50 teins, B. Weinstein, eds., Marcel Dekker, New York, p. 267 (1983). When protecting groups are single amino acid residues or See for example Alexander, J. et al. (1996) J. Med. Chem. polypeptides they optionally are substituted at R of substitu 39:48.0-486. ents A, A or A in a compound of the invention. These Amino Acid and Polypeptide Protecting Group and Conju 55 conjugates are produced by forming an amide bond between gates a carboxyl group of the amino acid (or C-terminal amino acid An amino acid or polypeptide protecting group of a com of a polypeptide for example). Similarly, conjugates are pound of the invention has the structure R'NHCH(R')C formed between R and an amino group of an amino acid or (O) , where R' is H, an amino acid or polypeptide residue, polypeptide. Generally, only one of any site in the parental or R, and R' is defined below. 60 molecule is amidated with an amino acid as described herein, R" is lower alkyl or lower alkyl (C-C) substituted with although it is within the scope of this invention to introduce amino, carboxyl, amide, carboxyl ester, hydroxyl, C-C, aryl, amino acids at more than one permitted site. Usually, a car guanidinyl, imidazolyl, indolyl. Sulfhydryl, Sulfoxide, and/or boxyl group of R is amidated with an amino acid. In general, alkylphosphate. R'also is taken together with the amino acid the C-amino or C-carboxyl group of the amino acid or the C. N to form a proline residue (R'= -CH-) ). However, 65 terminal amino or carboxyl group of a polypeptide are R" is generally the side group of a naturally-occurring amino bonded to the parental functionalities, i.e., carboxyl or amino acid Such as H. —CH. —CH(CH), —CH2—CH(CH), groups in the amino acid side chains generally are not used to US 7,871,991 B2 27 28 form the amide bonds with the parental compound (although acid, C.-methylglutamic acid, 1-aminocyclopropane-1-car these groups may need to be protected during synthesis of the boxylic acid, isoleucine, alloisoleucine, tert-leucine, B-meth conjugates as described further below). yltryptophan and C.-amino-B-ethyl-3-phenylpropionic acid; With respect to the carboxyl-containing side chains of 3-phenylserinyl; amino acids or polypeptides it will be understood that the 5 Aliphatic C-amino-O-hydroxy acids such as serine, B-hy carboxyl group optionally will be blocked, e.g., by R', esteri droxyleucine, B-hydroxynorleucine, B-hydroxynorvaline, fied with Roramidated. Similarly, the amino side chains R' and C.-amino-B-hydroxyStearic acid; optionally will be blocked with R' or substituted with R. C.-Amino, Cl-, y-, 6- ore-hydroxyacids such as homoserine, Such ester or amide-bonds with side chain amino or car Ö-hydroxynorvaline, Y-hydroxynorvaline and e-hydroxynor boxyl groups, like the esters or amides with the parental 10 leucine residues; canavine and canaline; Y-hydroxyomithine; molecule, optionally are hydrolyzable in vivo or in vitro 2-hexosaminic acids such as D-glucosaminic acid or D-ga under acidic (pH-3) or basic (pH>10) conditions. Alterna lactosaminic acid; tively, they are Substantially stable in the gastrointestinal tract C.-Amino-B-thiols such as penicillamine, B-thiolnorvaline of humans but are hydrolyzed enzymatically in blood or in or B-thiolbutyrine; intracellular environments. The esters or amino acid or 15 Other Sulfur containing amino acid residues including cys polypeptide amidates also are useful as intermediates for the teine; homocystine, 3-phenylmethionine, methionine, S-al preparation of the parental molecule containing free amino or lyl-L-cysteine Sulfoxide, 2-thiolhistidine, cystathionine, and carboxyl groups. The free acid or base of the parental com thiol ethers of cysteine or homocysteine; pound, for example, is readily formed from the esters or Phenylalanine, tryptophan and ring-Substituted C-amino amino acid or polypeptide conjugates of this invention by acids such as the phenyl- or cyclohexylamino acids C.-ami conventional hydrolysis procedures. nophenylacetic acid, C-aminocyclohexylacetic acid and When an amino acid residue contains one or more chiral C.-amino-C-cyclohexylpropionic acid; phenylalanine ana centers, any of the D. L. meso, threo or erythro (as appropri logues and derivatives comprising aryl, lower alkyl, hydroxy, ate) racemates, scalemates or mixtures thereof may be used. guanidino, oxyalkylether, nitro, Sulfur or halo-substituted In general, if the intermediates are to be hydrolyzed non 25 phenyl (e.g., tyrosine, methyltyrosine and o-chloro-, enzymatically (as would be the case where the amides are p-chloro-3,4-dichloro, o-, m- or p-methyl-, 2,4,6-trimethyl-, used as chemical intermediates for the free acids or free 2-ethoxy-5-nitro-, 2-hydroxy-5-nitro- and p-nitro-phenylala amines), D isomers are useful. On the other hand, L isomers nine); furyl-, thienyl-, pyridyl-, pyrimidinyl-, purinyl- or are more versatile since they can be susceptible to both non naphthyl-alanines; and tryptophan analogues and derivatives enzymatic and enzymatic hydrolysis, and are more efficiently 30 including kynurenine, 3-hydroxykynurenine, 2-hydroxytryp transported by amino acid or dipeptidyl transport systems in tophan and 4-carboxytryptophan; the gastrointestinal tract. C.-Amino substituted amino acids including sarcosine Examples of Suitable amino acids whose residues are rep (N-methylglycine), N-benzylglycine, N-methylalanine, resented by R or R' include the following: N-benzylalanine, N-methylphenylalanine, N-benzylpheny Glycine; 35 lalanine, N-methylvaline and N-benzylvaline; and Aminopolycarboxylic acids, e.g., aspartic acid, B-hydrox C.-Hydroxy and Substituted C-hydroxy amino acids includ yaspartic acid, glutamic acid, B-hydroxyglutamic acid, B-me ing serine, threonine, allothreonine, phosphoserine and phos thylaspartic acid, B-methylglutamic acid, B.B-dimethylaspar phothreonine. tic acid, Y-hydroxyglutamic acid, B.Y-dihydroxyglutamic Polypeptides are polymers of amino acids in which a car acid, B-phenylglutamic acid, Y-methyleneglutamic acid, 40 boxyl group of one amino acid monomer is bonded to an 3-aminoadipic acid, 2-aminopimelic acid, 2-aminoSuberic amino or imino group of the next amino acid monomer by an acid and 2-aminosebacic acid; amide bond. Polypeptides include dipeptides, low molecular Amino acid amides Such as glutamine and asparagine; weight polypeptides (about 1500-5000 MW) and proteins. Polyamino- or polybasic-monocarboxylic acids Such as Proteins optionally contain 3, 5, 10, 50, 75, 100 or more arginine, lysine, 3-aminoalanine, Y-aminobutyrine, ornithine, 45 residues, and Suitably are substantially sequence-homolo citruline, homoarginine, homocitrulline, hydroxylysine, allo gous with human, animal, plant or microbial proteins. They hydroxylsine and diaminobutyric acid; include enzymes (e.g., hydrogen peroxidase) as well as Other basic amino acid residues such as histidine, immunogens such as KLH, or antibodies or proteins of any Diaminodicarboxylic acids such as C.C.'-diaminosuccinic type against which one wishes to raise an immune response. acid, C.C.'-diaminoglutaric acid, C.C.'-diaminoadipic acid, 50 The nature and identity of the polypeptide may vary widely. C.C.'-diaminopimelic acid, C.C.'-diamino-B-hydroxypimelic The polypeptide amidates are useful as immunogens in acid, O.C.'-diaminoSuberic acid, C.C.'-diaminoaZelaic acid, raising antibodies against either the polypeptide (if it is not and C.C.'-diaminosebacic acid; immunogenic in the animal to which it is administered) or Imino acids such as proline, hydroxyproline, allohydrox against the epitopes on the remainder of the compound of this yproline, Y-methylproline, pipecolic acid, 5-hydroxypipe 55 invention. colic acid, and azetidine-2-carboxylic acid; Antibodies capable of binding to the parental non-peptidyl A mono- or di-alkyl (typically C-C branched or normal) compound are used to separate the parental compound from amino acid Such as alanine, Valine, leucine, allylglycine, mixtures, for example in diagnosis or manufacturing of the butyrine, norvaline, norleucine, heptyline, C.-methylserine, parental compound. The conjugates of parental compound C.-amino-C.-methyl-y-hydroxyvaleric acid, C.-amino-C.-me 60 and polypeptide generally are more immunogenic than the thyl-6-hydroxyvaleric acid, C.-amino-O-methyl-e-hydroxy polypeptides in closely homologous animals, and therefore caproic acid, isovaline, C.-methylglutamic acid, C.-ami make the polypeptide more immunogenic for facilitating rais noisobutyric acid, C.-aminodiethylacetic acid, ing antibodies against it. Accordingly, the polypeptide or C.-aminodiisopropylacetic acid, C.-aminodi-n-propylacetic protein may not need to be immunogenic in an animal typi acid, C-aminodiisobutylacetic acid, C.-aminodi-n-butylacetic 65 cally used to raise antibodies, e.g., rabbit, mouse, horse, or rat, acid, C.-aminoethylisopropylacetic acid, C.-amino-n-propy but the final product conjugate should be immunogenic in at lacetic acid, C.-aminodiisoamyacetic acid, C.-methylaspartic least one of Such animals. The polypeptide optionally con US 7,871,991 B2 29 30 tains a peptidolytic enzyme cleavage site at the peptide bond more amino acids in the D configuration are also compatible between the first and second residues adjacent to the acidic with peptide transport and can be utilized in the amidate heteroatom. Such cleavage sites are flanked by enzymatic compounds of this invention. Amino acids in the D configu recognition structures, e.g., a particular sequence of residues recognized by a peptidolytic enzyme. ration can be used to reduce the susceptibility of a di- or Peptidolytic enzymes for cleaving the polypeptide conju tripeptide to hydrolysis by proteases common to the brush gates of this invention are well known, and in particular border Such as aminopeptidase N. In addition, di- or tripep include carboxypeptidases. Carboxypeptidases digest tides alternatively are selected on the basis of their relative polypeptides by removing C-terminal residues, and are spe resistance to hydrolysis by proteases found in the lumen of the cific in many instances for particular C-terminal sequences. 10 intestine. For example, tripeptides or polypeptides lacking Such enzymes and their Substrate requirements in general are asp and/or glu are poor Substrates foraminopeptidase A, di- or well known. For example, a dipeptide (having a given pair of tripeptides lacking amino acid residues on the N-terminal residues and a free carboxyl terminus) is covalently bonded side of hydrophobic amino acids (leu, tyr, phe, Val, trp) are through its C.-amino group to the phosphorus or carbonatoms poor Substrates for endopeptidase, and peptides lacking a pro of the compounds herein. In embodiments where W is phos 15 residue at the penultimate positionata free carboxyl terminus phonate it is expected that this peptide will be cleaved by the appropriate peptidolytic enzyme, leaving the carboxyl of the are poor substrates for carboxypeptidase P. Similar consider proximal amino acid residue to autocatalytically cleave the ations can also be applied to the selection of peptides that are phosphonoamidate bond. either relatively resistant or relatively susceptible to hydroly Suitable dipeptidyl groups (designated by their single letter sis by cytosolic, renal, hepatic, serum or other peptidases. code) are AA, AR, AN, AD, AC, AE, AQ, AG, AH, AI, AL, Such poorly cleaved polypeptide amidates are immunogens AK, AM, AF, AP, AS, ATAW, AY, AV, RA, RR, RN, RD, RC, or are useful for bonding to proteins in order to prepare RE, RO, RG, RH, RI, RL, RK, RM, RF, RP, RS, RT, RW, RY, immunogens. RV, NA, NR, NN, ND, NC, NE, NO, NG, NH, NI, NL, NK, NM, NF, NP, NS, NT, NW, NY, NV, DA, DR, DN, DD, DC, 25 SPECIFIC EMBODIMENTS OF THE INVENTION DE, DQ, DG, DH, DI, DL, DK, DM, DF, DP, DS, DT, DW, DY, DV, CA, CR, CN, CD, CC, CE, CO, CG, CH, CI, CLCK, CM, CF, CP, CS, CT, CW, CY, CV, EA, ER, EN, ED, EC, EE, Specific values described for radicals, substituents, and EQ, EG, EH, EI, EL, EK, EM, EF, EP, ES, ET, EW, EY, EV, ranges, as well as specific embodiments of the invention QA, QR, QN. QD, QC, QE, QC, QG, QH, QI, QL, QK, QM, 30 described herein, are for illustration only; they do not exclude QF, QP, QS, QT, QW, QY, QV, GA, GR, GN, GD, GC, GE, other defined values or other values within defined ranges. GQ, GG, GH, GI, GL, GK, GM, GF, GP, GS, GT, GW, GY, In one specific embodiment of the invention A' is of the GV, HA, HR, HN, hd, HC, HE, HQ, HG, HH, HI, HL, HK, formula: HM, HF, HP, HS, HT, HW, HY, HV, IA, IR, IN, ID, IC, IE, IQ, IG, IH, II, IL, IK, IM, IF, IP, IS, IT, IW, IY, IV, LA, LR, LN, 35 LD, LC, LE, LO, LG, LH, LI, LL, LK, LM, LF, LP, LS, LT, Y2 - A. LW, LY, LV, KA, KR, KN, KD, KC, KE, KQ, KG, KH, KI, Y2 Yws KL, KK, KM, KF KP, KS, KT, KW, KY, KV, MA, MR, MN, MD, MC, ME, MQ, MG, MH, MI, ML, MK, MM, MF, MP, MS, MT, MW, MY, MV, FA, FR, FN, FD, FC, FE, FO, FG, 40 R2 R2 FH, FI, FL, FK, FM, FF, FP, FS, FT, FW, FY, FV, PA, PR, PN, af2. 2. PD, PC, PE, PQ, PG, PH, PI, PL, PK, PM, PF, PP, PS, PT, PW, PY, PV, SA, SR, SN, SD, SC, SE, SQ, SG, SH, SI, SL, SK, SM, SF, SPSS, ST, SW, SY, SV, TA TR, TN, TD, TC, TE, In another specific embodiment of the invention A' is of the TQ, TG, TH, TI, TL, TK, TM, TF, TP. TS, TT, TW, TY, TV, 45 formula: WA, WR, WN, WD, WC, WE, WQ, WG, WH, WI, WLWK, WM, WF, WPWS, WT, WW, WY, WV, YAYR,YN.YD,YC, YE,YO, YG, YHYI, YLYK, YM,YF,YPYS, YTYW,YY, Y2 1. A. YV, VA, VR, VN, VD, VC, VE, VQ, VG, VH, VI, VL, VK, Y2 Ywó VM, VF, VP, VS, VT, VW, VY and VV. 50 Tripeptide residues are also useful as protecting groups. When a phosphonate is to be protected, the sequence X R2 R2 pro-X (where X is any amino acid residue and X is an af2. 2. amino acid residue, a carboxyl ester of proline, or hydrogen) will be cleaved by luminal carboxypeptidase to yield X with 55 a free carboxyl, which in turn is expected to autocatalytically In anotherspecific embodiment of the invention A' is of the cleave the phosphonoamidate bond. The carboxy group of X formula: optionally is esterified with benzyl. Dipeptide or tripeptide species can be selected on the basis of known transport properties and/or Susceptibility to pepti 60 WS dases that can affect transport to intestinal mucosal or other Y2 NA3. cell types. Dipeptides and tripeptides lacking an O-amino group are transport Substrates for the peptide transporter R2 R2 found in brush border membrane of intestinal mucosal cells af2. 2. (Bai, J. P. F., (1992) Pharm Res. 9:969-978). Transportcom 65 petent peptides can thus be used to enhance bioavailability of the amidate compounds. Di- or tripeptides having one or US 7,871,991 B2 31 32 In another specific embodiment of the invention A' is of the In anotherspecific embodiment of the invention A' is of the formula: formula:

5 O R2 WS | N3A. O P O

2 (A) - O NR R2 R2 10 H H/ 2 af2.

whereinY is O or N(R); and M12d is 1,2,3,4,5,6,7 or 8. In another specific embodiment of the invention A' is of the 15 Inanother specific embodiment of the invention A' is of the formula: formula:

2O WSG

A: R R/ 2 2 R R af2. 25 wherein Wis a carbocycle independently substituted with 0 or 1 R groups; and W is a carbocycle or a heterocycle where W is inde- In another specific embodiment of the invention A' is of the pendently substituted with 0 or 1 R groups. A specific value formula: for M12a is 1. In another specific embodiment of the invention A' is of the formula: WSGNA3: 35 s

W3 s Y2 N A3. wherein W is a carbocycle or heterocycle where W is 40 independently substituted with 0 or 1 R groups. R2 R2 M2 2. In anotherspecific embodiment of the invention A' is of the formula:

45 In another specific embodiment of the invention A' is of the O R2 formula: O P O W3 50 1 xN orW3 x) N A3. H H/2 \1Y R2 R2 af2. 55 whereinY is O or N(R); and M12dis 1,2,3,4,5,6,7 or 8. In another specific embodiment of the invention A' is of the In a specific embodiment of the invention A is of the formula: formula:

w& 60 Y2 A: Y2 Nw. R2 R2 R2 R2 af2. 2. 65 wherein Wis a carbocycle independently substituted with 0 or 1 R groups; US 7,871,991 B2 33 34 In another specific embodiment of the invention A is of the In a specific embodiment of the invention A is of the formula: formula:

Yl

P Y2 N-RR R2 R2 10 n Y 2. af2. 2. R2 R2

af2. 2. In another specific embodiment of the invention M12b is 1. 15 In another specific embodiment of the invention M2b is 0. Y’ is a bond and W is a carbocycle or heterocycle where W In anotherspecific embodiment of the invention A is of the is optionally and independently substituted with 1, 2, or 3 R' formula: groups. 2O In another specific embodiment of the invention A is of the formula: Yl 25 c- WSa: Y2 N 21 R r1 Y: J, R2 R2 af2. 30 af2. wherein W is a carbocycle or heterocycle where W is optionally and independently substituted with 1, 2, or 3 R' In another specific embodiment of the invention A is of the groups. formula: In another specific embodiment of the invention M12a is 1. In another specific embodiment of the invention A is selected from phenyl, substituted phenyl, benzyl, substituted benzyl, pyridyl and substituted pyridyl. 40 M" In another specific embodiment of the invention A is of the P R formula: Y2a N 1 r1 Y- J, 45 2 R2 R2 Y2 Sw af2.

1 R2 R2 50 af2. 2. wherein Y is O or S; and Y is O, N(R) or S. In another specific embodiment of the invention A is of the In another specific embodiment of the invention A is of the formula: formula: 55 O W4. Y2 O N - 60 r1 Y 2. R2 R2 R2 R2 af2. af2. 2. 65 In another specific embodiment of the invention M12b is 1. wherein Y is O or N(R). US 7,871,991 B2 35 36 In another specific embodiment of the invention A is of the In anotherspecific embodiment of the invention A is of the formula: formula:

5 M P R 2 Y.2 FN N1 R 1O Y2b 10 ( 2 2 ) YR n 2s R. R. / Wis. R1 RI 1 2. af2d 15 In another specific embodiment of the invention W is phenyl. whereinY'2 is O or N(R);XY. and M12d is 1,2,3,4,5,6,7 or 8. In another specific embodiment of the invention A is of the In another specific embodiment of the invention A is of the 2O formula: formula:

O M" P| 25 Y.2a P R O 1. R 2- A N Y2 1 1. Y2b 2. 2 2 n s R R af2.

YW3 s H. H. 30 Y2a af2d whereinY” is O or N(R'); and M12dis 1,2,3,4,5,6,7 or 8. wherein Y is O or S; and Y is O, N(R) or S. In another specific embodiment of the invention M12d is 1. 35 In another specific embodiment of the invention A is of the In another specific embodiment of the invention A is of the formula: formula:

40

O P R

n 45 2x)\rR.2 R.2 / 21"W3

50 In another specific embodiment of the invention A is of the wherein Y is O or N(R). formula: In anotherspecific embodiment of the invention A is of the formula:

55 Y1 Y1 Y2 ( ) l N21 R 2-" ver R.2 R.2 / 60 ( R" R' )/ 21Wis. 1"W3 2.

65 In another specific embodiment of the invention W is a whereinY” is O or N(R'); and M12d is 1,2,3,4,5,6,7 or 8. carbocycle. In another specific embodiment of the invention R' is H. US 7,871,991 B2 37 38 In another specific embodiment of the invention A is of the In anotherspecific embodiment of the invention A is of the formula: formula:

N | --R O P us R2 21 2-S-S-S-S-),'-- O H. H. O \-OP R. 10 Y ORI In anotherspecific embodiment of the invention A is of the af2d R1 RI formula: 2.É.--O 15 wherein the phenyl carbocycle is substituted with 0, 1, 2, or 3 R groups. In another specific embodiment of the invention A is of the formula: 2O Yl

N wherein Y''' is O or S; and Y is O, N(R) or S. --R2 25 2 In anotherspecific embodiment of the invention A is of the formula: O O \-OP R. 2- af2d NH OR. 30 R2 R1 RI O P O Y2b 2 D2 In another specific embodiment of the invention A is of the 35 R4 R. af2. Yla 2: formula: wherein Y is O or S;Y is O or N(R); and Y is O, N(R) or S. 40 In anotherspecific embodiment of the invention A is of the formula:

O O Y- O CH 45 XN N ORI H. H. O

50 In another specific embodiment of the invention A is of the wherein Y is O or S;Y is O or N(R);Y is O or N(R'); formula: and M12d is 1, 2, 3, 4, 5, 6, 7 or 8. 55 In another specific embodiment of the invention A is of the formula:

O 60 \,-0 CH, 2- O X R O ORI H. H. O 65 whereinY is O or N(R); and M12dis 1,2,3,4,5,6,7 or 8. US 7,871,991 B2 39 40 In another specific embodiment of the invention A is of the In anotherspecific embodiment of the invention A is of the formula: formula:

O R2 O Y2d R2 O PNy25 N R;py. O P O Y -w Yla >1 Y2b NR2 R R af2. H. H. O 2 10 wherein Y is O or S;Y is O or N(R);Y is O or N(R'); and M12d is 1, 2, 3, 4, 5, 6, 7 or 8. In anotherspecific embodiment of the invention A is of the wherein Y is O or N(R). formula: In another specific embodiment of the invention A is of the 15 formula:

O | 2O C. P O >1 O~ NR2 whereinY is O or N(R); and M12d is 1,2,3,4,5,6,7 or 8. H. H. O 2 In another specific embodiment of the invention A is of the 25 formula: In another specific embodiment of the invention A is of the formula: O R2

30 O P O

Yl 3 rx\rH. H. -W y2b n Y2 Pn-RN -W: 35 wherein Y is O or N(R). R2 R2 af2. Y In anotherspecific embodiment of the invention A is of the formula: In another specific embodiment of the invention A is of the formula: 40 O 2. - R' R2 Yla n- N 3. Y -W s n Y2a |N. . Y& " 45 R" R/ 2 2 Yza -W 3. R R af2. wherein: Y is O or N(R); and M12d is 1, 2, 3, 4, 5, 6, 7 or 8. 50 In anotherspecific embodiment of the invention A is of the wherein Y''' is O or S; and Y is O, N(R) or S. formula: In another specific embodiment of the invention A is of the formula: 55

R2 O Y2Cn W-O R1 n Sy: R; 60 O PQ 2. N -W Yla n Y ORI 2 2 Y2b R R af2. R. R. af2d O

65 wherein Y''' is O or S;Y is O or N(R); and Y is O, N(R) wherein the phenyl carbocycle is substituted with 0, 1, 2, or 3 or S. R groups. US 7,871,991 B2 41 42 In another specific embodiment of the invention A is of the In a specific embodiment of the invention R is of the formula: formula:

R2 ne's Y2CYRy, Yla W-O RI 10 O R O ORI wherein Y"wrila is: O or S; and Y2e is O, N(R') or S. In a specific embodiment of the invention R is of the R1 RI af2d O formula: 15 R2 wherein the phenyl carbocycle is substituted with 0, 1, 2, or 3 R groups. Yê R: In another specific embodiment of the invention A is of the 2O s formula: Yla wherein Y''' is O or S; and Y is O or N(R). In a specific embodiment of the invention R is of the 25 formula: Me Me O V -O CH3 R2 O R X O OR. 30 O NRy. H. H. O

In a specific embodiment of the invention R’ is hydrogen or In a specific embodiment of the invention A' is of the 35 alkyl of 1 to 10 carbons. formula: In a specific embodiment of the invention R is of the formula:

40 city-i-o-r R2 O NR ne'sO 45 O wherein each R is independently (C-C)alkyl. In a specific embodiment of the invention R is indepen In a specific embodiment of the invention R is of the dently H, R', W, a protecting group, or the formula: formula: 50

Yl R. R. Yl Y

R:s 2 Y2 ls Y2 R. Y2 12 Yv2 Y2 afe 55 afe afic In a specific embodiment of the invention R is of the formula: wherein: R’ is independently H. W. R. or a protecting group; 60 R" is independently H or alkyl of 1 to 18 carbon atoms; R2 R2 R’ is independently H, R, R or R' wherein each R is independently substituted with 0 to 3 R' groups or taken Yê together at a carbon atom, two R groups form a ring of 3 to 8 65 af2. R carbons and the ring may be substituted with 0 to 3R groups; Yl wherein R is as defined herein. US 7,871,991 B2 43 44 In a specific embodiment of the invention Y is O or S In a specific embodiment of the inventionY is O, N(R) or S N In one specific embodiment of the invention R is a group NN n of the formula: 5 s 2 s 21 s

R. R. Yl

Yl R; 10 N 2- e f v2 M12 N. afe :1 21 s ( s N f s Yi, Y). Y). / H

15 wherein: S e N N m1a, m1b, m1 c, mild and mile are independently 0 or 1; \ f s f and W m12c is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; N S S R’ is H. W. R. or a protecting group; wherein W. R. Y and Y areas defined herein;- . 2O W carbocycles and heterocycles may be independently provided that: substituted with 0 to 3 R' groups, as defined above. For if m1a, m12c, and mild are 0, then mlb. mlc and mile are example, substituted W carbocycles include: 0: if m1a and m12c are 0 and mild is not 0, then m1b and m1c 25 are 0; OH if m1a and mild are 0 and m12c is not 0, then m1b and at /-/ least one of m1c and mile are 0; if m1a is 0 and m12c and mid are not 0, then m1b is 0; N if m12c and mild are 0 and m1a is not 0, then at least two of 30 - \- m1b, m1c and mile are 0; OH if m12c is 0 and m1a and mid are not 0, then at least one of m1b and m1c are 0; and if mild is 0 and m1a and m12c are not 0, then at least one of m1c and mile are 0. 35 C In compounds of the invention W carbocycles and W. o heterocycles may be independently substituted with 0 to 3 R' N groups. W may be a saturated, unsaturated or aromatic ring \ / comprising a mono- or bicyclic carbocycle or heterocycle. A W may have 3 to 10 ring atoms, e.g., 3 to 7 ring atoms. The C Wrings are saturated when containing 3 ring atoms, Satu rated or mono-unsaturated when containing 4 ring atoms, N Yo saturated, or mono- or di-unsaturated when containing 5 ring atoms, and Saturated, mono- or di-unsaturated, or aromatic as \ / NH2 when containing 6 ring atoms. A Wheterocycle may be a monocycle having 3 to 7 ring members (2 to 6 carbonatoms and 1 to 3 heteroatoms selected from N, O, P, and S) or a bicycle having 7 to 10 ring members / V (4 to 9 carbon atoms and 1 to 3 heteroatoms selected from N, so \ NH NH N NH O, P, and S). Wheterocyclic monocycles may have 3 to 6 ring \ / atoms (2 to 5 carbon atoms and 1 to 2 heteroatoms selected from N, O, and S); or 5 or 6 ring atoms (3 to 5 carbon atoms 2-N O N SH 2-x Ys O and 1 to 2 heteroatoms selected from NandS). Wheterocy- 2 clic bicycles have 7 to 10 ring atoms (6 to 9 carbon atoms and 55 1 to 2 heteroatoms selected from N, O, and S) arranged as a bicyclo 4.5, 5.5, 5.6, or 6.6 system; or 9 to 10 ring Examples of substituted phenyl carbocycles include: atoms (8 to 9 carbon atoms and 1 to 2 hetero atoms selected from NandS) arranged as a bicyclo[5.6 or 6.6 system. The Wheterocycle may be bonded to Y through a carbon, nitro- 60 gen,Wheterocycles Sulfur or other includeatom by for a stable example, covalent pyridyl, bond. dihydropy- HN X-st HN X-s, ridyl isomers, piperidine, pyridazinyl, pyrimidinyl, pyrazi- O O nyl. S-triazinyl, oxazolyl, imidazolyl, thiazolyl, isoxazolyl, pyrazolyl, isothiazolyl, furanyl, thiofuranyl, thienyl, and pyr- 65 rolyl. Walso includes, but is not limited to, examples such aS US 7,871,991 B2 45 46 In another embodiment of the invention the linking group -continued or linker is a divalent radical formed from a peptide. In another embodiment of the invention the linking group or linker is a divalent radical formed from an amino acid. 5 In another embodiment of the invention the linking group or linker is a divalent radical formed from poly-L-glutamic s X- s \ { acid, poly-L-aspartic acid, poly-L-histidine, poly-L-orni thine, poly-L-serine, poly-L-threonine, poly-L-tyrosine, poly-L-leucine, poly-L-lysine-L-phenylalanine, poly-L- 10 lysine or poly-L-lysine-L-tyrosine. \ . In another embodiment of the invention the linking group or linker is of the formula W (CH), wherein, n is between S) y about 1 and about 10; and W is —N(R)C(=O)— —C(=O) N(R)— —OC(=O)— —C(=O)C)— —O— —S , 15 S(O)— —S(O) , —C(-O)— —N(R)—, or a direct bond; wherein each R is independently H or (C-C)alkyl. In another embodiment of the invention the linking group or linker is methylene, ethylene, or propylene. y- NH2 In another embodiment of the invention the linking group or linker is attached to the phosphonate group through a carbon atom of the linker. Intracellular Targeting Linking Groups and Linkers The optionally incorporated phosphonate group of the compounds of the invention may cleave in vivo in stages after The invention provides conjugates that comprise an HIV 25 inhibiting compound that is optionally linked to one or more they have reached the desired site of action, i.e. inside a cell. phosphonate groups either directly (e.g. through a covalent One mechanism of action inside a cell may entail a first bond) or through a linking group (i.e. a linker). The nature of cleavage, e.g. by esterase, to provide a negatively-charged the linker is not critical provided it does not interfere with the “locked-in' intermediate. Cleavage of a terminal ester group ability of the phosphonate containing compound to function 30 ing in a compound of the invention thus affords an unstable as a therapeutic agent. The phosphonate or the linker can be intermediate which releases a negatively charged “locked in linked to the compound (e.g. a compound of formula A) at any intermediate. synthetically feasible position on the compound by removing After passage inside a cell, intracellular enzymatic cleav a hydrogen or any portion of the compound to provide an open age or modification of the phosphonate or prodrug compound may result in an intracellular accumulation of the cleaved or valence for attachment of the phosphonate or the linker. 35 modified compound by a “trapping mechanism. The cleaved In one embodiment of the invention the linking group or or modified compound may then be “locked-in' the cell by a linker (which can be designated “L”) can include all or a significant change in charge, polarity, or other physical prop portions of the group A' A' A', or W described herein. erty change which decreases the rate at which the cleaved or In another embodiment of the invention the linking group modified compound can exit the cell, relative to the rate at or linker has a molecular weight of from about 20 daltons to 40 which it entered as the phosphonate prodrug. Other mecha about 400 daltons. nisms by which a therapeutic effect are achieved may be In another embodiment of the invention the linking group operative as well. Enzymes which are capable of an enzy or linker has a length of about 5 angstroms to about 300 matic activation mechanism with the phosphonate prodrug angStroms. compounds of the invention include, but are not limited to, In another embodiment of the invention the linking group 45 amidases, esterases, microbial enzymes, phospholipases, or linker separates the DRUGanda P(=Y) residue by about cholinesterases, and phosphatases. 5 angstroms to about 200 angstroms, inclusive, in length. From the foregoing, it will be apparent that many different In another embodiment of the invention the linking group drugs can be derivatized in accord with the present invention. or linker is a divalent, branched or unbranched, saturated or 50 Numerous Such drugs are specifically mentioned herein. unsaturated, hydrocarbon chain, having from 2 to 25 carbon However, it should be understood that the discussion of drug atoms, wherein one or more (e.g. 1, 2, 3, or 4) of the carbon families and their specific members for derivatization accord atoms is optionally replaced by (—O—), and wherein the ing to this invention is not intended to be exhaustive, but chain is optionally Substituted on carbon with one or more merely illustrative. (e.g. 1, 2, 3, or 4) Substituents selected from (C-C)alkoxy, 55 HIV-Inhibitory Compounds (C-C)cycloalkyl, (C-C)alkanoyl, (C-C)alkanoyloxy, The compounds of the invention include those with HIV (C-C)alkoxycarbonyl, (C-C)alkylthio, azido, cyano, inhibitory activity. The compounds of the inventions option nitro, halo, hydroxy, oxo (=O), carboxy, aryl, aryloxy, het ally bear one or more (e.g. 1, 2, 3, or 4) phosphonate groups, eroaryl, and heteroaryloxy. which may be a prodrug moiety. In another embodiment of the invention the linking group 60 The term “HIV-inhibitory compound” includes those com or linker is of the formula W-A wherein A is (C-C)alkyl, pounds that inhibit HIV. (C-C24)alkenyl, (C-C24)alkynyl, (C-Cs)cycloalkyl, (C- Typically, compounds of the invention have a molecular Co)aryl or a combination thereof, wherein W is N(R)C weight of from about 400 amu to about 10,000 amu; in a (=O)— —C(=O)N(R)— —OC(=O)— —C(=O)C)—, specific embodiment of the invention, compounds have a O— —S— —S(O)— —S(O) , —N(R)—, 65 molecular weight of less than about 5000 amu; in another —C(=O)—, or a direct bond; wherein each R is indepen specific embodiment of the invention, compounds have a dently H or (C-C)alkyl. molecular weight of less than about 2500 amu; in another US 7,871,991 B2 47 48 specific embodiment of the invention, compounds have a that the compound or conjugate of the invention is at least molecular weight of less than about 1000 amu; in another about 90 wt.% free from biological materials; in another specific embodiment of the invention, compounds have a specific embodiment, the term means that the compound or molecular weight of less than about 800 amu; in another conjugate of the invention is at least about 98 wt.% free from specific embodiment of the invention, compounds have a biological materials; and in another embodiment, the term molecular weight of less than about 600 amu; and in another means that the compound or conjugate of the invention is at specific embodiment of the invention, compounds have a least about 99 wt.% free from biological materials. In another molecular weight of less than about 600 amu and a molecular specific embodiment, the invention provides a compound or weight of greater than about 400 amu. conjugate of the invention that has been synthetically pre The compounds of the invention also typically have a logD 10 pared (e.g., ex vivo). (polarity) less than about 5. In one embodiment the invention Cellular Accumulation provides compounds having a logD less than about 4; in In one embodiment, the invention is provides compounds another one embodiment the invention provides compounds capable of accumulating in human PBMC (peripheral blood having a logD less than about 3; in another one embodiment mononuclear cells). PBMC refer to blood cells having round the invention provides compounds having a logD greater than 15 lymphocytes and monocytes. Physiologically, PBMC are about -5; in another one embodiment the invention provides critical components of the mechanism against infection. compounds having a logD greater than about -3; and in PBMC may be isolated from heparinized whole blood of another one embodiment the invention provides compounds normal healthy donors or buffy coats, by standard density having a logD greater than about 0 and less than about 3. gradient centrifugation and harvested from the interface, Selected substituents within the compounds of the inven washed (e.g. phosphate-buffered saline) and stored in freez tion are present to a recursive degree. In this context, “recur ing medium. PBMC may be cultured in multi-well plates. At sive substituent’ means that a substituent may recite another various times of culture, Supernatant may be either removed instance of itself. Because of the recursive nature of such for assessment, or cells may be harvested and analyzed Substituents, theoretically, a large number may be present in (Smith R. et al (2003) Blood 102(7):2532-2540). The com any given embodiment. For example, R contains a R” sub 25 pounds of this embodiment may further comprise a phospho stituent. R” can be R, which in turn can be R. If R is selected nate or phosphonate prodrug. More typically, the phospho to be R, thena second instance of R' can be selected. One of nate or phosphonate prodrug can have the structure A as ordinary skill in the art of medicinal chemistry understands described herein. that the total number of such substituents is reasonably lim Typically, compounds of the invention demonstrate ited by the desired properties of the compound intended. Such 30 improved intracellular half-life of the compounds or intrac properties include, by of example and not limitation, physical ellular metabolites of the compounds in human PBMC when properties such as molecular weight, solubility or log P appli compared to analogs of the compounds not having the phos cation properties such as activity against the intended target, phonate or phosphonate prodrug. Typically, the half-life is and practical properties such as ease of synthesis. improved by at least about 50%, more typically at least in the By way of example and not limitation, W. RandR are all 35 range 50-100%, still more typically at least about 100%, more recursive Substituents in certain embodiments. Typically, typically yet greater than about 100%. each of these may independently occur 20, 19, 18, 17, 16, 15, In one embodiment of the invention the intracellular half 14, 13, 12, 11, 10,9,8,7,6, 5, 4, 3, 2, 1, or 0, times in a given life of a metabolite of the compound in human PBMCs is embodiment. More typically, each of these may indepen improved when compared to an analog of the compound not dently occur 12 or fewer times in a given embodiment. More 40 having the phosphonate or phosphonate prodrug. In Such typically yet, W will occur 0 to 8 times, R” will occur 0 to 6 embodiments, the metabolite may be generated intracellu times and R will occur 0 to 10 times in a given embodiment. larly, e.g. generated within human PBMC. The metabolite Even more typically, W will occur 0 to 6 times, R' will occur may be a product of the cleavage of a phosphonate prodrug 0 to 4 times and R will occur 0 to 8 times in a given embodi within human PBMCs. The optionally phosphonate-contain ment. 45 ing phosphonate prodrug may be cleaved to form a metabolite Recursive substituents are an intended aspect of the inven having at least one negative charge at physiological pH. The tion. One of ordinary skill in the art of medicinal chemistry phosphonate prodrug may be enzymatically cleaved within understands the versatility of such substituents. To the degree human PBMC to form a phosphonate having at least one that recursive Substituents are present in an embodiment of active hydrogen atom of the form P OH. the invention, the total number will be determined as set forth 50 above. Stereoisomers Whenever a compound described herein is substituted with The compounds of the invention may have chiral centers, more than one of the same designated group, e.g., "R" or e.g., chiral carbon or phosphorus atoms. The compounds of “R”, then it will be understood that the groups may be the the invention thus include racemic mixtures of all stereoiso same or different, i.e., each group is independently selected. 55 mers, including enantiomers, diastereomers, and atropiso Wavy lines indicate the site of covalent bond attachments to mers. In addition, the compounds of the invention include the adjoining groups, moieties, or atoms. enriched or resolved optical isomers at any or all asymmetric, In one embodiment of the invention, the compound is in an chiral atoms. In other words, the chiral centers apparent from isolated and purified form. Generally, the term "isolated and the depictions are provided as the chiral isomers or racemic purified” means that the compound is substantially free from 60 mixtures. Both racemic and diastereomeric mixtures, as well biological materials (e.g. blood, tissue, cells, etc.). In one as the individual optical isomers isolated or synthesized, Sub specific embodiment of the invention, the term means that the stantially free of their enantiomeric or diastereomeric part compound or conjugate of the invention is at least about 50 ners, are all within the scope of the invention. The racemic wt.% free from biological materials; in another specific mixtures are separated into their individual, Substantially embodiment, the term means that the compound or conjugate 65 optically pure isomers through well-known techniques such of the invention is at least about 75 wt.% free from biological as, for example, the separation of diastereomeric salts formed materials; in another specific embodiment, the term means with optically active adjuncts, e.g., acids or bases followed by US 7,871,991 B2 49 50 conversion back to the optically active Substances. In most The compounds herein are labeled in conventional fashion instances, the desired optical isomer is synthesized by means using functional groups such as hydroxyl or amino. of stereospecific reactions, beginning with the appropriate Within the context of the invention samples suspected of Stereoisomer of the desired starting material. containing HIV include natural or man-made materials such The compounds of the invention can also exist as tauto- 5 as living organisms; tissue or cell cultures; biological samples meric isomers in certain cases. All though only one delocal Such as biological material samples (blood, serum, urine, ized resonance structure may be depicted, all Such forms are cerebrospinal fluid, tears, sputum, saliva, tissue samples, and contemplated within the scope of the invention. For example, the like); laboratory samples; food, water, or air samples: ene-amine tautomers can exist for purine, pyrimidine, imida bioproduct samples such as extracts of cells, particularly Zole, guanidine, amidine, and tetrazole systems and all their 10 recombinant cells synthesizing a desired glycoprotein; and possible tautomeric forms are within the scope of the inven the like. Typically the sample will be suspected of containing tion. HIV. Samples can be contained in any medium including Salts and Hydrates water and organic solvent/water mixtures. Samples include The compositions of this invention optionally comprise living organisms such as humans, and man made materials salts of the compounds herein, especially pharmaceutically 15 Such as cell cultures. acceptable non-toxic salts containing, for example, Na', Li". The treating step of the invention comprises adding the K", Ca' and Mg". Such salts may include those derived by composition of the invention to the sample or it comprises combination of appropriate cations such as alkali and alkaline adding a precursor of the composition to the sample. The earth metal ions or ammonium and quaternary amino ions addition step comprises any method of administration as with an acid anion moiety, typically a carboxylic acid. described above. Monovalent salts are preferred if a water soluble salt is If desired, the activity of HIV after application of the com desired. position can be observed by any method including direct and Metal salts typically are prepared by reacting the metal indirect methods of detecting HIV activity. Quantitative, hydroxide with a compound of this invention. Examples of qualitative, and semiquantitative methods of determining metal salts which are prepared in this way are salts containing 25 HIV activity are all contemplated. Typically one of the Li, Na', and K". A less soluble metal salt can be precipitated screening methods described above are applied, however, any from the solution of a more soluble salt by addition of the other method such as observation of the physiological prop Suitable metal compound. erties of a living organism are also applicable. In addition, salts may be formed from acid addition of Many organisms contain HIV. The compounds of this certain organic and inorganic acids, e.g., HCl, HBr, HSO 30 invention are useful in the treatment or prophylaxis of condi HPO or organic sulfonic acids, to basic centers, typically tions associated with HIV activation in animals or in man. amines, or to acidic groups. Finally, it is to be understood that However, in screening compounds capable of inhibiting the compositions herein comprise compounds of the inven HIV it should be kept in mind that the results of enzyme tion in their unionized, as well as Zwitterionic form, and assays may not correlate with cell culture assays. Thus, a cell combinations with Stoichiometric amounts of water as in 35 based assay should be the primary Screening tool. hydrates. Screens for HIV Inhibitors Also included within the scope of this invention are the Compositions of the invention are screened for inhibitory salts of the parental compounds with one or more amino activity against HIV by any of the conventional techniques for acids. Any of the amino acids described above are Suitable, 40 evaluating enzyme activity. Within the context of the inven especially the naturally-occurring amino acids found as pro tion, typically compositions are first screened for inhibition of tein components, although the amino acid typically is one HIV in vitro and compositions showing inhibitory activity are bearing a side chain with a basic or acidic group, e.g., lysine, then screened for activity in vivo. Compositions having in arginine or glutamic acid, or a neutral group Such as glycine, vitro Ki (inhibitory constants) of less then about 5x10 M. serine, threonine, alanine, isoleucine, or leucine. 45 typically less than about 1x107M and preferably less than Methods of Inhibition of HIV about 5x10 Mare preferred for in vivo use. Another aspect of the invention relates to methods of inhib iting the activity of HIV comprising the step of treating a Useful in vitro screens have been described in detail. sample Suspected of containing HIV with a composition of Pharmaceutical Formulations the invention. 50 The compounds of this invention are formulated with con Compositions of the invention may act as inhibitors of HIV. ventional carriers and excipients, which will be selected in as intermediates for such inhibitors or have other utilities as accord with ordinary practice. Tablets will contain excipients, described below. The inhibitors will generally bind to loca glidants, fillers, binders and the like. Aqueous formulations tions on the Surface or in a cavity of the liver. Compositions are prepared in sterile form, and when intended for delivery binding in the liver may bind with varying degrees of revers 55 by other than oral administration generally will be isotonic. ibility. Those compounds binding substantially irreversibly All formulations will optionally contain excipients such as are ideal candidates for use in this method of the invention. those set forth in the Handbook of Pharmaceutical Excipients Once labeled, the substantially irreversibly binding compo (1986). Excipients include ascorbic acid and other antioxi sitions are useful as probes for the detection of HIV. Accord dants, chelating agents such as EDTA, carbohydrates Such as ingly, the invention relates to methods of detecting NS3 in a 60 dextrin, hydroxyalkylcellulose, hydroxyalkylmethylcellu sample Suspected of containing HIV comprising the steps of lose, stearic acid and the like. The pH of the formulations treating a sample Suspected of containing HIV with a com ranges from about 3 to about 11, but is ordinarily about 7 to position comprising a compound of the invention bound to a 10. label; and observing the effect of the sample on the activity of While it is possible for the active ingredients to be admin the label. Suitable labels are well known in the diagnostics 65 istered alone it may be preferable to present them as pharma field and include stable free radicals, fluorophores, radioiso ceutical formulations. The formulations, both for veterinary topes, enzymes, chemiluminescent groups and chromogens. and for human use, of the invention comprise at least one US 7,871,991 B2 51 52 active ingredient, as above defined, together with one or more so-called emulsifying wax, and the wax together with the oil acceptable carriers therefor and optionally other therapeutic and fat make up the so-called emulsifying ointment base ingredients. The carrier(s) must be “acceptable' in the sense which forms the oily dispersed phase of the cream formula of being compatible with the other ingredients of the formu tions. lation and physiologically innocuous to the recipient thereof. Emulgents and emulsion stabilizers suitable for use in the The formulations include those suitable for the foregoing formulation of the invention include Tween(R) 60, SpanR 80. administration routes. The formulations may conveniently be cetostearyl alcohol, benzyl alcohol, myristyl alcohol, glyc presented in unit dosage form and may be prepared by any of eryl mono-stearate and sodium lauryl Sulfate. the methods well known in the art of pharmacy. Techniques The choice of suitable oils or fats for the formulation is and formulations generally are found in Remington's Phar 10 based on achieving the desired cosmetic properties. The maceutical Sciences (Mack Publishing Co., Easton, Pa.). cream should preferably be a non-greasy, non-staining and Such methods include the step of bringing into association the washable product with Suitable consistency to avoid leakage active ingredient with the carrier which constitutes one or from tubes or other containers. Straight or branched chain, more accessory ingredients. In general the formulations are mono- or dibasic alkyl esters such as di-isoadipate, isocetyl prepared by uniformly and intimately bringing into associa 15 Stearate, propylene glycol diester of coconut fatty acids, iso tion the active ingredient with liquid carriers or finely divided propyl myristate, decyl oleate, isopropyl palmitate, butyl Solid carriers or both, and then, if necessary, shaping the stearate, 2-ethylhexyl palmitate or a blend of branched chain product. esters known as Crodamol CAP may be used, the last three Formulations of the present invention suitable for oral being preferred esters. These may be used alone or in com administration may be presented as discrete units such as bination depending on the properties required. Alternatively, capsules, cachets or tablets each containing a predetermined high melting point lipids such as white soft paraffin and/or amount of the active ingredient; as a powder or granules; as a liquid paraffin or other mineral oils are used. Solution or a Suspension in an aqueous or non-aqueous liquid; Pharmaceutical formulations according to the present or as an oil-in-water liquid emulsion or a water-in-oil liquid invention comprise one or more compounds of the invention emulsion. The active ingredient may also be administered as 25 together with one or more pharmaceutically acceptable car a bolus, electuary or paste. riers or excipients and optionally other therapeutic agents. A tablet is made by compression or molding, optionally Pharmaceutical formulations containing the active ingredient with one or more accessory ingredients. Compressed tablets may be in any form suitable for the intended method of may be prepared by compressing in a Suitable machine the administration. When used for oral use for example, tablets, active ingredient in a free-flowing form Such as a powder or 30 troches, lozenges, aqueous or oil Suspensions, dispersible granules, optionally mixed with a binder, lubricant, inert dilu powders or granules, emulsions, hard or soft capsules, syrups ent, preservative, surface active or dispersing agent. Molded or elixirs may be prepared. Compositions intended for oral tablets may be made by molding in a suitable machine a use may be prepared according to any method known to the mixture of the powdered active ingredient moistened with an art for the manufacture of pharmaceutical compositions and inert liquid diluent. The tablets may optionally be coated or 35 Such compositions may contain one or more agents including scored and optionally are formulated so as to provide slow or Sweetening agents, flavoring agents, coloring agents and pre controlled release of the active ingredient therefrom. serving agents, in order to provide a palatable preparation. For administration to the eye or other external tissues e.g., Tablets containing the active ingredient in admixture with mouth and skin, the formulations are preferably applied as a non-toxic pharmaceutically acceptable excipient which are topical ointment or cream containing the active ingredient(s) 40 suitable for manufacture of tablets are acceptable. These in an amount of, for example, 0.075 to 20% w/w (including excipients may be, for example, inert diluents, such as cal active ingredient(s) in a range between 0.1% and 20% in cium or sodium carbonate, lactose, lactose monohydrate, increments of 0.1% w/w such as 0.6% w/w, 0.7% w/w, etc.), croScarmellose Sodium, povidone, calcium or sodium phos preferably 0.2 to 15% w/w and most preferably 0.5 to 10% phate; granulating and disintegrating agents, such as maize w/w. When formulated in an ointment, the active ingredients 45 starch, or alginic acid; binding agents, such as cellulose, may be employed with either a paraffinic or a water-miscible microcrystalline cellulose, starch, gelatin oracacia; and lubri ointment base. Alternatively, the active ingredients may be cating agents. Such as magnesium Stearate, Stearic acid or talc. formulated in a cream with an oil-in-water cream base. Tablets may be uncoated or may be coated by known tech If desired, the aqueous phase of the cream base may niques including microencapsulation to delay disintegration include, for example, at least 30% w/w of a polyhydric alco 50 and adsorption in the gastrointestinal tract and thereby pro hol, i.e. an alcohol having two or more hydroxyl groups such vide a Sustained action over a longer period. For example, a as propylene glycol, butane 1,3-diol, mannitol, Sorbitol, glyc time delay material Such as glyceryl monostearate or glyceryl erol and polyethylene glycol (including PEG 400) and mix distearate alone or with a wax may be employed. tures thereof. The topical formulations may desirably include Formulations for oral use may be also presented as hard a compound which enhances absorption or penetration of the 55 gelatin capsules where the active ingredient is mixed with an active ingredient through the skin or other affected areas. inert Solid diluent, for example calcium phosphate or kaolin, Examples of such dermal penetration enhancers include dim or as Soft gelatin capsules wherein the active ingredient is ethyl Sulphoxide and related analogs. mixed with water oran oil medium, Such as peanut oil, liquid The oily phase of the emulsions of this invention may be paraffin or olive oil. constituted from known ingredients in a known manner. 60 Aqueous Suspensions of the invention contain the active While the phase may comprise merely an emulsifier (other materials in admixture with excipients—suitable for the wise known as an emulgent), it desirably comprises a mixture manufacture of aqueous Suspensions. Such excipients of at least one emulsifier with a fat or an oil or with both a fat include a Suspending agent, such as Sodium carboxymethyl and an oil. Preferably, a hydrophilic emulsifier is included cellulose, methylcellulose, hydroxypropyl methylcellulose, together with a lipophilic emulsifier which acts as a stabilizer. 65 Sodium alginate, polyvinylpyrrolidone, gum tragacanth and It is also preferred to include both an oil and a fat. Together, gum acacia, and dispersing or wetting agents such as a natu the emulsifier(s) with or without stabilizer(s) make up the rally occurring phosphatide (e.g., lecithin), a condensation US 7,871,991 B2 53 54 product of an alkylene oxide with a fatty acid (e.g., polyoxy compositions (weight: weight). The pharmaceutical compo ethylene Stearate), a condensation product of ethylene oxide sition can be prepared to provide easily measurable amounts with a long chain aliphatic alcohol (e.g., heptadecaethyl for administration. For example, an aqueous solution eneoxycetanol), a condensation product of ethylene oxide intended for intravenous infusion may contain from about 3 to with a partial ester derived from a fatty acid and a hexitol 500 ug of the active ingredient per milliliter of solution in anhydride (e.g., polyoxyethylene Sorbitan monooleate). The order that infusion of a suitable volume at a rate of about 30 aqueous Suspension may also contain one or more preserva mL/hr can occur. tives Such as ethyl or n-propyl p-hydroxy-benzoate, one or Formulations suitable for administration to the eye include more coloring agents, one or more flavoring agents and one or eye drops wherein the active ingredient is dissolved or Sus more Sweetening agents, such as Sucrose or saccharin. 10 pended in a suitable carrier, especially an aqueous solvent for Oil Suspensions may be formulated by Suspending the the active ingredient. The active ingredient is preferably active ingredient in a vegetable oil. Such as arachis oil, olive present in such formulations in a concentration of 0.5 to 20%, oil, Sesame oil or coconut oil, or in a mineral oil such as liquid advantageously 0.5 to 10% particularly about 1.5% w/w. paraffin. The oral Suspensions may contain a thickening Formulations suitable for topical administration in the agent, such as beeswax, hard paraffin or cetyl alcohol. Sweet 15 mouth include lozenges comprising the active ingredient in a ening agents, such as those set forth above, and flavoring flavored basis, usually Sucrose and acacia or tragacanth; pas agents may be added to provide a palatable oral preparation. tilles comprising the active ingredient in an inert basis such as These compositions may be preserved by the addition of an gelatin and glycerin, or Sucrose and acacia; and mouthwashes antioxidant Such as ascorbic acid. comprising the active ingredient in a suitable liquid carrier. Dispersible powders and granules of the invention suitable Formulations for rectal administration may be presented as for preparation of an aqueous suspension by the addition of a Suppository with a Suitable base comprising for example water provide the active ingredient in admixture with a dis cocoa butter or a salicylate. persing or wetting agent, a suspending agent, and one or more Formulations Suitable for intrapulmonary or nasal admin preservatives. Suitable dispersing or wetting agents and Sus istration have a particle size for example in the range of 0.1 to pending agents are exemplified by those disclosed above. 25 500 microns (including particle sizes in a range between 0.1 Additional excipients, for example Sweetening, flavoring and and 500 microns in increments microns such as 0.5, 1, 30 coloring agents, may also be present. microns, 35 microns, etc.), which is administered by rapid The pharmaceutical compositions of the invention may inhalation through the nasal passage or by inhalation through also be in the form of oil-in-water emulsions. The oily phase the mouth so as to reach the alveolar sacs. Suitable formula may be a vegetable oil. Such as olive oil or arachis oil, a 30 tions include aqueous or oily solutions of the active ingredi mineral oil. Such as liquid paraffin, or a mixture of these. ent. Formulations suitable for aerosol or dry powder admin Suitable emulsifying agents include naturally-occurring istration may be prepared according to conventional methods gums, such as gum acacia and gum tragacanth, naturally and may be delivered with other therapeutic agents such as occurring phosphatides, such as soybean lecithin, esters or compounds heretofore used in the treatment or prophylaxis of partial esters derived from fatty acids and hexitol anhydrides, 35 conditions associated with HIV activity. Such as Sorbitan monooleate, and condensation products of Formulations suitable for vaginal administration may be these partial esters with ethylene oxide. Such as polyoxyeth presented as pessaries, tampons, creams, gels, pastes, foams ylene Sorbitan monooleate. The emulsion may also contain or spray formulations containing in addition to the active Sweetening and flavoring agents. Syrups and elixirs may be ingredient Such carriers as are known in the art to be appro formulated with Sweetening agents, such as glycerol, Sorbitol 40 priate. or Sucrose. Such formulations may also contain a demulcent, Formulations suitable for parenteral administration a preservative, a flavoring or a coloring agent. include aqueous and non-aqueous sterile injection solutions The pharmaceutical compositions of the invention may be which may contain anti-oxidants, buffers, bacteriostats and in the form of a sterile injectable preparation, such as a sterile solutes which render the formulation isotonic with the blood injectable aqueous or oleaginous Suspension. This suspen 45 of the intended recipient; and aqueous and non-aqueous ster sion may be formulated according to the known art using ille Suspensions which may include Suspending agents and those Suitable dispersing or wetting agents and Suspending thickening agents. agents which have been mentioned above. The sterile inject The formulations are presented in unit-dose or multi-dose able preparation may also be a sterile injectable solution or containers, for example sealed ampoules and vials, and may Suspension in a non-toxic parenterally acceptable diluent or 50 be stored in a freeze-dried (lyophilized) condition requiring Solvent. Such as a solution in 1,3-butane-diol or prepared as a only the addition of the sterile liquid carrier, for example lyophilized powder. Among the acceptable vehicles and Sol water for injection, immediately prior to use. Extemporane vents that may be employed are water, Ringer's solution and ous injection Solutions and Suspensions are prepared from isotonic sodium chloride solution. In addition, sterile fixed sterile powders, granules and tablets of the kind previously oils may conventionally be employed as a solventor Suspend 55 described. Preferred unit dosage formulations are those con ing medium. For this purpose any bland fixed oil may be taining a daily dose or unit daily Sub-dose, as herein above employed including synthetic mono- or diglycerides. In addi recited, or an appropriate fraction thereof, of the active ingre tion, fatty acids Such as oleic acid may likewise be used in the dient. preparation of injectables. It should be understood that in addition to the ingredients The amount of active ingredient that may be combined 60 particularly mentioned above the formulations of this inven with the carrier material to produce a single dosage form will tion may include other agents conventional in the art having vary depending upon the host treated and the particular mode regard to the type of formulation in question, for example of administration. For example, a time-release formulation those Suitable for oral administration may include flavoring intended for oral administration to humans may contain agents. approximately 1 to 1000 mg of active material compounded 65 The invention further provides veterinary compositions with an appropriate and convenient amount of carrier material comprising at least one active ingredient as above defined which may vary from about 5 to about 95% of the total together with a veterinary carrier therefor. US 7,871,991 B2 55 56 Veterinary carriers are materials useful for the purpose of clic 2',3'-dideoxy-2',3'-didehydroguanosine), 3'-azido-2',3'- administering the composition and may be solid, liquid or dideoxyuridine, 5-fluorothymidine, (E)-5-(2-bromovinyl)- gaseous materials which are otherwise inert or acceptable in 2'-deoxyuridine (BVDU), 2-chlorodeoxyadenosine, the veterinary art and are compatible with the active ingredi 2-deoxycoformycin, 5-fluorouracil, 5-fluorouridine, ent. These veterinary compositions may be administered 5-fluoro-2'-deoxyuridine, 5-trifluoromethyl-2'-deoxyuridine, orally, parenterally or by any other desired route. 6-azauridine, 5-fluoroorotic acid, methotrexate, triacetyluri Compounds of the invention can also be formulated to dine, 1-(2'-deoxy-2'-fluoro-1-f-arabinosyl)-5-iodocytidine provide controlled release of the active ingredient to allow (FIAC), tetrahydro-imidazo(4,5,1-jk)-(1,4)-benzodiazepin-2 less frequent dosing or to improve the pharmacokinetic or (1H)-thione (TIBO), 2-nor-cyclicGMP, 6-methoxypurine toxicity profile of the active ingredient. Accordingly, the 10 invention also provided compositions comprising one or arabinoside (ara-M), 6-methoxypurine arabinoside 2'-O-Val more compounds of the invention formulated for Sustained or erate, cytosine arabinoside (ara-C), 2',3'-dideoxynucleosides controlled release. such as 2',3'-dideoxycytidine (ddC), 2',3'-dideoxyadenosine Effective dose of active ingredient depends at least on the (ddA) and 2',3'-dideoxyinosine (ddI), acyclic nucleosides nature of the condition being treated, toxicity, whether the 15 Such as acyclovir, penciclovir, famciclovir, ganciclovir, compound is being used prophylactically (lower doses), the HPMPC, PMEA, PMEG, PMPA, PMPDAP, FPMPA, method of delivery, and the pharmaceutical formulation, and HPMPA, HPMPDAP, (2R,5R)-9->tetrahydro-5-(phospho will be determined by the clinician using conventional dose nomethoxy)-2-furanyladenine, (2R,5R)-1->tetrahydro-5- escalation studies. It can be expected to be from about 0.0001 (phosphonomethoxy)-2-furanylthymine, other antivirals to about 100 mg/kg body weight per day. Typically, from including ribavirin (adenine arabinoside), 2-thio-6-azauri about 0.01 to about 10 mg/kg body weight per day. More dine, tubercidin, aurintricarboxylic acid, 3-deaZaneoplano typically, from about 0.01 to about 5 mg/kg body weight per cin, neoplanocin, rimantidine, adamantine, and foScarnet (tri day. More typically, from about 0.05 to about 0.5 mg/kg body Sodium phosphonoformate), antibacterial agents including weight per day. For example, the daily candidate dose for an bactericidal fluoroquinolones (ciprofloxacin, pefloxacin and adult human of approximately 70 kg body weight will range 25 the like), aminoglycoside bactericidal antibiotics (streptomy from 1 mg to 1000 mg, preferably between 5 mg and 500 mg. cin, gentamicin, amicacin and the like) B-lactamase inhibitors and may take the form of single or multiple doses. (cephalosporins, penicillins and the like), other antibacterials including tetracycline, isoniazid, rifampin, cefoperaZone, Routes of Administration claithromycin and azithromycin, antiparasite or antifungal One or more compounds of the invention (herein referred 30 agents including pentamidine (1.5-bis(4-aminophenoxy) to as the active ingredients) are administered by any route pentane), 9-deaza-inosine, Sulfamethoxazole, Sulfadiazine, appropriate to the condition to be treated. Suitable routes quinapyramine, quinine, fluconazole, ketoconazole, itra include oral, rectal, nasal, topical (including buccal and Sub conazole, Amphotericin B, 5-fluorocytosine, clotrimazole, lingual), vaginal and parenteral (including Subcutaneous, hexadecylphosphocholine and nystatin, renal excretion intramuscular, intravenous, intradermal, intrathecal and epi 35 inhibitors such as probenicid, nucleoside transport inhibitors dural), and the like. It will be appreciated that the preferred Such as dipyridamole, dilaZep and nitrobenzylthioinosine, route may vary with for example the condition of the recipi immunomodulators such as FK506, cyclosporin A, thymosin ent. An advantage of the compounds of this invention is that C-1, cytokines including TNF and TGF-B, interferons includ they are orally bioavailable and can be dosed orally. ing IFN-O, IFN-B, and IFN-Y, interleukins including various Combination Therapy 40 interleukins, macrophage/granulocyte colony stimulating The compounds of the invention may be employed in com factors including GM-CSF, G-CSF, M-CSF, cytokine antago bination with other therapeutic agents for the treatment or nists including anti-TNF antibodies, anti-interleukin antibod prophylaxis of the infections or conditions indicated above. ies, soluble interleukin receptors, protein kinase C inhibitors Examples of Such further therapeutic agents include agents and the like. that are effective for the treatment or prophylaxis of viral, 45 In addition, the therapeutic agents disclosed in Tables 98 parasitic or bacterial infections or associated conditions or for and 99 directed to HIV may be used in combination with treatment of tumors or related conditions include 3'-azido-3'- compounds of the present invention. For example, Table 98 deoxythymidine (zidovudine, AZT), 2'-deoxy-3'-thiacytidine discloses exemplary HIV/AIDS therapeutics, and Table 99 (3TC), 2',3'-dideoxy-2',3'-didehydroadenosine (D4A), 2',3'- discloses Exemplary HIV Antivirals with their corresponding dideoxy-2',3'-didehydrothymidine (D4T), carbovir (carbocy U.S. patent numbers.

TABLE 98 Exemplary HIV/AIDS Therapeutics

Mechanism Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Launched- AZT Azidothymidine AZTEC Anti-HIV Agents Reverse GlaxoSmithKline 1987 BW-ASO9U Zidovudine Retrovir Transcriptase (Originator) Cpd S Inhibitors Launched- NSC- Dideoxycytidine Hivid Anti-HIV Agents Reverse National Cancer 1992 606170 Transcriptase Institute (US) Inhibitors (Originator) Ro-24- Zalcitabine Roche

RO-242O27 US 7,871,991 B2 57 58

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization didC ddCyd Launched BMY-27857 Sanilvudine Zerit Anti-HIV Agents Reverse Bristol-Myers 1994 Transcriptase Squibb Inhibitors (Originator) DTH Stavudine Chemical INSERM Delivery (Originator) Systems d4T ddeThd Launched BMY-4O900 Didanosine Videx Anti-HIV Agents Reverse Bristol-Myers 1991 Transcriptase Squibb Inhibitors (Originator) DDI Dideoxyinosine Bristol-Myers Squibb (Orphan Drug) NSC 612049 d2I ddIno Launched rIL-2 Aldesleukin Macrolin Anti-HIV Agents IL-2 Chiron 1989 (Originator) rhIL-2 Recombinant Proleukin Breast Cancer Nat. Inst. Allergy interleukin-2 herapy & Infectious Dis.

herapy Myelodysplastic Syndrome

herapy Non-Hodgkin's Lymphoma Therapy Renal Cancer Therapy Launched R-56 Saquinavir Fortovase Anti-HIV Agents HIV Protease Chugai 1995 mesilate Inhibitors Pharmaceutical (Originator) Ro-31 Invirase Chugai 8959,003 Pharmaceutical (Orphan Drug) Fortovase Roche (softgel (Originator) capsules) Launched Human Alferon Anti Guangdong 1989 leukocyte LDO Cytomegalovirus interferon alpha Drugs Interferon alfa-n3 Alferon N Anti-HIV Agents HemispheRx (human Gel leukocyte derived) Alferon N Anti-Hepatitis C Interferon Injection Virus Drugs Sciences (Originator) Altemol Anti-Papilloma Virus Drugs Cellferon Antiviral Drugs Genital Warts, Treatment for Multiple Sclerosis, Agents for Oncolytic Drugs Severe Acute Respiratory Syndrome (SARS), US 7,871,991 B2 59 60

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Treatment of Treatment of Female Sexual Dysfunction Launched BI-RG-587 Nevirapine Viramune Anti-HIV Agents Reverse Boehringer 1996 Transcriptase Ingelheim Inhibitors (Originator) BIRG-0587 Nippon Boehringer Ingelheim Roxane Launched 1592U89 Abacavir Ziagen Anti-HIV Agents Reverse GlaxoSmithKline 1999 sulfate sulfate Transcriptase (Originator) Inhibitors GlaxoSmithKline (Orphan Drug) Phase III CD4-IgG CD4 AIDS Medicines Genentech Immunoadhesin (Originator) Recombinant Immunomodulators Nat. Inst. Allergy CD4 & Infectious Dis. immunoglobulin G Recombinant soluble CD4 immunoglobulin G Launched (-)-BCH-189 Lamivudine 3TC Agents for Liver Reverse GlaxoSmithKline 1995 Cirrhosis Transcriptase (-)-SoldC Epivir Anti-HIV Agents Inhibitors Shire BioChem (Originator) 3TC Epivir Anti-Hepatitis B HBV Virus Drugs GG-714 Heptodin GR Heptovir 109714X BCH-790 Lamivir (fomer code) Zeffix Zefix Phase II KNI-272 Kynostatin-272 Anti-HIV Agents HIV Protease apan Energy Inhibitors (Originator) NSC 6S 1714 Launched (-)-FTC Emtricitabine Coviracil Anti-HIV Agents Reverse Emory University 2003 Transcriptase (Originator) 524W91 Emtriva Anti-Hepatitis B Inhibitors Gilead Virus Drugs BW apan Tobacco Launched Delavirdine Rescriptor Anti-HIV Agents Reverse 1997 mesilate Transcriptase Inhibitors (Originator) Pfizer (Orphan Drug) Pre-Registered AG-1661 HIV-1 Remune AIDS Vaccines le Immunogen Response (Originator) RG-83894 Roemmers RG-83894 Trinity Medical 103 Group Launched L-735524 Indinavir Sulfate Crixivan Anti-HIV Agents HIV Protease Banyu 1996 Inhibitors MK-639 Merck & Co. (Originator) Phase I ph AZT Azidothymidine Anti-HIV Agents Reverse Russian phosphonate Transcriptase Academy of Inhibitors Sciences (Originator) Nicavir Phosphazid Phase II NSC (+)-Calanolide A Anti-HIV Agents Reverse Advanced Life 675451 Transcriptase Sciences Inhibitors NSC-664737 Calanolide A Treatment of Sarawak (racemate) Tuberculosis MediChem US 7,871,991 B2 61 62

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization US Department of Health & Human Services (Originator) Phase II SA8 Anti-HIV Agents Anti-CD4 Biogen Idec (Originator) Hu-SA8 Humanized Tanox Monoclonal Antibodies TNX-355 Viral Entry Inhibitors Launched 141W94 Amprenavir Agenerase Anti-HIV Agents HIV Protease GlaxoSmithKline 1999 KVX-478 Prozei Inhibitors Kissei VX-478 Vertex (Originator) Launched DMP-266 Efavirenz Stocrin Anti-HIV Agents Reverse Banyu 1998 Transcriptase inhibitors L-743726 Sustiva Banyu (Orphan Drug) L-743725 Bristol-Myers ((+)- Squibb enantiomer) (Originator) L-741211 (racemate) Launched A-84538 Ritonavir Norwir Anti-HIV Agents HIV Protease Abbott 1996 Inhibitors (Originator) ABTS38 Dainippon Pharmaceutical Launched AG-1343 Nelfinavir Viracept Anti-HIV Agents HIV Protease Agouron 1997 mesilate Inhibitors (Originator) LY-312857 apan Tobacco AG-1346 (free base) Phase III PRO-2OOO Anti-HIV Agents Viral Entry Inhibitors PRO-2OOO.S Microbicides

Council Palligent (Originator) Phase III Gd-Tex Gadolinium Xcytrin Anti-HIV Agents National Cancer texaphyrin institute Motexafin Antineoplastic Pharmacyclics gadolinium Enhancing (Originator) Agents PCI-0120 Brain Cancer Therapy Glioblastoma MultiformeTherapy Head and Neck Cancer Therapy Lung Cancer herapy

herapy Lymphoma Therapy Non-Small Cell Lung Cancer herapy adiosensitizers enal Cancer US 7,871,991 B2 63 64

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Launched DP-178 Enfluvirtide FuZeon Anti-HIV Agents Viral Fusion Duke University 2003 Inhibitors (Originator) R-698 Pentafuside Roche T-20 Trimeris (Originator) Phase II BC-IL Buffy coat MultiKine AIDS Medicines Cel-Sci interleukins (Originator) Cancer University of Immunotherapy Maryland Cervical Cancer Therapy Head and Neck Cancer Therapy Prostate Cancer Therapy Phase II FP-21399 Anti-HIV Agents Viral Fusion EMD Lexigen Inhibitors (Originator) Fuji Photo Film (Originator) Phase II Semapimod Anti-HIV Agents Deoxyhypusine AXxima hydrochloride Synthase Inhibitors CNI-1493 Antipsoriatics Mitogen Cytokine Activated PharmaSciences Protein Kinase (MAPK) Inhibitors Inflammatory Nitric Oxide Picower Institute Bowel Disease, Synthase for Medical Agents for Inhibitors Research (Originator) Pancreatic Disorders, Treatment of Renal Cancer Therapy Phase II ALVAC AIDS Vaccines ANRS MN12O TMGMP ALVAC Merck & Co. wCP205 wCP205 Nat. Inst. Allergy & Infectious Dis. Sanofi Pasteur (Originator) Virogenetics (Originator) Walter Reed Army Institute Phase III CY-2301 Theradigm AIDS Vaccines Epimmune HIV (Originator) EP HIV-1090 DNA Vaccines DM EP-1090 Nat. Inst. Allergy & Infectious Dis. National institutes of Health Phase II Anti-HIV Agents Viral Entry Epicyte Inhibitors PRO-542 Formatech GTC Biotherapeutics Progenics (Originator) Phase I UC-781 Anti-HIV Agents Reverse Biosyn Transcriptase Inhibitors Microbicides Cellegy Uniroyal (Originator) University of Pittsburgh (Originator) US 7,871,991 B2 65 66

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Preclinical ProVax AIDS Vaccines Progenics (Originator) Phase II ACH Elvucitabine Anti-HIV Agents DNA Achillion 126443 Polymerase Inhibitors Anti-Hepatitis B Reverse Vion Virus Drugs Transcriptase Inhibitors beta-L-F4C Yale University (Originator) Preclinical CVN Cyanovirin N Anti-HIV Agents Viral Entry Biosyn Inhibitors Microbicides National Cancer Institute (US) (Originator) Launched PNU Tipranavir Aptivus Anti-HIV Agents HIV Protease Boehringer 2005 14O690 Inhibitors Ingelheim U-140690 Pfizer (Originator) PNU 14O690E (diNasalt) Phase III ADA Azodicarbonamide Anti-HIV Agents National Cancer Institute (US) (Originator) NSC Rega Institute for 674447 Medical Research (Originator) Launched Bis(POC)PM Tenofovir Wiread AIDS Medicines Reverse Gilead 2001 PA disoproxil Transcriptase (Originator) fumarate Inhibitors GS-4331-05 Anti-HIV Agents Japan Tobacco Japan Tobacco (Orphan Drug) Phase II PA-457 Anti-HIV Agents Viral Biotech Maturation Research Inhibitors Laboratories (Originator) Panacos University North Carolina, Chapel Hill (Originator) ViroLogic Phase II Anticort Anti-HIV Agents HMG-CoA Altachem Reductase mRNA Expression Inhibitors SP-01A Oncolytic Drugs Viral Entry Georgetown Inhibitors University (Originator) Samaritan Pharmaceuticals Launched BMS-232632 Atazanavir ReyataZ Anti-HIV Agents HIV Protease Bristol-Myers 2003 05 sulfate Inhibitors Squibb CGP-73547 Bristol-Myers Squibb (Orphan Drug) BMS-232632 Novartis (free base) (Originator) Launched AZT3TC Lamivudine Combivir Anti-HIV Agents Reverse GlaxoSmithKline 1997 Zidovudine Transcriptase (Originator) Inhibitors Zidovudine? Lamivudine Phase III AIDSVAX AIDS Vaccines Genentech BB (Originator) AIDSVAX Nat. Inst. Allergy gp120 B/B & Infectious Dis. WaxGen Phase II (-)-BCH Anti-HIV Agents Reverse Avexa 10652 Transcriptase US 7,871,991 B2 67

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization (-)-dOTC Inhibitors Shire Pharmaceuticals (Originator) AVX-754 BCH-106.18 SPD-754 Phase II D-D4FC Reverset Anti-HIV Agents DNA Bristol-Myers Polymerase Squibb Inhibitors (Originator) DPC-817 Reverse Incyte Transcriptase Inhibitors RVT Pharmasset beta-D- D4FC Phase III VIR-201 AIDS Vaccines Virax (Originator) Preclinical DDE-46 Anti-HIV Agents Antimitotic Paradigm Drugs Pharmaceuticals WH-07 Oncolytic Drugs Apoptosis Parker Hughes Inducers Institute (Originator) Vaginal Caspase 3 Spermicides Activators Caspase 8 Activators Caspase 9 Activators Microtubule inhibitors Preclinical HI-113 Sampidine Anti-HIV Agents Reverse Parker Hughes Transcriptase Institute Inhibitors (Originator) STAMP Stampidine d4T pBPMAP Preclinical WHI-OS Anti-HIV Agents Paradigm Pharmaceuticals Vaginal Parker Hughes Spermicides institute (Originator) Preclinical Anti-HIV Agents Murine mmPheron Monoclonal Anti-Hepatitis C Antibodies mmune Network Virus Drugs MAb 1F7 nNexus Sidney Kimmel Cancer Center (Originator) University of British Columbia IND Filed MDI-P Anti-HIV Agents Dana-Farber Cancer Institute Antibacterial Medical Drugs Discoveries (Originator) Asthma. Therapy Cystic Fibrosis, Treatment of Septic Shock, Treatment of Phase I PA-14 Anti-HIV Agents Anti-CD195 Epicyte (CCR5) PRO-140 Humanized Progenics Monoclonal (Originator) Antibodies Viral Entry Protein Design Inhibitors Labs Phase II EpiBr Immunitin Anti-HIV Agents Colthurst (Originator) HE-2OOO Inactivin Anti-Hepatitis B Edenland Virus Drugs Anti-Hepatitis C Hollis-Eden Virus Drugs (Originator) US 7,871,991 B2 69 70

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Antimalarials Cystic Fibrosis, Treatment of Immunomodulators Treatment of Tuberculosis Phase II ALVAC AIDS Vaccines ANRS wCP1452 wCP1452 Nat. Inst. Allergy & Infectious Dis. Sanofi Pasteur (Originator) Virogenetics (Originator) Phase II (+)-FTC Racivir Anti-HIV Agents Pharmasset (Originator) PSI-SOO4 Anti-Hepatitis B Virus Drugs Phase III Cellulose Female Viral Entry Polydex sulfate Contraceptives Inhibitors (Originator) Ushercell Microbicides Phase I SF-2 rgp120 AIDS Vaccines Chiron (Originator) rgp120 SF-2 Nat. Inst. Allergy & Infectious Dis. Phase I MIV-1SO Anti-HIV Agents Reverse Medivir Transcriptase (Originator) Inhibitors Microbicides Population Council Phase III Cytolin Anti-HIV Agents Anti- Amerimmune CD11a CD18 (Originator) (LFA-1) Murine Cytodyn Monoclonal Antibodies Phase III 1OD1 mAb Anti-HIV Agents Anti-CD152 Bristol-Myers (CTLA-4) Squibb Anti-CTLA-4 Breast Cancer Human Medarex MAb Therapy Monoclonal (Originator) Antibodies MDX-010 Head and Neck Medarex Cancer Therapy (Orphan Drug) MDX- Melanoma National Cancer CTLA4 Therapy Institute MDX-101 Prostate Cancer (formerly) Therapy Renal Cancer Therapy Phase IIIII 1018-ISS AIDS Medicines Oligonucleotides Dynavax (Originator) ISS-1018 Antiallergy/Antiasthmatic Gilead Drugs Drugs for Sanofi Pasteur Allergic Rhinitis mmunomodulators Non-Hodgkin's Lymphoma Therapy Vaccine adjuvants Phase III HGTV43 Stealth Anti-HIV Agents Enzo (Originator) Vector Gene Delivery Systems Phase II R-147681 Dapivirine Anti-HIV Agents Reverse IPM Transcriptase Inhibitors TMC-120 Microbicides Janssen (Originator) Tibotec (Originator) US 7,871,991 B2 71 72

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Phase II DPC-083 Anti-HIV Agents Reverse Bristol-Myers Transcriptase Squibb Inhibitors (Originator) Launched Lamivudine Triziwir Anti-HIV Agents GlaxoSmithKline 2OOO zidovudine (Originator) abacavir sulfate Launched 908 Fosamprenavir Lexiva Anti-HIV Agents HIV Protease GlaxoSmithKline 2003 calcium Inhibitors (Originator) GW Telzir Chemical Vertex 433908G Delivery (Originator) Systems GW-433908 (free acid) VX-175 (free acid) Phase I DNAHIV AIDS Vaccines GlaxoSmithKline vaccine Powderect HIV PowderMed DNA vaccine (Originator) Phase III PC-515 Carraguard Microbicides Population Council (Originator) Phase II R-16533S Etravirine Anti-HIV Agents Reverse Janssen Transcriptase (Originator) Inhibitors TMC-12S Tibotec (Originator) Preclinical SP-1093V. Anti-HIV Agents DNA McGill University Polymerase Inhibitors Reverse Supratek Transcriptase (Originator) Inhibitors Phase III AIDSVAX AIDS Vaccines Genentech BE (Originator) AIDSVAX WaxGen gp120 BE Walter Reed Army Institute Launched ABT-378.r Lopinavirritonavir Kaletra Anti-HIV Agents HIV Protease Abbott 2OOO Inhibitors (Originator) ABT Severe Acute Gilead 378ritonavir Respiratory Syndrome (SARS), Treatment of Phase I Anti-HIV Agents Reverse Shire Transcriptase Pharmaceuticals Inhibitors (Originator) SPD-756 Phase III BAYSO Adargileukin Anti-HIV Agents IL-2 Bayer 4798 alfa Immunomodulators (Originator) Oncolytic Drugs Phase I 2O4937 Anti-HIV Agents Reverse GlaxoSmithKline Transcriptase Inhibitors MIV-210 Anti-Hepatitis B Medivir Virus Drugs (Originator) Phase III BufferGel Microbicides Johns Hopkins University (Originator) Vaginal National Spermicides Institutes of Health ReProtect (Originator) Phase I Ad5-FL gag AIDS Vaccines Merck & Co. (Originator) Ad5-gag DNA Vaccines Phase III ALVAC AIDS Vaccines Nat. Inst. Allergy E12OTMG & Infectious Dis. ALVAC Sanofi Pasteur US 7,871,991 B2 73

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization wCP1521 (Originator) wCP1521 Virogenetics (Originator) Walter Reed Army Institute Phase II MVA-BN AIDS Vaccines Bavarian Nordic Nef (Originator) MVA-HIV-1 LAI-nef MVA-nef Phase I DNAMVA Multiprotein AIDS Vaccines Emory University SHIV-89.6 DNAMVA (Originator) vaccine GeoVax Nat. Inst. Allergy & Infectious Dis. Phase II MVAHIVA AIDS Vaccines Impfstoffwerk Dessau-Tornau GmbH (Originator) International AIDS Vaccine Initiative Uganda Virus Research Institute University of Oxford Phase I HIV-Therapore AIDS Vaccines Avant vaccine (Originator) Nat. Inst. Allergy & Infectious Dis. Walter Reed Army Institute Phase III Glyminox Oramed Anti-HIV Agents Biosyn (Originator) SAVVY Antibacterial Cellegy Drugs Antifungal Agents Microbicides Treatment of Opportunistic Infections Vaginal Spermicides Phase I BRI-7013 VivaGel Microbicides Biomolecular Research Institute (Originator) SPL-7013 Starpharma Phase III SDS Sodium dodecyl Invisible Anti-HIV Agents Universite Laval sulfate Condom (Originator) SLS Sodium lauryl Anti-Herpes sulfate Simplex Virus Drugs Antiviral Drugs Microbicides Vaginal Spermicides Phase III Anti-HIV Agents Human Epicyte Monoclonal Antibodies Viral Entry Polymun Inhibitors (Originator) Universitaet Wien (Originator) Phase I AK-671 Ancriviroc Anti-HIV Agents Chemokine Schering-Plough CCR5 (Originator) Antagonists SCH Viral Entry 351125 Inhibitors US 7,871,991 B2 75 76

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization SCH-C Schering C Phase I DNAPLG AIDS Vaccines Chiron microparticles (Originator) DNA Vaccines Nat. Inst. Allergy & Infectious Dis. Phase I AAV2-gag AIDS Vaccines International PR-DELTA AIDS Vaccine RT Initiative tgAAC-09 DNA Vaccines Targeted Genetics (Originator) tgAAC09 AAV Phase I AVX-101 AIDS Vaccines AlphaVax (Originator) AVX-101 DNA Vaccines Nat. Inst. Allergy VEE & Infectious Dis. Phase I gp160 AIDS Vaccines ANRS MNLAI-2 Sanofi Pasteur (Originator) Walter Reed Army Institute Preclinical THPB 2-OH-propyl Trappsol Anti-HIV Agents Cyclodextrin beta HPB Technologies cyclodextrin Development O-(2- (Originator) Hydroxypropyl)- beta cyclodextrin Preclinical MPI-498.39 Anti-HIV Agents Myriad Genetics (Originator) Phase I BMS Anti-HIV Agents Viral Entry Bristol-Myers 378.806 Inhibitors Squibb BMS-806 (Originator) Phase I T-cell HIV AIDS Vaccines Hadassah Vaccine Medical Organization (Originator) Weizmann Institute of Science Phase III TMC-114 Darunavir Anti-HIV Agents HIV Protease Johnson & Inhibitors Johnson Tibotec (Originator) University of Illinois (Originator) Preclinical MV-O26048 Anti-HIV Agents Reverse Medivir Transcriptase (Originator) Inhibitors Roche Preclinical K5-N, OS(H) Anti-HIV Agents Angiogenesis Glycores 2000 Inhibitors Microbicides Viral Fusion San Raffaele Inhibitors Scientific Institute Oncolytic Drugs Universita degli Studi di Bari (Originator) Universita degli Studi di Brescia (Originator) Phase III UK-427857 Maraviroc Anti-HIV Agents Chemokine Pfizer CCR5 (Originator) Antagonists Viral Entry Inhibitors Phase I BILR-3SS Anti-HIV Agents Reverse Boehringer Transcriptase Ingelheim Inhibitors (Originator) US 7,871,991 B2 77 78

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization BILR-3SS BS Launched Abacavir Epzicom Anti-HIV Agents Reverse GlaxoSmithKline 2004 sulfateflamivudine Transcriptase (Originator) Inhibitors Kivexa Preclinical DermaVir AIDS Vaccines Genetic Immunity (Originator) DNA Vaccines Research Institute Genetic Human Ther. Phase III 2G12 Anti-HIV Agents Human Epicyte Monoclonal Antibodies Viral Entry Polymun Inhibitors (Originator) Universitaet Wien (Originator) Phase I L Anti-HIV Agents HIV Integrase Merck & Co. OOO870810 Inhibitors (Originator) L-870810 Phase I L-87O812 Anti-HIV Agents HIV Integrase Merck & Co. Inhibitors (Originator) Phase I VRX-496 Anti-HIV Agents University of Pennsylvania Antisense VIRXSYS Therapy (Originator) Preclinical SAMMA Microbicides Viral Entry Mount Sinai Inhibitors School of Medicine (Originator) Rush University Medical Center (Originator) Phase I Ad5gag2 AIDS Vaccines Merck & Co. (Originator) MRKAd5 Nat. Inst. Allergy HIV-1 gag & Infectious Dis. MRKAd5gag Sanofi Pasteur Phase I BG-777 Anti Virocell Cytomegalovirus (Originator) Drugs Anti-HIV Agents Anti-Influenza Virus Drugs Antibacterial Drugs Immunomodulators Preclinical Sulphonated Contraceptives Panjab Hesperidin Microbicides University (Originator) Phase II 695634 Anti-HIV Agents Reverse GlaxoSmithKline Transcriptase (Originator) inhibitors GW-5634 GW-695634 Phase II GW-678248 Anti-HIV Agents Reverse GlaxoSmithKline Transcriptase (Originator) inhibitors GW-8248 Preclinical R-1495 Anti-HIV Agents Reverse Medivir Transcriptase inhibitors Roche Preclinical SMP-717 Anti Reverse Advanced Life Cytomegalovirus Transcriptase Sciences Drugs inhibitors (Originator) Anti-HIV Agents Phase III AMD-070 Anti-HIV Agents AnorMED (Originator) ) Antagonists Viral Entry Nat. Inst. Allergy inhibitors & Infectious Dis. US 7,871,991 B2 79 80

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization National Institutes of Health Preclinical TGF-alpha Anti-HIV Agents Centocor Antiparkinsonian Kaleidos Pharma Drugs National Cancer Institute (US) (Originator) National Institutes of Health (Originator) Phase II 873140 Anti-HIV Agents Chemokine GlaxoSmithKline CCR5 Antagonists AK-602 Viral Entry Ono (Originator) Inhibitors GW-873 140 ONO-4128 Phase I TAK-220 Anti-HIV Agents Chemokine Takeda CCR5 (Originator) Antagonists Viral Entry Inhibitors Launched V-1 Immunitor AIDS Vaccines Immunitor (Originator) Treatment of AIDS-Associated Disorders Phase I TAK-652 Anti-HIV Agents Chemokine Takeda CCR5 (Originator) Antagonists Viral Entry Inhibitors IND Filed Block Aide? Anti-HIV Agents Viral Entry Adventrx CR Inhibitors Pharmaceuticals M. D. Anderson Cancer Center (Originator) Phase II R-278474 Rilpivirine Anti-HIV Agents Reverse Janssen Transcriptase (Originator) Inhibitors TMC-278 Preclinical KPC-2 Anti-HIV Agents Kucera Pharmaceutical (Originator) Preclinical INK-2O Anti-HIV Agents Kucera Pharmaceutical (Originator) Chemical Delivery Systems Phase I CCR5 mAb Anti-HIV Agents Anti-CD195 Human Genome (CCR5) Sciences (Originator) CCR5mAb004 Human Monoclonal Antibodies Viral Entry Inhibitors Preclinical MIV-170 Anti-HIV Agents Reverse Medivir Transcriptase (Originator) Inhibitors Phase I DP6-001 HIV DNA AIDS Vaccines Advanced vaccine BioScience DNA Vaccines CytRx University of Massachusetts (Originator) US 7,871,991 B2 81 82

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Phase II AG-OO1859 Anti-HIV Agents HIV Protease Pfizer Inhibitors (Originator) AG-1859 Phase III GTU AIDS Vaccines FIT Biotech MultiV (Originator) DNA Vaccines International AIDS Vaccine Initiative Preclinical Eradicaide AIDS Vaccines Adventrx Pharmaceuticals M. D. Anderson Cancer Center (Originator) Launched Tenofovir Truvada Anti-HIV Agents Reverse Gilead 2004 disoproxil Transcriptase (Originator) fumaratef Inhibitors Japan Tobacco emtricitabine Preclinical Block Aide,VP Anti-HIV Agents Viral Entry Adventrx Inhibitors Pharmaceuticals (Originator) Preclinical TPFA Thiovir Anti-HIV Agents Reverse Adventrx Transcriptase Pharmaceuticals Inhibitors Cervical Cancer National Cancer Therapy Institute Genital Warts, University of Treatment for Southern California (Originator) Phase III MetX MetaboliteX Anti-HIV Agents Tripep (Originator) alpha-HGA Preclinical NV-OSA Anti-HIV Agents Reverse Idenix Transcriptase (Originator) Inhibitors Phase III IR-103 AIDS Vaccines Immune Response Preclinical MX-100 Anti-HIV Agents HIV Protease Pharmacor Inhibitors (Originator) PL-100 Procyon Biopharma (Originator) ViroLogic Phase I Anti-HIV Agents Fresenius (Originator) Gene Therapy Georg-Speyer Haus (Originator) Phase I SCH-D Anti-HIV Agents Chemokine Schering-Plough CCR5 (Originator) Antagonists Sch-417690 Viral Entry Inhibitors Preclinical ImmunoVex AIDS Vaccines BioVex HIV (Originator) Phase I CYT-99-007 Anti-HIV Agents Cytheris (Originator) rhIL-7 Immunomodulators Nat. Inst. Allergy & Infectious Dis. National Cancer Institute Phase I recombinanto AIDS Vaccines Chiron gp140/MF59 (Originator) adjuvant Nat. Inst. Allergy & Infectious Dis. Phase II BMS Anti-HIV Agents Viral Entry Bristol-Myers 488043 Inhibitors Squibb (Originator) Preclinical KP-1212 Anti-HIV Agents Koronis (Originator) SN-1212 US 7,871,991 B2 83 84

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Preclinical AMD-887 Anti-HIV Agents Chemokine AnorMED CCR5 (Originator) Antagonists Viral Entry Inhibitors Phase I KP-1461 Anti-HIV Agents Koronis (Originator) SN-1461 Chemical Delivery Systems Preclinical DES-10 Anti-HIV Agents AusAm Biotechnologies (Originator) Anti-Herpes National Virus Drugs Institutes of Health Preclinical APP-069 Anti-HIV Agents Aphios (Originator) Preclinical PC-815 MIV Anti-HIV Agents Medivir 150/Carraguard (Originator) MIV-1SOPC Microbicides Population 515 Council (Originator) Preclinical FGI-345 Anti-HIV Agents Functional Genetics (Originator) Preclinical Anti-HIV Agents Nutra Pharma (Originator) ReceptoPharm (Originator) Preclinical Tenofovir Anti-HIV Agents Reverse Bristol-Myers disoproxil Transcriptase Squibb fumaratef Inhibitors (Originator) emtricitabine? Gilead efavirenz (Originator) Merck & Co. (Originator) Preclinical MVA-BN HIV AIDS Vaccines Bavarian Nordic Polytope (Originator) Preclinical MVA-BN HIV AIDS Vaccines Bavarian Nordic Multiantigen (Originator) Preclinical PBS-119 Immunostimulants Phoenix Biosciences (Originator) Phase II HIV-1 Tat Toxoid AIDS Vaccines Neovacs vaccine Tat Toxoid Sanofi Pasteur vaccine Univ. Maryland Biotechnology Institute Phase III Thymus nuclear Anti-HIV Agents Viral Genetics WGV-1 protein Phase I VCR-ADV. AIDS Vaccines GenVec O14 (Originator) WRC Nat. Inst. Allergy HIVADVO14 & Infectious Dis. OO-VP Preclinical SP-010 Anti-HIV Agents Georgetown University (Originator) SP-10 Cognition Samaritan Disorders, Pharmaceuticals Treatment of Phase III GS-91.37 Anti-HIV Agents HIV Integrase Gilead Inhibitors JTK-303 Japan Tobacco (Originator) Phase III RNA-loaded AIDS Vaccines Argos dendritic cell CancerVaccines Therapeutics vaccine (Originator) Melanoma Therapy US 7,871,991 B2 85 86

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Renal Cancer Therapy Phase I IFN-alpha Antiferon AIDS Vaccines Neovacs kinoid (Originator) Systemic Lupus Sanofi Pasteur Erythematosus, Agents for Vaccines Phase II DNAHIVA AIDS Vaccines International AIDS Vaccine Initiative HIVA DNA Vaccines ML Laboratories (Originator) Uganda Virus Research Institute University of Oxford Phase I DEBIO-O2S Anti-HIV Agents Debiopharm (Originator) UNIL-O2S Anti-Hepatitis C Virus Drugs Ischemic Stroke, Treatment of Preclinical HIV vaccine AIDS Vaccines Berna Biotech (Originator) MV-HIV vaccine Phase I 82578O DNA Vaccines GlaxoSmithKline (Originator) Viral Vaccines Phase I C-1605 AIDS Medicines Merck & Co. (Originator) Phase I ADMVA AIDS Vaccines Aaron Diamond AIDS Research Center Impfstoffwerk Dessau-Tornau GmbH (Originator) International AIDS Vaccine Initiative Preclinical BL-1OSO AIDS Medicines BioLineRx Hebrew University (Originator) Yissum Phase I CAP Cellulose Microbicides Viral Entry New York Blood acetate Inhibitors Center phthalate Vaginal Spermicides Preclinical Anti-HIV Agents Quigley Pharma (Originator) Phase II MRKAd5 AIDS Vaccines Merck & Co. HIV-1 (Originator) gag polinef MRKAd5 Nat. Inst. Allergy HIV-1 & Infectious Dis. trivalent MRKAd5gag? polinef Preclinical Carry Vac AIDS Vaccines Tripep HIV (Originator) Vaccine Research Institute of San Diego Preclinical HIV-RAS AIDS Medicines Tripep (Originator) US 7,871,991 B2 87 88

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Preclinical PL-337 Anti-HIV Agents HIV Protease Procyon Inhibitors Biopharma (Originator) Phase I DNA-C AIDS Vaccines EuroVacc Foundation DNA-HIVC Universitaet Regensburg (Originator) Phase II Lipo-5 AIDS Vaccines ANRS INSERM (Originator) Nat. Inst. Allergy & Infectious Dis. Sanofi Pasteur (Originator) Phase I Lipo-6T AIDS Vaccines ANRS INSERM (Originator) Sanofi Pasteur (Originator) Phase EnvPro AIDS Vaccines St. Jude Children's Res. Hosp. (Originator) Phase TCB-M358 AIDS Vaccines Nat. Inst. Allergy & Infectious Dis. Therion (Originator) Phase TBC-M335 AIDS Vaccines Nat. Inst. Allergy & Infectious Dis. Therion (Originator) Phase TBC-F357 AIDS Vaccines Nat. Inst. Allergy & Infectious Dis. Therion (Originator) Phase TBC-F349 AIDS Vaccines Nat. Inst. Allergy & Infectious Dis. Therion (Originator) Phase TBC- AIDS Vaccines Nat. Inst. Allergy M358.TBC- & Infectious Dis. M355 Therion (Originator) Phase I TBC- AIDS Vaccines Nat. Inst. Allergy F357 TBC- & Infectious Dis. F349

Phase I HIV CTL Multiepitope CTL AIDS Vaccines Nat. Inst. Allergy MEP peptide vaccine & Infectious Dis.

Phase I WRC-DNA- AIDS Vaccines National O09 Institutes of Health (Originator) WRC- DNA Vaccines HIVDNAO09 OO-VP Preclinical REP-9 Anti-HIV Agents Oligonucleotides REPLICor (Originator) Antiviral Drugs Preclinical PPL-100 Anti-HIV Agents HIV Protease Procyon Inhibitors Biophamia (Originator) Chemical Delivery Systems US 7,871,991 B2 89 90

TABLE 98-continued Exemplary HIV/AIDS Therapeutics Mechanism t Code Generic Brand Therapeutic of Action Highest Phase Name Name Name Group Group Organization Phase III BI-201 Anti-HIV Agents Human BioInvent Monoclonal (Originator) Antibodies

diagnostic assays for therapeutic dosing of the compounds of TABLE 99 the invention even if they possess no HIV-inhibitory activity 15 of their own. Exemplary HIV Antivirals and Patent Numbers Recipes and methods for determining stability of com Ziagen (Abacavir sulfate, U.S. Pat. No. 5,034,394) pounds in Surrogate gastrointestinal secretions are known. Epzicom (Abacavir Sulfate/lamivudine, U.S. Pat. No. 5,034,394) Compounds are defined hereinas stable in the gastrointestinal Hepsera (Adefovir dipivoxil, U.S. Pat. No. 4,724.233) Agenerase (Amprenavir, U.S. Pat. No. 5,646,180) tract where less than about 50 mole percent of the protected Reyataz (Atazanavir Sulfate, U.S. Pat. No. 5,849.911) groups are deprotected in Surrogate intestinal or gastric juice Rescriptor (Delavirdine mesilate, U.S. Pat. No. 5,563,142) upon incubation for 1 hour at 37° C. Simply because the Hivid (Dideoxycytidine; Zalcitabine, U.S. Pat. No. 5,028,595) compounds are stable to the gastrointestinal tract does not Videx (Dideoxyinosine; Didanosine, U.S. Pat. No. 4,861,759) Sustiva (Efavirenz, U.S. Pat. No. 5,519,021) mean that they cannot be hydrolyzed in vivo. The phospho Emtriva (Emtricitabine, U.S. Pat. No. 6,642,245) nate prodrugs of the invention typically will be stable in the Lexiva (Fosamprenavir calcium, U.S. Pat. No. 6,436,989) 25 digestive system but are substantially hydrolyzed to the Virudin; Triapten; Foscavir (Foscarnet sodium, U.S. Pat. No. 6,476,009) parental drug in the digestive lumen, liver or other metabolic Crixivan (Indinavir Sulfate, U.S. Pat. No. 5,413.999) Epivir (Lamivudine, U.S. Pat. No. 5 047,407) organ, or within cells in general. Combivir (Lamivudine/Zidovudine, U.S. Pat. No. 4,724.232) Aluviran (Lopinavir) Exemplary Methods of Making the Compounds of the Inven Kaletra (Lopinaviriritonavir, U.S. Pat. No. 5,541,206) 30 tion. Viracept (Nelfinavir mesilate, U.S. Pat. No. 5,484.926) Viramune (Nevirapine, U.S. Pat. No. 5,366,972) The invention also relates to methods of making the com Norvir (Ritonavir, U.S. Pat. No. 5,541,206) positions of the invention. The compositions are prepared by nvirase: Fortovase (Saquinavir mesilate, U.S. Pat. No. 5,196,438) any of the applicable techniques of organic synthesis. Many Zerit (Stavudine, U.S. Pat. No. 4,978,655) Such techniques are well known in the art. However, many of Truvada (Tenofovir disoproxil fumaratefemtricitabine, 35 U.S. Pat. No. 5,210,085) the known techniques are elaborated in Compendium of Aptivus (Tipranavir) Organic Synthetic Methods (John Wiley & Sons, New York), Retrovir (Zidovudine: Azidothymidine, U.S. Pat. No. 4,724.232) Vol. 1, Ian T. Harrison and Shuyen Harrison, 1971; Vol. 2, Ian T. Harrison and Shuyen Harrison, 1974; Vol. 3. Louis S. Hegedus and Leroy Wade, 1977; Vol. 4, Leroy G. Wade, jr., 40 Metabolites of the Compounds of the Invention 1980; Vol. 5, Leroy G. Wade, Jr., 1984; and Vol. 6, Michael B. Smith; as well as March, J., Advanced Organic Chemistry, Also falling within the scope of this invention are the in Third Edition, (John Wiley & Sons, New York, 1985), Com vivo metabolic products of the compounds described herein. prehensive Organic Synthesis, Selectivity Strategy & Efi Such products may result for example from the oxidation, ciency in Modern Organic Chemistry. In 9 Volumes, Barry M. reduction, hydrolysis, amidation, esterification and the like of 45 Trost, Editor-in-Chief (Pergamon Press, New York, 1993 the administered compound, primarily due to enzymatic pro printing). cesses. Accordingly, the invention includes compounds pro A number of exemplary methods for the preparation of the duced by a process comprising contacting a compound of this compositions of the invention are provided below. These invention with a mammal for a period of time sufficient to 50 methods are intended to illustrate the nature of Such prepara yield a metabolic product thereof. Such products typically are tions and are not intended to limit the scope of applicable identified by preparing a radiolabelled (e.g., C'' or H) com methods. pound of the invention, administering it parenterally in a Generally, the reaction conditions such as temperature, detectable dose (e.g., greater than about 0.5 mg/kg) to an reaction time, solvents, work-up procedures, and the like, will 55 be those common in the art for the particular reaction to be animal Such as rat, mouse, guinea pig, monkey, or to man, performed. The cited reference material, together with mate allowing Sufficient time for metabolism to occur (typically rial cited therein, contains detailed descriptions of such con about 30 seconds to 30 hours) and isolating its conversion ditions. Typically the temperatures will be -100° C. to 200° products from the urine, blood or other biological samples. C., solvents will be aprotic or protic, and reaction times will These products are easily isolated since they are labeled (oth 60 be 10 seconds to 10 days. Work-up typically consists of ers are isolated by the use of antibodies capable of binding quenching any unreacted reagents followed by partition epitopes surviving in the metabolite). The metabolite struc between a water/organic layer system (extraction) and sepa tures are determined in conventional fashion, e.g., by MS or rating the layer containing the product. NMR analysis. In general, analysis of metabolites is done in Oxidation and reduction reactions are typically carried out the same way as conventional drug metabolism studies well 65 at temperatures near room temperature (about 20° C.), known to those skilled in the art. The conversion products, so although for metal hydride reductions frequently the tem long as they are not otherwise found in Vivo, are useful in perature is reduced to 0°C. to -100°C., solvents are typically US 7,871,991 B2 91 92 aprotic for reductions and may be either protic or aprotic for water insensitive reactions or nitrogen or argon for oxygen or oxidations. Reaction times are adjusted to achieve desired water sensitive), etc., are intended unless otherwise indicated. conversions. The knowledge of similar reactions known in the art of Condensation reactions are typically carried out at tem organic synthesis are used in selecting the conditions and peratures near room temperature, although for non-equili apparatus for “treating in a given process. In particular, one brating, kinetically controlled condensations reduced tem of ordinary skill in the art of organic synthesis selects condi peratures (0°C. to -100°C.) are also common. Solvents can tions and apparatus reasonably expected to successfully carry be either protic (common in equilibrating reactions) or apro out the chemical reactions of the described processes based tic (common in kinetically controlled reactions). on the knowledge in the art. Standard synthetic techniques such as azeotropic removal 10 Modifications of each of the exemplary schemes and in the of reaction by-products and use of anhydrous reaction condi examples (hereafter “exemplary schemes”) leads to various tions (e.g., inert gas environments) are common in the art and analogs of the specific exemplary materials produce. The will be applied when applicable. above-cited citations describing Suitable methods of organic synthesis are applicable to such modifications. Schemes and Examples 15 In each of the exemplary Schemes it may be advantageous General aspects of these exemplary methods are described to separate reaction products from one another and/or from below and in the Examples. Each of the products of the starting materials. The desired products of each step or series following processes is optionally separated, isolated, and/or of steps is separated and/or purified (hereinafter separated) to purified prior to its use in Subsequent processes. the desired degree of homogeneity by the techniques com Generally, the reaction conditions such as temperature, mon in the art. Typically Such separations involve multiphase reaction time, solvents, work-up procedures, and the like, will extraction, crystallization from a solvent or solvent mixture, be those common in the art for the particular reaction to be distillation, Sublimation, or chromatography. Chromatogra performed. The cited reference material, together with mate phy can involve any number of methods including, for rial cited therein, contains detailed descriptions of such con example: reverse-phase and normal phase; size exclusion; ion ditions. Typically the temperatures will be -100° C. to 200° 25 exchange; high, medium, and low pressure liquid chromatog C., solvents will be aprotic or protic, and reaction times will raphy methods and apparatus; Small scale analytical; simu be 10 seconds to 10 days. Work-up typically consists of lated moving bed (SMB) and preparative thin or thick layer quenching any unreacted reagents followed by partition chromatography, as well as techniques of Small scale thin between a water/organic layer system (extraction) and sepa layer and flash chromatography. rating the layer containing the product. 30 Another class of separation methods involves treatment of Oxidation and reduction reactions are typically carried out a mixture with a reagent selected to bind to or render other at temperatures near room temperature (about 20° C.), wise separable a desired product, unreacted starting material, although for metal hydride reductions frequently the tem reaction by product, or the like. Such reagents include adsor perature is reduced to 0°C. to -100°C., solvents are typically bents or absorbents such as activated carbon, molecular aprotic for reductions and may be either protic or aprotic for 35 sieves, ion exchange media, or the like. Alternatively, the oxidations. Reaction times are adjusted to achieve desired reagents can be acids in the case of a basic material, bases in conversions. the case of an acidic material, binding reagents such as anti Condensation reactions are typically carried out at tem bodies, binding proteins, selective chelators such as crown peratures near room temperature, although for non-equili ethers, liquid/liquidion extraction reagents (LIX), or the like. brating, kinetically controlled condensations reduced tem 40 Selection of appropriate methods of separation depends on peratures (0°C. to -100°C.) are also common. Solvents can the nature of the materials involved. For example, boiling be either protic (common in equilibrating reactions) or apro point, and molecular weight in distillation and Sublimation, tic (common in kinetically controlled reactions). presence or absence of polar functional groups in chromatog Standard synthetic techniques such as azeotropic removal raphy, stability of materials in acidic and basic media in of reaction by-products and use of anhydrous reaction condi 45 multiphase extraction, and the like. One skilled in the art will tions (e.g., inert gas environments) are common in the art and apply techniques most likely to achieve the desired separa will be applied when applicable. tion. The terms “treated”, “treating”, “treatment, and the like, A single stereoisomer, e.g., an enantiomer, Substantially when used in connection with a chemical synthetic operation, free of its stereoisomer may be obtained by resolution of the mean contacting, mixing, reacting, allowing to react, bring 50 racemic mixture using a method Such as formation of diaste ing into contact, and other terms common in the art for indi reomers using optically active resolving agents (Stereochem cating that one or more chemical entities is treated in Such a istry of Carbon Compounds, (1962) by E. L. Eliel, McGraw manner as to convert it to one or more other chemical entities. Hill; Lochmuller, C. H., (1975).J. Chromatogr., 113:(3)283 This means that “treating compound one with compound 302). Racemic mixtures of chiral compounds of the invention two' is synonymous with “allowing compound one to react 55 can be separated and isolated by any Suitable method, includ with compound two', 'contacting compound one with com ing: (1) formation of ionic, diastereomeric salts with chiral pound two”, “reacting compound one with compound two'. compounds and separation by fractional crystallization or and other expressions common in the art of organic synthesis other methods, (2) formation of diastereomeric compounds for reasonably indicating that compound one was “treated'. with chiral derivatizing reagents, separation of the diastere “reacted”, “allowed to react', etc., with compound two. For 60 omers, and conversion to the pure stereoisomers, and (3) example, treating indicates the reasonable and usual manner separation of the Substantially pure or enriched Stereoisomers in which organic chemicals are allowed to react. Normal directly under chiral conditions. concentrations (0.01M to 10M, typically 0.1M to 1M), tem Under method (1), diastereomeric salts can be formed by peratures (-100° C. to 250° C., typically -78° C. to 150° C., reaction of enantiomerically pure chiral bases such as bru more typically -78°C. to 100° C., still more typically 0°C. to 65 cine, quinine, ephedrine, Strychnine, C.-methyl-3-phenyl 100° C.), reaction vessels (typically glass, plastic, metal), ethylamine (amphetamine), and the like with asymmetric Solvents, pressures, atmospheres (typically airfor oxygen and compounds bearing acidic functionality. Such as carboxylic US 7,871,991 B2 93 94 acid and Sulfonic acid. The diastereomeric salts may be example, chlorophosphonate addition on to 5'-hydroxy of induced to separate by fractional crystallization orionic chro nucleoside is a well known method for preparation of nucleo matography. For separation of the optical isomers of amino side phosphate monoesters. The activated precursor can be compounds, addition of chiral carboxylic or Sulfonic acids, prepared by several well known methods. Chlorophospho Such as camphorsulfonic acid, tartaric acid, mandelic acid, or 5 nates useful for synthesis of the prodrugs are prepared from lactic acid can result in formation of the diastereomeric salts. the substituted-1,3-propanediol (Wissner, et al. (1992) J. Alternatively, by method (2), the substrate to be resolved is Med. Chem. 35:1650). Chlorophosphonates are made by oxi reacted with one enantiomer of a chiral compound to form a dation of the corresponding chlorophospholanes (Anderson, diastereomeric pair (Eliel, E. and Wilen, S. (1994) Stere et al., (1984).J. Org. Chem. 49: 1304) which are obtained by ochemistry of Organic Compounds, John Wiley & Sons, Inc., 10 reaction of the substituted diol with phosphorus trichloride. p. 322). Diastereomeric compounds can be formed by react Alternatively, the chlorophosphonate agent is made by treat ing asymmetric compounds with enantiomerically pure ing substituted-1,3-diols with phosphorusoxychloride (Pa chiral derivatizing reagents, such as menthyl derivatives, fol tois, et al. (1990).J. Chem. Soc. Perkin Trans. I, 1577). Chlo lowed by separation of the diastereomers and hydrolysis to rophosphonate species may also be generated in situ from yield the free, enantiomerically enriched xanthene. A method 15 corresponding cyclic phosphites (Silverburg, et al., (1996) of determining optical purity involves making chiral esters, Tetrahedron lett., 37:771-774), which in turn can be either Such as a menthyl ester, e.g., (-) menthyl chloroformate in the made from chlorophospholane or phosphoramidate interme presence of base, or Mosher ester, C.-methoxy-O-(trifluorom diate. Phosphoroflouridate intermediate prepared either from ethyl)phenyl acetate (Jacob III. (1982) J. Org. Chem. pyrophosphate orphosphoric acid may also act as precursor 47:4165), of the racemic mixture, and analyzing the NMR in preparation of cyclic prodrugs (Watanabe et al., (1988) spectrum for the presence of the two atropisomeric diastere Tetrahedron lett., 29:5763-66). omers. Stable diastereomers of atropisomeric compounds can Phosphonate prodrugs of the present invention may also be be separated and isolated by normal- and reverse-phase chro prepared from the free acid by Mitsunobu reactions (Mit matography following methods for separation of atropiso sunobu, (1981) Synthesis, 1: Campbell, (1992).J. Org. Chem. meric naphthyl-isoquinolines (Hoye, T., WO 96/15111). By 25 57:6331), and other acid coupling reagents including, but not method (3), a racemic mixture of two enantiomers can be limited to, carbodiimides (Alexander, et al. (1994) Collect. separated by chromatography using a chiral stationary phase Czech. Chem. Commun. 59:1853; Casara et al. (1992) Bioorg. (Chiral Liquid Chromatography (1989) W. J. Lough, Ed. Med. Chem. Lett. 2:145; Ohashi et al. (1988) Tetrahedron Chapman and Hall, New York: Okamoto, (1990).J. of Chro Lett., 29:1189), and benzotriazolyloxytris-(dimethylamino) matogr: 513:375-378). Enriched or purified enantiomers can 30 phosphonium salts (Campagne etal (1993) Tetrahedron Lett. be distinguished by methods used to distinguish other chiral 34:6743). molecules with asymmetric carbon atoms, such as optical Aryl halides undergo Ni" catalyzed reaction with phos rotation and circular dichroism. phite derivatives to give aryl phosphonate containing com Examples General Section pounds (Balthazar, etal (1980).J. Org. Chem. 45:5425). Phos A number of exemplary methods for the preparation of 35 phonates may also be prepared from the chlorophosphonate compounds of the invention are provided herein, for example, in the presence of a palladium catalyst using aromatic triflates in the Examples hereinbelow. These methods are intended to (Petrakis et al (1987).J. Am. Chem. Soc. 109:2831; Lu et al illustrate the nature of Such preparations are not intended to (1987) Synthesis 726). In another method, aryl phosphonate limit the scope of applicable methods. Certain compounds of esters are prepared from aryl phosphates under anionic rear 40 rangement conditions (Melvin (1981) Tetrahedron Lett. the invention can be used as intermediates for the preparation 22:3375; Casteel et al (1991) Synthesis, 691). N-Alkoxyaryl of other compounds of the invention. For example, the inter salts with alkali metal derivatives of cyclic alkylphosphonate conversion of various phosphonate compounds of the inven provide general synthesis for heteroaryl-2-phosphonate link tion is illustrated below. ers (Redmore (1970).J. Org. Chem. 35:4114). These above Interconversions of the Phosphonates R-Link-P(O)(OR), 45 mentioned methods can also be extended to compounds R-Link-P(O)(OR')(OH) and R-Link-P(O)(OH). where the W group is C-heterocycle. Cyclic-1,3-propanyl The following schemes 32-38 describe the preparation of prodrugs of phosphonates are also synthesized from phos phosphonateesters of the general structure R-link-P(O)(OR") phonic diacids and Substituted propane-1,3-diols using a cou in which the groups R' may be the same or different. The R' pling reagent such as 1,3-dicyclohexylcarbodiimide (DCC) groups attached to a phosphonate ester, or to precursors 50 in presence of a base (e.g., pyridine). Other carbodiimide thereto, may be changed using established chemical transfor based coupling agents like 1,3-disopropylcarbodiimide or mations. The interconversion reactions of phosphonates are water soluble reagent, 1-(3-dimethylaminopropyl)-3-ethyl illustrated in Scheme S32. The group R in Scheme 32 repre carbodiimide hydrochloride (EDCI) can also be utilized for sents the substructure, i.e. the drug “scaffold, to which the the synthesis of cyclic phosphonate prodrugs. substituent link-P(O)(OR') is attached, either in the com 55 The conversion of a phosphonate diester S32.1 into the pounds of the invention, or in precursors thereto. At the point corresponding phosphonate monoester S32.2 (Scheme 32, in the synthetic route of conducting a phosphonate intercon Reaction 1) is accomplished by a number of methods. For version, certain functional groups in R may be protected. The example, the ester S32.1 in which R" is an aralkyl group such methods employed for a given phosphonate transformation as benzyl, is converted into the monoester compound S32.2 depend on the nature of the substituent R', and of the sub 60 by reaction with a tertiary organic base such as diazabicy strate to which the phosphonate group is attached. The prepa clooctane (DABCO) or quinuclidine, as described in J. Org. ration and hydrolysis of phosphonate esters is described in Chem. (1995) 60:2946. The reaction is performed in an inert Organic Phosphorus Compounds, G. M. Kosolapoff, L. hydrocarbon solvent such as toluene or xylene, at about 110° Maeir, eds, Wiley, 1976, p. 9ff. C. The conversion of the diester S32.1 in which R" is an aryl In general, synthesis of phosphonate esters is achieved by 65 group Such as phenyl, or an alkenyl group Such as allyl, into coupling a nucleophile amine or alcohol with the correspond the monoester S32.2 is effected by treatment of the ester ing activated phosphonate electrophilic precursor. For S32.1 with a base such as aqueous sodium hydroxide in US 7,871,991 B2 95 96 acetonitrile or lithium hydroxide in aqueous tetrahydrofuran. ducted in a polar organic solvent such as dimethylformamide Phosphonate diesters S32.1 in which one of the groups R' is or acetonitrile, in the presence of a base Such as cesium aralkyl, Such as benzyl, and the other is alkyl, is converted into carbonate. Alternatively, the phosphonate monoester is trans the monoesters S32.2 in which R" is alkyl by hydrogenation, formed into the phosphonate diester in a two step procedure. for example using a palladium on carbon catalyst. Phospho In the first step, the phosphonate monoester S32.2 is trans nate diesters in which both of the groups R' are alkenyl, such formed into the chloro analog RP(O)(OR")C1 by reaction as allyl, is converted into the monoester S32.2 in which R' is with thionyl chloride or oxalyl chloride and the like, as alkenyl, by treatment with chlorotris(triphenylphosphine) described in Organic Phosphorus Compounds, G. M. Koso rhodium (Wilkinson's catalyst) in aqueous ethanol at reflux, lapoff, L. Maeir, eds, Wiley, 1976, p. 17, and the thus-ob optionally in the presence of diazabicyclooctane, for example 10 tained product RP(O)(OR")C1 is then reacted with the by using the procedure described in J. Org. Chem. (1973) hydroxy compound R'OH, in the presence of a base such as 38:3224, for the cleavage of allyl carboxylates. triethylamine, to afford the phosphonate diester S32.1. The conversion of a phosphonate diester S32.1 or a phos A phosphonic acid R-link-P(O)(OH) is transformed into a phonate monoester S32.2 into the corresponding phosphonic phosphonate monoester RP(O)(OR')(OH) (Scheme 32, acid S32.3 (Scheme 32, Reactions 2 and 3) can be effected by 15 Reaction 5) by means of the methods described above of for reaction of the diester or the monoester with trimethylsilyl the preparation of the phosphonate diester R-link-P(O) bromide, as described in J. Chem. Soc., Chem. Comm., (1979) (OR"), S32.1, except that only one molar proportion of the 739. The reaction is conducted in an inert solvent such as, for component ROH or R'Br is employed. Dialkyl phospho example, dichloromethane, optionally in the presence of a nates may be prepared according to the methods of Quast et silylating agent Such as bis(trimethylsilyl)trifluoroacetamide, all (1974) Synthesis 490; Stowell et al (1990) Tetrahedron at ambient temperature. A phosphonate monoester S32.2 in Lett. 3261; U.S. Pat. No. 5,663,159. which R" is aralkyl such as benzyl, is converted into the A phosphonic acid R-link-P(O)(OH), S32.3 is transformed corresponding phosphonic acid S32.3 by hydrogenation over into a phosphonate diester R-link-P(O)(OR"), S32.1 a palladium catalyst, or by treatment with hydrogen chloride (Scheme 32, Reaction 6) by a coupling reaction with the in an ethereal solvent Such as dioxane. A phosphonate 25 hydroxy compound ROH, in the presence of a coupling monoester S32.2 in which R" is alkenyl such as, for example, agent such as Aldrithiol-2 (Aldrich) and triphenylphosphine. allyl, is converted into the phosphonic acid S32.3 by reaction The reaction is conducted in a basic solvent such as pyridine. with Wilkinson's catalyst in an aqueous organic solvent, for Alternatively, phosphonic acids S32.3 are transformed into example in 15% aqueous acetonitrile, or in aqueous ethanol, phosphonic esters S32.1 in which R" is aryl, by means of a for example using the procedure described in Helv. Chim. 30 coupling reaction employing, for example, dicyclohexylcar Acta. (1985) 68:618. Palladium catalyzed hydrogenolysis of bodiimide in pyridine at ca 70° C. Alternatively, phosphonic phosphonateesters S32.1 in which R" is benzyl is described in acids S32.3 are transformed into phosphonic esters S32.1 in J. Org. Chem. (1959) 24:434. Platinum-catalyzed hydro which R' is alkenyl, by means of an alkylation reaction. The genolysis of phosphonate esters S32.1 in which R" is phenyl phosphonic acid is reacted with the alkenyl bromide R'Brin is described in J. Am. Chem. Soc. (1956) 78:2336. 35 a polar organic solvent such as acetonitrile Solution at reflux The conversion of a phosphonate monoester S32.2 into a temperature, the presence of a base such as cesium carbonate, phosphonate diester S32.1 (Scheme 32, Reaction 4) in which the newly introduced R' group is alkyl, aralkyl, haloalkyl to afford the phosphonic ester S32.1. such as chloroethyl, or aralkyl is effected by a number of reactions in which the substrate S32.2 is reacted with a 40 hydroxy compound ROH, in the presence of a coupling Scheme 32 agent. Typically, the second phosphonate ester group is dif O O 1 ferent than the first introduced phosphonate ester group, i.e. R-link-P-OR -- R-link-P-OR R" is followed by the introduction of R where each of R' and ORI OH R’ is alkyl, aralkyl, haloalkyl such as chloroethyl, or aralkyl 45 S32.1 S32.2 (Scheme 32, Reaction 4a) whereby S32.2 is converted to O O S32.1a. Suitable coupling agents are those employed for the 2 preparation of carboxylate esters, and include a carbodiimide R-link-P-OR Ho- R-link-P-OH Such as dicyclohexylcarbodiimide, in which case the reaction ORI OH is preferably conducted in a basic organic solvent Such as 50 pyridine, or (benzotriazol-1-yloxy)tripyrrolidinophospho S32.1 S32.3 nium hexafluorophosphate (PYBOP, Sigma), in which case O O the reaction is performed in a polar solvent such as dimeth R-link-P-OR---ol He-3 R-link-P-OH ylformamide, in the presence of a tertiary organic base such as OH OH diisopropylethylamine, or Aldrithiol-2 (Aldrich) in which 55 case the reaction is conducted in a basic solvent Such as S32.2 S32.3 pyridine, in the presence of a triaryl phosphine Such as triph O O enylphosphine. Alternatively, the conversion of the phospho R-link-P-OR---ol He-4 R-link-P-OR nate monoester S32.2 to the diester S32.1 is effected by the OH ORI use of the Mitsunobu reaction, as described above. The sub 60 strate is reacted with the hydroxy compound ROH, in the S32.2 S32.1 presence of diethylazodicarboxylate and a triarylphosphine O O Such as triphenyl phosphine. Alternatively, the phosphonate 4a | monoester S32.2 is transformed into the phosphonate diester R-link-P-OR Ho- R-link-P-OR S32.1, in which the introduced R' group is alkenyl or aralkyl, 65 OH OR2 by reaction of the monoester with the halide R'Br, in which S32.2 S32.1a R" is as alkenyl or aralkyl. The alkylation reaction is con US 7,871,991 B2 97 98 lamine or triethylamine. The hydroxyl component R"OH is -continued selected from the group of compounds S33.19-S33.24 shown O in Scheme 33, and similar compounds. For example, if the R-link-P-OH - - Ris--or component R"OH is hydroxybenztriazole S33.19, N-hydrox y succinimide S33.20, or pentachlorophenol, S33.21, the OH OH mixed carbonate S33.10 is obtained by the reaction of the S32.3 S32.2 chloroformate with the hydroxyl compound in an ethereal O O Solvent in the presence of dicyclohexylamine, as described in 6 | R-link-P-OH He- R-link-P-OR Can. J. Chem., 1982, 60,976. A similar reaction in which the 10 component R"OH is pentafluorophenol S33.22 or 2-hydroxy OH ORI pyridine S33.23 is performed in an ethereal solvent in the S32.3 S32.1 presence of triethylamine, as described in Syn., 1986, 303, and Chem. Ber: 118, 468, 1985. Scheme 33 Example 4 illustrates the preparation of car Preparation of Phosphonate Carbamates. 15 bamates in which an alkyloxycarbonylimidazole S33.8 is Phosphonate esters may contain a carbamate linkage. The employed. In this procedure, an alcohol S33.5 is reacted with preparation of carbamates is described in Comprehensive an equimolar amount of carbonyl diimidazole S33.11 to pre Organic Functional Group Transformations, A. R. Katritzky, pare the intermediate S33.8. The reaction is conducted in an ed., Pergamon, 1995, Vol. 6, p. 416ff, and in Organic Func aprotic organic solvent Such as dichloromethane or tetrahy tional Group Preparations, by S. R. Sandler and W. Karo, drofuran. The acyloxyimidazole S33.8 is then reacted with an Academic Press, 1986, p. 260ff. The carbamoyl group may be equimolar amount of the amine R'NH to afford the carbam formed by reaction of a hydroxy group according to the ate S33.7. The reaction is performed in an aprotic organic methods known in the art, including the teachings of Ellis, US Solvent such as dichloromethane, as described in Tet. Lett., 2002/0103378 A1 and Hajima, U.S. Pat. No. 6,018,049. 42, 2001, 5227, to afford the carbamate S33.7. Scheme 33 illustrates various methods by which the car 25 Scheme 33, Example 5 illustrates the preparation of car bamate linkage is synthesized. As shown in Scheme 33, in the bamates by means of an intermediate alkoxycarbonylbenz general reaction generating carbamates, an alcohol S33.1, is triazole S33.13. In this procedure, an alcohol ROH is reacted converted into the activated derivative S33.2 in which LV is a at ambient temperature with an equimolar amount of benz leaving group Such as halo, imidazolyl, benztriazolyl and the triazole carbonyl chloride S33.12, to afford the alkoxycarbo 30 nyl product S33.13. The reaction is performed in an organic like, as described herein. The activated derivative S33.2 is Solvent Such as benzene or toluene, in the presence of a then reacted with an amine S33.3, to afford the carbamate tertiary organic amine such as triethylamine, as described in product S33.4. Examples 1-7 in Scheme 33 depict methods Synthesis., 1977, 704. The product is then reacted with the by which the general reaction is effected. Examples 8-10 amine R'NH2 to afford the carbamate S33.7. The reaction is illustrate alternative methods for the preparation of carbam 35 conducted in toluene or ethanol, at from ambient temperature ates. to about 80° C. as described in Synthesis., 1977, 704. Scheme 33, Example 1 illustrates the preparation of car Scheme 33, Example 6 illustrates the preparation of car bamates employing a chloroformyl derivative of the alcohol bamates in which a carbonate (R"O)CO, S33.14, is reacted S33.5. In this procedure, the alcohol S33.5 is reacted with with an alcohol S33.5 to afford the intermediate alkyloxycar phosgene, in an inert Solvent Such as toluene, at about 0°C., 40 bonyl intermediate S33.15. The latter reagent is then reacted as described in Org. Syn. Coll. Vol. 3, 167, 1965, or with an with the amine R'NH to afford the carbamate S33.7. The equivalent reagent Such as trichloromethoxy chloroformate, procedure in which the reagent S33.15 is derived from as described in Org. Syn. Coll. Vol. 6,715, 1988, to afford the hydroxybenztriazole S33.19 is described in Synthesis, 1993, chloroformate S33.6. The latter compound is then reacted 908; the procedure in which the reagent S33.15 is derived with the amine component S33.3, in the presence of an 45 from N-hydroxysuccinimide S33.20 is described in Tet. Lett., organic or inorganic base, to afford the carbamate S33.7. For 1992, 2781; the procedure in which the reagent S33.15 is example, the chloroformyl compound S33.6 is reacted with derived from 2-hydroxypyridine S33.23 is described in Tet. the amine S33.3 in a water-miscible solvent such as tetrahy Lett., 1991, 4251; the procedure in which the reagent S33.15 drofuran, in the presence of aqueous sodium hydroxide, as is derived from 4-nitrophenol S33.24 is described in Synthe described in Org. Syn. Coll. Vol. 3, 167, 1965, to yield the 50 sis. 1993, 103. The reaction between equimolar amounts of carbamate S33.7. Alternatively, the reaction is performed in the alcohol ROH and the carbonate S33.14 is conducted in an dichloromethane in the presence of an organic base Such as inert organic solvent at ambient temperature. diisopropylethylamine or dimethylaminopyridine. Scheme 33, Example 7 illustrates the preparation of car Scheme 33, Example 2 depicts the reaction of the chloro bamates from alkoxycarbonyl azides S33.16. In this proce formate compound S33.6 with imidazole to produce the imi 55 dure, an alkyl chloroformate S33.6 is reacted with an azide, dazolide S33.8. The imidazolide product is then reacted with for example sodium azide, to afford the alkoxycarbonyl azide the amine S33.3 to yield the carbamate S33.7. The prepara S33.16. The latter compound is then reacted with an equimo tion of the imidazolide is performed in an aprotic solvent such laramount of the amine R'NH2 to afford the carbamate S33.7. as dichloromethane at 0°, and the preparation of the carbam The reaction is conducted at ambient temperature in a polar ate is conducted in a similar solvent at ambient temperature, 60 aprotic Solvent such as dimethylsulfoxide, for example as optionally in the presence of a base such as dimethylaminopy described in Synthesis., 1982, 404. ridine, as described in J. Med. Chem., 1989, 32,357. Scheme 33, Example 8 illustrates the preparation of car Scheme 33 Example 3, depicts the reaction of the chloro bamates by means of the reaction between an alcohol ROH formate S33.6 with an activated hydroxyl compound R"OH, and the chloroformyl derivative of an amine S33.17. In this to yield the mixed carbonate ester S33.10. The reaction is 65 procedure, which is described in Synthetic Organic Chemis conducted in an inert organic solvent such as ether or dichlo try, R. B. Wagner, H. D. Zook, Wiley, 1953, p. 647, the romethane, in the presence of a base such as dicyclohexy reactants are combined at ambient temperature in an aprotic US 7,871,991 B2 99 Solvent such as acetonitrile, in the presence of a base such as triethylamine, to afford the carbamate S33.7. -continued Scheme 33, Example 9 illustrates the preparation of car NN N bamates by means of the reaction between an alcohol ROH M N RNH S33.3 and an isocyanate S33.18. In this procedure, which is 1. Her ROCONHR described in Synthetic Organic Chemistry, R. B. Wagner, H. R D. Zook, Wiley, 1953, p. 645, the reactants are combined at O O1 ambient temperature in an aprotic solvent such as ether or S33.13 S33.7 dichloromethane and the like, to afford the carbamate S33.7. 10 (R"O)C=O R'NH2 Scheme 33, Example 10 illustrates the preparation of car (6) ROH - - ROCOR" -- ROCONHR bamates by means of the reaction between an alcohol ROH S33.5 S33.15 S33.15 S333 S33.7 RNH 33.3 and an amine R'NH2. In this procedure, which is described in (7) ROH -- ROCOCl -- ROCON -> Chem. Lett. 1972,373, the reactants are combined at ambient S33.5 S33.6 S33.16 temperature in an aprotic organic solvent Such as tetrahydro 15 ROCONHR furan, in the presence of a tertiary base such as triethylamine, S33.7 and selenium. Carbon monoxide is passed through the solu (8) ROH RNHCOCI ROCONHR' He tion and the reaction proceeds to afford the carbamate S33.7. S33.5 S33.17 S33.7 (9) ROH RNCO ROCONHR --- S33.5 S33.18 S33.7 Scheme 33. Preparation of carbamates. (10) ROH R'NH2 ROCONHR Ho General reaction S33.5 S33.3 S33.7 R'NH2 OH ROH -> ROCOLy -- ROCONHR 25 O C C S33.1 S33.2 S33.3 S33.4 R"OH = N Examples NM -OH R'NH2S33.3 C C (1) ROH -- ROCOC - - ROCONHR OH O C S33.5 S33.6 S33.7 30 S33.19 S33.20 S33.21 H

OH OH OH O)N (2) ROH -- ROCOC – H 35 F F S33.5 S33.6 NN

1-\ RNH S33.3 F F 2 O N N ROCONHR NO R1 Y Na F 2 O 40 S33.22 S33.23 S33.24 S33.7 S33.7 ROH R'NH2 (3) ROH -- ROCOC -- ROCOOR" -- Preparation of Carboalkoxy-Substituted Phosphonate Bisa S33.5 S33.6 S33.9 S33.10 S33.3 midates, Monoamidates, Diesters and Monoesters. ROCONHR 45 A number of methods are available for the conversion of S33.7 phosphonic acids into amidates and esters. In one group of O methods, the phosphonic acid is either converted into an (4) ROH 2\ l 1N isolated activated intermediate Such as a phosphorylchloride, S33.5 N N N N or the phosphonic acid is activated in situ for reaction with an 50 amine or a hydroxy compound. The conversion of phosphonic acids into phosphoryl chlo S33.11 rides is accomplished by reaction with thionyl chloride, for / \ R'NH2S33.3 example as described in J. Gen. Chem. USSR, 1983, 53,480, Zh. Obschei Khim., 1958, 28, 1063, or J. Org. Chem., 1994, R1 "-ne" ROCONHR 55 59, 6144, or by reaction with oxalyl chloride, as described in O J. Am. Chem. Soc., 1994, 116, 3251, or J. Org. Chem., 1994, S33.8 S33.7 59, 6144, or by reaction with phosphorus pentachloride, as described in J. Org. Chem., 2001, 66, 329, or in J. Med. NN N Chem., 1995, 38, 1372. The resultant phosphoryl chlorides M 60 are then reacted with amines or hydroxy compounds in the N presence of a base to afford the amidate or ester products. Phosphonic acids are converted into activated imidazolyl es derivatives by reaction with carbonyl diimidazole, as S33.12 described in J. Chem. Soc., Chem. Comm. (1991) 312, or (5) ROH He 65 Nucleosides & Nucleotides (2000) 19:1885. Activated sulfo S33.5 nyloxy derivatives are obtained by the reaction of phosphonic acids with trichloromethylsulfonyl chloride or with triisopro US 7,871,991 B2 101 102 pylbenzenesulfonyl chloride, as described in Tet. Lett. (1996) phosphonate diesters, (Scheme 37). Scheme 38 illustrates 7857, or Bioorg. Med. Chem. Lett. (1998) 8:663. The acti synthesis of gem-dialkyl amino phosphonate reagents. vated sulfonyloxy derivatives are then reacted with amines or hydroxy compounds to afford amidates or esters. Scheme 34 illustrates various methods for the conversion Alternatively, the phosphonic acid and the amine or of phosphonate diesters S34.1 into phosphonbisamidates hydroxy reactant are combined in the presence of a diimide S34.5. The diester S34.1, prepared as described previously, is coupling agent. The preparation of phosphonic amidates and hydrolyzed, either to the monoester S34.2 or to the phospho esters by means of coupling reactions in the presence of nic acid S34.6. The methods employed for these transforma dicyclohexyl carbodiimide is described, for example, in J. tions are described above. The monoester S34.2 is converted Chem. Soc., Chem. Comm. (1991) 312 or Coll. Czech. Chem. 10 into the monoamidate S34.3 by reaction with an aminoester Comm. (1987) 52:2792. The use of ethyl dimethylaminopro S34.9, in which the group R is Horalkyl; the group R' is a pyl carbodiimide for activation and coupling of phosphonic divalent alkylene moiety such as, for example, CHCH acids is described in Tet. Lett., (2001) 42:8841, or Nucleo CHCHCH, CH(CH(CH)), CH(CHPh), and the like, or a sides & Nucleotides (2000) 19:1885. 15 side chain group present in natural or modified aminoacids; A number of additional coupling reagents have been and the group R is C-C2 alkyl, such as methyl, ethyl, described for the preparation of amidates and esters from propyl, isopropyl, or isobutyl, C-C aryl, such as phenyl or phosphonic acids. The agents include Aldrithiol-2, and Substituted phenyl: or C-C arylalkyl, such as benzyl or PYBOP and BOP, as described in J. Org. Chem., 1995, 60, benzyhydryl. The reactants are combined in the presence of a 5214, and J. Med. Chem. (1997) 40:3842, mesitylene-2-sul coupling agent Such as a carbodiimide, for example dicyclo fonyl-3-nitro-1,2,4-triazole (MSNT), as described in J. Med. hexylcarbodiimide, as described in J. Am. Chem. Soc., (1957) Chem. (1996) 39:4958, diphenylphosphoryl azide, as 79:3575, optionally in the presence of an activating agent described in J. Org. Chem. (1984) 49: 1158, 1-(2,4,6-triiso Such as hydroxybenztriazole, to yield the amidate product propylbenzenesulfonyl-3-nitro-1,2,4-triazole (TPSNT) as 25 described in Bioorg. Med. Chem. Lett. (1998) 8:1013, bro S34.3. The amidate-forming reaction is also effected in the motris(dimethylamino)phosphonium hexafluorophosphate presence of coupling agents such as BOP, as described in J. (BroP), as described in Tet. Lett., (1996) 37:3997, 2-chloro Org. Chem. (1995) 60:5214, Aldrithiol, PYBOP and similar 5,5-dimethyl-2-oxo-1,3,2-dioxaphosphinane, as described in coupling agents used for the preparation of amides and esters. Nucleosides Nucleotides 1995, 14, 871, and diphenyl chloro 30 Alternatively, the reactants S34.2 and S34.9 are transformed phosphate, as described in J. Med. Chem., 1988, 31, 1305. into the monoamidate S34.3 by means of a Mitsunobu reac Phosphonic acids are converted into amidates and esters by tion. The preparation of amidates by means of the Mitsunobu means of the Mitsunobu reaction, in which the phosphonic reaction is described in J. Med. Chem. (1995) 38:2742. acid and the amine or hydroxy reactant are combined in the 35 Equimolar amounts of the reactants are combined in an inert presence of a triaryl phosphine and a dialkyl azodicarboxy Solvent such as tetrahydrofuran in the presence of a triary1 late. The procedure is described in Org. Lett., 2001, 3, 643, or phosphine and a dialkylazodicarboxylate. The thus-obtained J. Med. Chem., 1997, 40, 3842. monoamidate ester S34.3 is then transformed into amidate Phosphonic esters are also obtained by the reaction phosphonic acid S34.4. The conditions used for the hydroly between phosphonic acids and halo compounds, in the pres 40 sis reaction depend on the nature of the R' group, as described ence of a suitable base. The method is described, for example, previously. The phosphonic acid amidate S34.4 is then in Anal. Chem., 1987, 59, 1056, or J. Chem. Soc. Perkin reacted with an aminoester S34.9, as described above, to yield Trans., I, 1993, 19, 2303, or J. Med. Chem., 1995, 38, 1372, or the bisamidate product S34.5, in which the amino substitu Tet. Lett., 2002, 43, 1161. 45 ents are the same or different. Alternatively, the phosphonic Schemes 34-37 illustrate the conversion of phosphonate acid S34.6 may be treated with two different amino ester esters and phosphonic acids into carboalkoxy-Substituted reagents simulataneously, i.e. S34.9 where R, R' or Rare phosphonbisamidates (Scheme 34), phosphonamidates different. The resulting mixture of bisamidate products S34.5 (Scheme 35), phosphonate monoesters (Scheme 36) and may then be separable, e.g. by chromatography.

Scheme 34

R-link-B-" -- R-link-E-' -- Ric-k -> 34.7 ORI OH OH S34.1 S34.2A S34.6 US 7,871,991 B2

-continued

R-link-E-OR HeR2NH(R1b)COR5 R-link-E-OR R-link-P-OH Lw S34.9 N-R N-R (RB) (R) COR5 COR5 S34.1 S34.3 S34.4

/ S. / R-link-1''' so- R-link-kN COR so- R-link-E-N 4t S. (R") (R+)-COR (Lv or OH) (16) R2 (Lv or OH) N COR)S. S34.7 S34.5 S34.11

Hal(R:)COR R-link-E-NH2 S34.12 R-link-E-NR 4t S. Ex6 N (R")CO2R NH2 / (RCOR5 S34.10 S34.5

An example of this procedure is shown in Scheme 34, which LV is a leaving group such as chloro, imidazolyl, tri Example 1. In this procedure, a dibenzylphosphonate S34.14 isopropylbenzenesulfonyloxy etc. The conversion of phos is reacted with diazabicyclooctane (DABCO) in toluene at phonic acids into chlorides S34.7 (LV-Cl) is effected by reflux, as described in J. Org. Chem., 1995, 60,2946, to afford reaction with thionyl chloride or oxalyl chloride and the like, the monobenzyl phosphonate S34.15. The product is then 35 as described in Organic Phosphorus Compounds, G. M. reacted with equimolar amounts of ethylalaninate S34.16 and Kosolapoff, L. Maeir, eds. Wiley, 1976, p. 17. The conversion dicyclohexyl carbodiimide in pyridine, to yield the amidate of phosphonic acids into monoimidazolides S34.7 product S34.17. The benzyl group is then removed, for (LV-imidazolyl) is described in J. Med. Chem., 2002, 45, example by hydrogenolysis over a palladium catalyst, to give 40 1284 and in J. Chem. Soc. Chem. Comm., 1991, 312. Alter the monoacid product S34.18 which may be unstable accord natively, the phosphonic acid is activated by reaction with ing to J. Med. Chem. (1997) 40(23):3842. This compound triisopropylbenzenesulfonyl chloride, as described in S34.18 is then reacted in a Mitsunobu reaction with ethyl Nucleosides and Nucleotides, 2000, 10, 1885. The activated leucinate S34.19, triphenyl phosphine and diethylazodicar product is then reacted with the aminoester S34.9, in the boxylate, as described in J. Med. Chem., 1995, 38, 2742, to 45 presence of a base, to give the bisamidate S34.5. The reaction produce the bisamidate product S34.20. is performed in one step, in which case the nitrogen Substitu Using the above procedures, but employing in place of ents present in the product S34.5 are the same, or in two steps, ethyl leucinate S34.19 or ethyl alaninate S34.16, different via the intermediate S34.11, in which case the nitrogen sub aminoesters S34.9, the corresponding products S34.5 are stituents can be different. obtained. 50 Examples of these methods are shown in Scheme 34, Alternatively, the phosphonic acid S34.6 is converted into Examples 3 and 5. In the procedure illustrated in Scheme 34, the bisamidate S34.5 by use of the coupling reactions Example 3, a phosphonic acid S34.6 is reacted with ten molar described above. The reaction is performed in one step, in equivalents of thionyl chloride, as described in Zh. Obschei which case the nitrogen-related Substituents present in the Khim., 1958, 28, 1063, to give the dichloro compound product S34.5 are the same, or in two steps, in which case the 55 S34.23. The product is then reacted at reflux temperature in a nitrogen-related substituents can be different. polar aprotic Solvent Such as acetonitrile, and in the presence An example of the method is shown in Scheme 34, of a base such as triethylamine, with butyl serinate S34.24 to Example 2. In this procedure, a phosphonic acid S34.6 is afford the bisamidate product S34.25. reacted in pyridine solution with excess ethyl phenylalaninate Using the above procedures, but employing, in place of S34.21 and dicyclohexylcarbodiimide, for example as 60 butyl serinate S34.24, different aminoesters S34.9, the corre described in J. Chem. Soc., Chem. Comm., 1991, 1063, to give sponding products S34.5 are obtained. the bisamidate product S34.22. In the procedure illustrated in Scheme 34, Example 5, the Using the above procedures, but employing, in place of phosphonic acid S34.6 is reacted, as described in J. Chem. ethyl phenylalaninate, different aminoesters S34.9, the cor Soc. Chem. Comm., 1991, 312, with carbonyl diimidazole to responding products S34.5 are obtained. 65 give the imidazolide S34.S32. The product is then reacted in As a further alternative, the phosphonic acid S34.6 is con acetonitrile Solution at ambient temperature, with one molar verted into the mono or bis-activated derivative S34.7, in equivalent of ethyl alaninate S34.33 to yield the monodis US 7,871,991 B2 105 106 placement product S34.S34. The latter compound is then Using the above procedures, but employing, in place of reacted with carbonyl diimidazole to produce the activated ethyl 2-bromo-3-methylbutyrate S34.38, different haloesters intermediate S34.35, and the product is then reacted, under S34.12 the corresponding products S34.5 are obtained. the same conditions, with ethyl N-methylalaninate S34.33a to The procedures shown in Scheme 34 are also applicable to give the bisamidate product S34.36. the preparation of bisamidates in which the aminoester moi Using the above procedures, but employing, in place of ety incorporates different functional groups. Scheme 34. ethylalaninate S34.33 or ethyl N-methylalaninate S34.33a, Example 7 illustrates the preparation of bisamidates derived different aminoesters S34.9, the corresponding products from tyrosine. In this procedure, the monoimidazolide S34.5 are obtained. S34.32 is reacted with propyl tyrosinate S34.40, as described The intermediate monoamidate S34.3 is also prepared 10 in Example 5, to yield the monoamidate S34.41. The product from the monoester S34.2 by first converting the monoester is reacted with carbonyl diimidazole to give the imidazolide into the activated derivative S34.8 in which LV is a leaving group such as halo, imidazolyl etc, using the procedures S34.42, and this material is reacted with a further molar described above. The product S34.8 is then reacted with an equivalent of propyl tyrosinate to produce the bisamidate aminoester S34.9 in the presence of a base such as pyridine, to 15 product S34.43. give an intermediate monoamidate product S34.3. The latter Using the above procedures, but employing, in place of compound is then converted, by removal of the R' group and propyl tyrosinate S34.40, different aminoesters S34.9, the coupling of the product with the aminoester S34.9, as corresponding products S34.5 are obtained. The aminoesters described above, into the bisamidate S34.5. employed in the two stages of the above procedure can be the An example of this procedure, in which the phosphonic same or different, so that bisamidates with the same or dif acid is activated by conversion to the chloro derivative ferent amino Substituents are prepared. S34.26, is shown in Scheme 34, Example 4. In this procedure, Scheme 35 illustrates methods for the preparation of phos the phosphonic monobenzyl ester S34.15 is reacted, in phonate monoamidates. dichloromethane, with thionyl chloride, as described in Tet. Letters., 1994, 35, 4097, to afford the phosphoryl chloride 25 In one procedure, a phosphonate monoester S34.1 is con S34.26. The product is then reacted in acetonitrile solution at verted, as described in Scheme 34, into the activated deriva ambient temperature with one molar equivalent of ethyl tive S34.8. This compound is then reacted, as described 3-amino-2-methylpropionate S34.27 to yield the monoami above, with an aminoester S34.9, in the presence of a base, to date product S34.28. The latter compound is hydrogenated in afford the monoamidate product S35.1. ethylacetate over a 5% palladium on carbon catalyst to pro 30 The procedure is illustrated in Scheme 35, Example 1. In duce the monoacid product S34.29. The product is subjected this method, a monophenyl phosphonate S35.7 is reacted to a Mitsunobu coupling procedure, with equimolar amounts with, for example, thionyl chloride, as described in J. Gen. ofbutylalaninate S34.30, triphenyl phosphine, diethylazodi Chem. USSR., 1983,32.367, to give the chloro product S35.8. carboxylate and triethylamine in tetrahydrofuran, to give the The product is then reacted, as described in Scheme 34, with bisamidate product S34.31. 35 ethylalaninate S3, to yield the amidate S35.10. Using the above procedures, but employing, in place of Using the above procedures, but employing, in place of ethyl 3-amino-2-methylpropionate S34.27 or butyl alaninate ethylalaninate S35.9, different aminoesters S34.9, the corre S34.30, different aminoesters S34.9, the corresponding prod sponding products S35.1 are obtained. ucts S34.5 are obtained. 40 Alternatively, the phosphonate monoester S34.1 is The activated phosphonic acid derivative S34.7 is also converted into the bisamidate S34.5 via the diamino com coupled, as described in Scheme 34, with an aminoester pound S34.10. The conversion of activated phosphonic acid S34.9 to produce the amidate S335.1. If necessary, the R' derivatives such as phosphorylchlorides into the correspond substituent is then altered, by initial cleavage to afford the phosphonic acid S35.2. The procedures for this transforma ing amino analogs S34.10, by reaction with ammonia, is 45 described in Organic Phosphorus Compounds, G. M. Koso tion depend on the nature of the R' group, and are described lapoff, L. Maeir, eds, Wiley, 1976. The bisamino compound above. The phosphonic acid is then transformed into the ester S34.10 is then reacted at elevated temperature with a amidate product S35.3, by reaction with the hydroxy com haloester S34.12 (Hal=halogen, i.e. F, Cl, Br, I), in a polar pound ROH, in which the group R is aryl, heterocycle, alkyl, cycloalkyl, haloalkyl etc, using the same coupling pro organic solvent such as dimethylformamide, in the presence 50 of a base such as 4,4-dimethylaminopyridine (DMAP) or cedures (carbodiimide, Aldrithiol-2, PYBOP. Mitsunobu potassium carbonate, to yield the bisamidate S34.5. Alterna reaction etc) described in Scheme 34 for the coupling of tively, S34.6 may be treated with two different amino ester amines and phosphonic acids. reagents simulataneously, i.e. S34.12 where R' or R are different. The resulting mixture of bisamidate products S34.5 55 may then be separable, e.g. by chromatography. Scheme 34 Example 1 An example of this procedure is shown in Scheme 34, Example 6. In this method, a dichlorophosphonate S34.23 is R-link-E-OBn -- reacted with ammonia to afford the diamide S34.37. The reaction is performed in aqueous, aqueous alcoholic or alco 60 OB holic solution, at reflux temperature. The resulting diamino S34.14 compound is then reacted with two molar equivalents of ethyl O 2-bromo-3-methylbutyrate S34.38, in a polar organic solvent | H2NCH(Me)COEt R-link-P -OH S34.16 such as N-methylpyrrolidinone at ca. 150°C., in the presence He of a base such as potassium carbonate, and optionally in the 65 OB presence of a catalytic amount of potassium iodide, to afford S34.15 the bisamidate product S34.39.

US 7,871,991 B2 109

-continued -continued

Me R-link-E-O O Y- COEt MeNHCH(Me)COEt NH --

Rin-1-Ní S34.33a Her Im. COPr S34.35 10

Me HO O )-cost S34.41 R-link-E-NH 15 N-Me R-link--" Me NH COEt He S34.36 COPr

25 HO Scheme 34 Example 6 S34.41 PrOC

R-link-B- -- R-link-E-NH 30 C NH S34.23 OH COPr Rink-1-Nil BrCH(Pri)COEt 35 He NH S34.38 2 HO S34.37 S34.43 40 Pri Examples of this method are shown in Scheme 35, O )-cost Examples 2 and 3. In the sequence shown in Example 2, a R-link-E-N monobenzyl phosphonate S35.11 is transformed by reaction with ethyl alaninate, using one of the methods described NH 45 above, into the monoamidate S35.12. The benzyl group is Pri then removed by catalytic hydrogenation in ethylacetate solu tion over a 5% palladium on carbon catalyst, to afford the COEt phosphonic acid amidate S35.13. The product is then reacted S34.39 in dichloromethane solution at ambient temperature with 50 equimolar amounts of 1-(dimethylaminopropyl)-3-ethylcar bodiimide and trifluoroethanol S35.14, for example as described in Tet. Lett., 2001, 42,8841, to yield the amidate ester S35.15. 55 In the sequence shown in Scheme 35, Example 3, the Scheme 34 Example 7 monoamidate S35.13 is coupled, in tetrahydrofuran solution HO at ambient temperature, with equimolar amounts of dicyclo hexyl carbodiimide and 4-hydroxy-N-methylpiperidine S35.16, to produce the amidate ester product S35.17. 60 Using the above procedures, but employing, in place of the O ethyl alaninate product. S35.12 different monoacids S35.2, | OH HN COPr and in place of trifluoroethanol S35.14 or 4-hydroxy-N-me R-link-P HerS334.40 thylpiperidine S35.16, different hydroxy compounds ROH, Im. the corresponding products S35.3 are obtained. 65 Alternatively, the activated phosphonate ester S34.8 is S34.32 reacted with ammonia to yield the amidate S35.4. The prod uct is then reacted, as described in Scheme 34, with a US 7,871,991 B2 111 112 haloester S35.5, in the presence of a base, to produce the uct S34.11. The latter compound is then reacted with the amidate product S35.6. If appropriate, the nature of the R' hydroxy compound ROH in a polar organic solvent such as group is changed, using the procedures described above, to dimethylformamide, in the presence of a base Such as diiso give the product S35.3. The method is illustrated in Scheme 35. Example 4. In this sequence, the monophenyl phosphoryl propylethylamine, to yield the monoamidate ester S35.3. chloride S35.18 is reacted, as described in Scheme 34, with The method is illustrated in Scheme 35. Example 5. In this ammonia, to yield the amino product S35.19. This material is method, the phosphoryl dichloride S35.22 is reacted in then reacted in N-methylpyrrolidinone solution at 170° with dichloromethane solution with one molar equivalent of ethyl butyl 2-bromo-3-phenylpropionate S35.20 and potassium N-methyl tyrosinate S35.23 and dimethylaminopyridine, to carbonate, to afford the amidate product S35.21. 10 generate the monoamidate S35.24. The product is then Using these procedures, but employing, in place of butyl - 2-bromo-3-phenylpropionate S35.20, different haloesters reacted with phenol S35.25 in dimethylformamide contain S35.5, the corresponding products S35.6 are obtained. ing potassium carbonate, to yield the ester amidate product The monoamidate products S35.3 are also prepared from S35.26. the doubly activated phosphonate derivatives S34.7. In this Using these procedures, but employing, in place of ethyl procedure, examples of which are described in Synlett., 1998, N-methyl tyrosinate S35.23 or phenol S35.25, the ami 1,73, the intermediate S34.7 is reacted with a limited amount noesters 34.9 and/or the hydroxy compounds ROH, the cor of the aminoester S34.9 to give the mono-displacement prod- responding products S35.3 are obtained.

Scheme 35 O O O

R-link-P-OR -- R-link-P-OR - - R-link-P-OH -- S35.3 OH S34.9 N-R N-R S34.1 (RB) (RB) COR5 COR5 S35.1 S35.2 R2NH(R+b)CORS | S34.9 /

O O O R-link-P-OR - R-link-P-OR -Hal(R:)COR - - -- R-link-P-OR| S35.5 Lw NH2 NH S34.8 S35.4 (RB) COR5b S35.6

A R. 3 Rink- Lw so- R-link- re N ROH- R-link-P-OR Lw Lw " N-R S34.7 COR5 (RB) S34.11 COR5 S35.3 US 7,871,991 B2

Scheme 35 Example 1 Scheme 35 Example 4 O O O O |OPh |-OPh HNCH(MeCO.E. R-link-1|-OPh He- R-link-1|-OPh --BrCH(Bn)CO.Bu Rink 1" - Rink 1 "2NC(MP S35.20 OH C S35.9 C NH2 S35.7 S35.8 S35.18 S35.19 10 R-link-1 OPh R-link-1 OH NH Bn NH 15 COBu Me S35.21 COEt S35.10

Scheme 35 Example 5 HO

Scheme 35 Example 2 25

OB OB R-link-1 He- R-link-1 He O Me He -Cl SN COEt OH NH R-link-P Her M S35.23 S35.11 Me C COEt S35.22 S35.12 R-link-1 C V 35 O CFCHOH O N-Me R-link-1|-OH He-S35.14 R-link-1|OCHCF HO COEt NH NH S35.24 Me Me 40 PhOH COEt COEt S35.25 S35.13 S35.15

45 R-link-P-O N-Me Scheme 35 Example 3 HO OH COEt OH 50 R-link-1 N S35.26

VNH HerMe1 S35.16 Scheme 36 illustrates methods for the preparation of car Me boalkoxy-substituted phosphonate diesters in which one of COEt 55 the ester groups incorporates a carboalkoxy Substituent. S35.13 In one procedure, a phosphonate monoester S34.1, pre pared as described above, is coupled, using one of the meth ods described above, with a hydroxyester S36.1, in which the groups R' and R are as described in Scheme 34. For R-link-P-O N-Me 60 example, equimolar amounts of the reactants are coupled in NH the presence of a carbodiimide Such as dicyclohexyl carbo diimide, as described in Aust. J. Chem., 1963, 609, optionally Me in the presence of dimethylaminopyridine, as described in COEt Tet., 1999, 55, 12997. The reaction is conducted in an inert S35.17 65 Solvent at ambient temperature. The procedure is illustrated in Scheme 36, Example 1. In this method, a monophenyl phosphonate S36.9 is coupled, in US 7,871,991 B2 115 116 dichloromethane solution in the presence of dicyclohexyl The procedure is illustrated in Scheme 36, Example 3. In carbodiimide, with ethyl 3-hydroxy-2-methylpropionate this sequence, a monophenylphosphonate S36.9 is reacted, in S36.10 to yield the phosphonate mixed diester S36.11. acetonitrile solution at 70° C., with ten equivalents of thionyl Using this procedure, but employing, in place of ethyl chloride, so as to produce the phosphoryl chloride S36.19. 3-hydroxy-2-methylpropionate S36.10, different hydroxyes The product is then reacted with ethyl 4-carbamoyl-2-hy ters S33.1, the corresponding products S33.2 are obtained. droxybutyrate S36.20 in dichloromethane containing triethy The conversion of a phosphonate monoester S34.1 into a lamine, to give the mixed diester S36.21. mixed diester S36.2 is also accomplished by means of a Using the above procedures, but employing, in place of Mitsunobu coupling reaction with the hydroxyester S36.1, as 10 ethyl 4-carbamoyl-2-hydroxybutyrate S36.20, different described in Org. Lett., 2001, 643. In this method, the reac hydroxyesters S36.1, the corresponding products S36.2 are tants 34.1 and S36.1 are combined in a polar solvent such as obtained. tetrahydrofuran, in the presence of a triarylphosphine and a The mixed phosphonate diesters are also obtained by an dialkylazodicarboxylate, to give the mixed diester S36.2. The alternative route for incorporation of the RO group into R" substituent is varied by cleavage, using the methods 15 intermediates S36.3 in which the hydroxyester moiety is described previously, to afford the monoacid product S36.3. already incorporated. In this procedure, the monoacid inter The product is then coupled, for example using methods mediate S36.3 is converted into the activated derivative S36.6 in which LV is a leaving group Such as chloro, imidazole, and described above, with the hydroxy compound ROH, to give the like, as previously described. The activated intermediate the diester product S36.4. is then reacted with the hydroxy compound ROH, in the The procedure is illustrated in Scheme 36, Example 2. In presence of a base, to yield the mixed diester product S36.4. this method, a monoallyl phosphonate S36.12 is coupled in The method is illustrated in Scheme 36, Example 4. In this tetrahydrofuran solution, in the presence of triphenylphos sequence, the phosphonate monoacid S36.22 is reacted with phine and diethylazodicarboxylate, with ethyl lactate S36.13 trichloromethanesulfonyl chloride in tetrahydrofuran con to give the mixed diester S36.14. The product is reacted with 25 taining collidine, as described in J. Med. Chem., 1995, 38. tris(triphenylphosphine) rhodium chloride (Wilkinson cata 4648, to produce the trichloromethanesulfonyloxy product lyst) in acetonitrile, as described previously, to remove the S36.23. This compound is reacted with 3-(morpholinom allyl group and produce the monoacid product S36.15. The ethyl)phenol S36.24 in dichloromethane containing triethy latter compound is then coupled, in pyridine Solution at ambi lamine, to yield the mixed diester product S36.25. 30 Using the above procedures, but employing, in place of ent temperature, in the presence of dicyclohexyl carbodiim with 3-(morpholinomethyl)phenol S36.24, differentalcohols ide, with one molar equivalent of 3-hydroxypyridine S36.16 ROH, the corresponding products S36.4 are obtained. to yield the mixed diester S36.17. The phosphonate esters S36.4 are also obtained by means Using the above procedures, but employing, in place of the of alkylation reactions performed on the monoesters S34.1. ethyl lactate S36.13 or 3-hydroxypyridine, a different 35 The reaction between the monoacid S34.1 and the haloester hydroxyester S36.1 and/or a different hydroxy compound S36.7 is performed in a polar solvent in the presence of a base ROH, the corresponding products S36.4 are obtained. Such as diisopropylethylamine, as described in Anal. Chem., The mixed diesters S36.2 are also obtained from the 1987, 59, 1056, or triethylamine, as described in J. Med. monoesters S34.1 via the intermediacy of the activated Chem., 1995, 38, 1372, or in a non-polar solvent such as monoesters S36.5. In this procedure, the monoester S34.1 is 40 benzene, in the presence of 18-crown-6, as described in Syn. converted into the activated compound S36.5 by reaction Comm., 1995, 25,3565. with, for example, phosphorus pentachloride, as described in The method is illustrated in Scheme 36, Example 5. In this procedure, the monoacid S36.26 is reacted with ethyl J. Org. Chem., 2001, 66, 329, or with thionyl chloride or 2-bromo-3-phenylpropionate S36.27 and diisopropylethy oxalyl chloride (LV-Cl), or with triisopropylbenzenesulfonyl 45 lamine in dimethylformamide at 80°C. to afford the mixed chloride in pyridine, as described in Nucleosides and Nucle diester product S36.28. otides, 2000, 19, 1885, or with carbonyl diimidazole, as Using the above procedure, but employing, in place of described in J. Med. Chem., 2002, 45, 1284. The resultant ethyl 2-bromo-3-phenylpropionate S36.27, different activated monoester is then reacted with the hydroxyester haloesters S36.7, the corresponding products S36.4 are S36.1, as described above, to yield the mixed diester S36.2. obtained.

Scheme 36

O O HOR' (1 equiv.) R-link-P-OR R-link- |-OH Ha-Rib-COOR3 O OH A (RB) COR5 S36.4

Ha-Rib-COORS S33.7

US 7,871,991 B2 120 performed in the presence of an excess of the hydroxyester, to -continued afford the diester product S37.3 in which the ester substitu HO ents are identical, or sequentially with limited amounts of local r different hydroxyesters, to prepare diesters S37.3 in which Rink, O 5 the ester substituents are different. O S36.24 The methods are illustrated in Scheme 37. Examples 3 and Me 4. As shown in Example 3, the phosphoryl dichloride S35.22 COEt is reacted with three molar equivalents of ethyl 3-hydroxy-2- S36.23 10 (hydroxymethyl)propionate S37.9 in tetrahydrofuran con taining potassium carbonate, to obtain the diester product S37.10. Using the above procedure, but employing, in place of RickO r O 15 ethyl 3-hydroxy-2-(hydroxymethyl)propionate S37.9, differ Me ent hydroxyesters S37.2, the corresponding products S37.3 COEt are obtained. S36.25 Scheme 37, Example 4 depicts the displacement reaction between equimolar amounts of the phosphoryl dichloride 2O S35.22 and ethyl 2-methyl-3-hydroxypropionate S37.11, to yield the monoester product S37.12. The reaction is con Scheme 36 Example 5 ducted in acetonitrile at 70° in the presence of diisopropyl ethylamine. The product S37.12 is then reacted, under the same conditions, with one molar equivalent of ethyl lactate R-link-OH BrCH(Bn)CO2EtBrCH(B)COEt R-OCH(Bn)CO:Et 25 S36.27 S37.13, to give the diester product S37.14. OCH2CF OCH2CF Using the above procedures, but employing, in place of S36.26 S36.28 ethyl 2-methyl-3-hydroxypropionate S37.11 and ethyllactate S37.13, sequential reactions with different hydroxyesters 30 S37.2, the corresponding products S37.3 are obtained. Scheme 37 illustrates methods for the preparation of phos phonate diesters in which both the ester substituents incorpo rate carboalkoxy groups. Scheme 37 The compounds are prepared directly or indirectly from the phosphonic acids S34.6. In one alternative, the phosphonic 35 acid is coupled with the hydroxyester S37.2, using the con R-link-E-OH —- R-link-B- ditions described previously in Schemes 34-36, such as cou pling reactions using dicyclohexyl carbodiimide or similar O(R+b)COR5b O(R)COR reagents, or under the conditions of the Mitsunobu reaction, S37.5 37.4 to afford the diester product S37.3 in which the ester substitu- 40 S37.1 ents are identical. This method is illustrated in Scheme 37. Example 1. In this sia N sia procedure, the phosphonic acid S34.6 is reacted with three HO(R)COR4b. 5 molar equivalents of butyl lactate S37.5 in the presence of S37.2 4b. Sb R-link-E-OH —t R-O(R")COR Aldrithiol-2 and triphenylphosphine in pyridine at ca. 70° C., 4s Hal(Rb)COR3b to afford the diester S37.6. OH (R")CO O(R4b)COR5b S37.1 Using the above procedure, but employing, in place of S34.6 S37.3 butyl lactate S37.5, different hydroxyesters S37.2, the corre sponding products S37.3 are obtained. Alternatively, the diesters S37.3 are obtained by alkylation so -6S37.2 st of the phosphonic acid S34.6 with a haloester S37.1. The alkylation reaction is performed as described in Scheme 36 - LV -LV for the preparation of the esters S36.4. R-link-P st - R-link-P This method is illustrated in Scheme 37. Example 2. In this Lw O(R')COR5b procedure, the phosphonic acid S34.6 is reacted with excess 55 S34.7 S37.4 ethyl 3-bromo-2-methylpropionate S37.7 and diisopropyl ethylamine in dimethylformamide at ca. 80°C., as described in Anal. Chem., 1987, 59, 1056, to produce the diester S37.8. Using the above procedure, but employing, in place of ethyl 3-bromo-2-methylpropionate S37.7, different 60 Scheme 37 Example 1 haloesters S37.1, the corresponding products S37.3 are obtained. HOCH(CH2)COB The diesters S37.3 are also obtained by displacement reac R-link-OH Bochticob. R-link-P - OCH(CH3)COBu tions of activated derivatives S34.7 of the phosphonic acid OH OCH(CH3)COBu with the hydroxyesters S37.2. The displacement reaction is 65 S34.6 S37.6 performed in a polar solvent in the presence of a suitable base, as described in Scheme 36. The displacement reaction is US 7,871,991 B2 122

Scheme 37 Example 2 Scheme 38a. O H-OH BrCH3CH(CH3)COEt 5 R-link-P —s - X- OH He- HessHP(O)(OCH3)2 HN NR NaH OH S34.6 S38.16 10 O O R-link-P -OCH2CH(CH3)COEt Xu -OCH3 Xu -OH OCH2CH(CH3)COEt RHN YoCH, CbzHN NoH S37.8 S38.17 S38.14 15

Scheme 37 Example 3 ENUMERATED EXEMPLARY EMBODIMENTS 1-CI (HOCH2)2CHCO2Et R-link-P — so - 1. A compound, including enantiomers thereof, of Formula C 1A, or a pharmaceutically acceptable salt or Solvate thereof, S35.22 25 R-link-P-OCHCH(CHOH)COEt 1A A9 Y2 Base OCH2CH(CHOH)COEt S37.10 R2 R2 30 R2a R3a

Scheme 37 Example 4 wherein: 35 C HOCH2CH(CH3)CO2Et A is A, A, or A: R-link-P S37.11 C S35.22 A is O HOCH(CH)COEt 40 Y2 ill-OCHCHCH. Co-El S37.13 Y2 Yw6. 2 2 C R R af2. 2. S37.12 45 A is Y2 R-OCH3CH(CH3)CO:Et Y2 Yw3. OCH(CH3)COEt 2 2 S37.14 R R af2. 50 2. A is: 2,2-Dimethyl-2-aminoethylphosphonic acid intermediates can be prepared by the route in Scheme 5. Condensation of Yl Yl 2-methyl-2-propanesulfinamide with acetone give Sulfinyl imine S38.11 (J. Org. Chem. 1999, 64, 12). Addition of dim 55 ethyl methylphosphonate lithium to S38.11 afford S38.12. Acidic methanolysis of S38.12 provide amine S38.13. Pro tection of amine with Cbz group and removal of methyl groups yield phosphonic acid S38.14, which can be converted to desired S38.15 (Scheme 38a) using methods reported ear 60 lier on. An alternative synthesis of compound S38.14 is also Y' is independently O, S, N(R), N(O)(R), N(OR), N(O) shown in Scheme 38b. Commercially available 2-amino-2- (OR), or N(N(R)(R)); methyl-1-propanol is converted to aziridines S38.16 accord ing to literature methods (J. Org. Chem. 1992, 57, 5813, Syn. Y is independently a bond,Y, N(R), N(O)(R), N(OR), Lett. 1997, 8, 893). Aziridine opening with phosphite give 65 N(O)(OR), N(N(R)(R)). —S(O)—, or —S(O)—S S38.17 (Tetrahedron Lett. 1980, 21, 1623). Reprotection) of (O) ; S38.17 affords S38.14. Y is O, S(O), S, or C(R): US 7,871,991 B2 123 124 R’ is independently H. R. R. W., a protecting group, or 4. The compound of embodiment 1 wherein R is selected the formula: from selected from the group consisting of H. halogen, alkyl, alkenyl, alkynyl, amino, amino acid, alkoxy, aryloxy, cyano, azido, haloalkyl, cycloalkyl, aryl, haloaryl, and heteroaryl. c. I-P's -1. |- R; 5. The compound of embodiment 1 that has the formula 1B 2 Y afe af2c Y2 afic Y2 afe 1B Base wherein: 10 R’ is independently H. W. R or a protecting group; R" is independently H or alkyl of 1 to 18 carbonatoms; RandR are independently H, R', R, or R' wherein each Risindependently substituted with 0 to 3R groups or, when taken together at a carbon atom, two R groups form a ring of 15 3 to 8 and the ring may be substituted with 0 to 3 R groups; 6. The compound of embodiment 1 that has the formula 1C R is R. R. R. R., or R, provided that when R is bound to a heteroatom, then R is R or R': R" is R, CN, N or NO; R is (—Y); R is R, N(R)(R), SR, S(O)R’, S(O).R., –S(O)(OR), S(O),(OR), OC(Y)R, OC(Y)OR, OC(Y)(N(R)(R)), SC(Y)R', SC(Y)OR', SC (Y)(N(R)(R)), N(R)C(Y)R’, N(R)C(Y)OR, or N(R)C(Y)(N(R)(R)); 25 R is C(Y)R’, C(Y)OR or C(Y)(N(R)(R)); 7. The compound of embodiment 1 that has the formula 1D R is F, Cl, Br or I: R" is an alkyl of 1 to 18 carbon atoms, alkenyl of 2 to 18 carbon atoms, or alkynyl of 2 to 18 carbon atoms; R is Hor R, wherein each R is substituted with 0 to 3 R' 30 A. Y Base groups: W3 is Wor W5; W is R., C(Y)R, C(Y)W, SOR, or PC —SOW: W is carbocycle or heterocycle wherein W is indepen 35 dently substituted with 0 to 3 R' groups; 8. The compound of embodiment 1 that has the formula 1E W is W independently substituted with 1, 2, or 3 A groups: M2 is 0, 1 or 2: 40 M12a is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; A. Base M12b is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; M1a, M1 c, and M1d are independently 0 or 1; and M12c is 0, 1,2,3,4,5,6,7,8,9, 10, 11 or 12; PC provided that the compound of Formula 1A is not of the 45 Structure 556-E.6 9. The compound of embodiment 1 that has the formula 1 F 556-E.6 NH2 50 O e Y Base HON | \, Ho1 P N1 O O N -/ 55 o 10. The compound of embodiment 1 that has the formula 1 G or its ethyl diester. 60 2. The compound of embodiment 1 wherein R* is selected 1G from the group consisting of H, halogen, alkyl, alkenyl, alky A3 Base nyl, amino, amino acid, alkoxy, aryloxy, cyano, azido, haloalkyl, cycloalkyl, aryl, haloaryl, and heteroaryl o

3. The compound of embodiment 1 wherein R* is selected 65 F from the group consisting of H, halo, alkyl, azido, cyano, or haloalkyl. US 7,871,991 B2 125 126 11. The compound of embodiment 1 that has the formula 1H A is H, alkyl, alkenyl, alkynyl, amino, amino acid, alkoxy, aryloxy, cyano, haloalkyl, cycloalkyl, aryl, haloaryl, or heteroaryl, optionally substituted with R: 1H Y is O or S; A. O Base 5 Y is O, N(R), or S; and each R and R” is independently selected from the group consisting of H. halogen, alkyl, alkenyl, alkynyl, amino, amino acid, alkoxy, aryloxy, cyano, azido, haloalkyl, cycloalkyl, aryl, haloaryl, and heteroaryl; and 10 each R' is independently selected from the group consist 12. The compound of embodiment 1 that has the formula 1 I ing of H, halogen, alkyl, alkenyl, alkynyl, amino, amino acid, alkoxy, aryloxy, cyano, azido, haloalkyl, cycloalkyl, aryl, haloaryl, and heteroaryl; provided that the compound of For mula 1A is not of the structure 556-E.6 R3 15 556-E.6 ( 4 n Y4. NH2 2 O e A3 O N N 2O HON ( | \, HO -N10 O N N2-/

R3e 25 or its ethyl diester. wherein: 17. The compound of embodiment 16 wherein R* is selected Y is N or C(R). from the group consisting of H, halogen, alkyl, alkenyl, alky 13. The compound of embodiment 1 that has the formula 1J nyl, amino, amino acid, alkoxy, aryloxy, cyano, azido, 30 haloalkyl, cycloalkyl, aryl, haloaryl, and heteroaryl 18. The compound of embodiment 16 wherein R* is selected NH2 from the group consisting of H, halo, alkyl, azido, cyano, or haloalkyl. (N NN 35 19. The compound of embodiment 1 selected from: a) Formula 1A wherein A' is A: A. O N N2 b) Formula 1A wherein A' is

40 O F O N1 < OR; 14. The compound of embodiment 1 wherein R* is halo, alkyl, azido, cyano, or haloalkyl. 45 c) Formula 1A wherein: 15. The compound of embodiment 1 wherein R is a naturally A is occurring amino acid. 16. A compound, enantiomers thereof, or a pharmaceutically acceptable salt or Solvate thereof that is of the general struc- 50 OR ture of formula I O N1 K OR;

(I) and 55 each RandR is H: d) Formula 1A wherein: A is

60 wherein O 3 B is Base; O P|-OR Z is O, S, or C(R): N1 Nors. R is F, Cl, Br or I; A CHP(Y)(A)(YA), CHP(Y)(A)(A), 65 O H.P(Y)(YA)(YA), optionally substituted R is N(R)(R'); with R: each RandR is H. US 7,871,991 B2 127 128 e) Formula 1A wherein: 23. The compound of embodiment 1 wherein A is of the A is formula:

O

O P -OH n N1 NoH. O 10 \-O R1 O ORI R1 RI and each RandR is H. af2d O 20. The compound of embodiment 1, wherein A is of the formula: wherein the phenyl carbocycle is substituted with 0, 1, 2, or 3 R groups. 24. The compound of embodiment 1 wherein A is of the 2O formula: O R2 na O PN. 'N, H. H. af2d W3 O 25 y25 O O \l-OP CH3

30 "SXN N OR. H. H. wherein: Y is O or N(R); and O M12d is 1, 2, 3, 4, 5, 6, 7 or 8. 25. The compound of embodiment 1 wherein A is of the 21. The compound of embodiment 1 wherein A is of the 35 formula: formula:

40 Yl O P Y2C | NN 25 YRy, Pa R' R2 R2 W3 Yla Y2 Ny. af2. y251 45 R2 R2 af2. 2. wherein: Y''' is O or S; Y is O or N(R); and 22. The compound of embodiment 1 wherein A is of the 50 Y is O, N(R) or S; and formula: each R and R is independently selected from the group consisting of H. halogen, alkyl, alkenyl, alkynyl, amino, amino acid, alkoxy, aryloxy, cyano, azido, haloalkyl, cycloalkyl, aryl, haloaryl, and heteroaryl. 55 26. The compound of embodiment 1 wherein A is of the formula: O O \-OP R' SS-1'N, ORI 60 | R1 RI af2d O cir-o-

65 wherein the phenyl carbocycle is substituted with 0, 1, 2, or 3 R groups. wherein each R is independently H or alkyl. US 7,871,991 B2 129 130 27. The compound of embodiment 1 which is isolated and 33. The compound of embodiment 1 that is selected from purified. Table Y. 28. A compound of formula MBFI, or prodrugs, solvates, or 34 The compound of embodiment 28 wherein K1 and K2 are Selected from Table 100. pharmaceutically acceptable salts or esters thereof 5 TABLE 100 (MBF I) O K K2 Ester K1-P O O B 10 Ala OP cPent /N-1 Ala OCHCF E K2 Ala OP 3-furan-4H Ala OP cBut F Phe(B) OP E Phe(A) OP E Ala(B) OP E 15 Phe OP sBucS) wherein Phe OP cBu each K1 and K2 are independently selected from the group Phe OCHCF iBu Ala(A) OP E consisting of A and - Y“A: Phe OP sBu(R) Y is O, N(R'), or S; Ala(B) OP CH-cPr B is Base; Ala(A) OP CH-cPr A is H. alkyl, alkenyl, alkynyl, amino, amino acid, Phe(B) OP nBu alkoxy, aryloxy, cyano, haloalkyl, cycloalkyl, aryl, haloaryl, Phe(A) OP nBu Phe OP CH-cPr or heteroaryl, optionally substituted with R', and Phe OP CH-cBu R’ is independently selected from the group consisting of Ala OP 3-pent H. halogen, alkyl, alkenyl, alkynyl, amino, amino acid, 25 ABA(B) OP E alkoxy, aryloxy, cyano, azido, haloalkyl, cycloalkyl, aryl, ABA(A) OP E Ala OP CH-cBu haloaryl, and heteroaryl; provided that when B is adenine, Met OP E then both K1 and K2 are not simultaneously both —OH or Pro OP Bn - OEt. Phe(B) OP iBu 30 Phe(A) OP iBu 29. The compound of embodiment 28 wherein B is selected Phe OP iPr form the group consisting of 2,6-diaminopurine, guanine, Phe OP Pr Ala OP CH-cPr adenine, cytosine, 5-fluoro-cytosine, monodeaza, and Phe OP E monoaza analogues thereof. Ala OP E ABA OP nPent 35 30. The compound of embodiment 28 wherein MBFI is of the Phe Phe Pr formula Phe Phe E Ala Ala E CHA OP Me MBFI Gly OP iPr NH2 ABA OP nBu 40 Phe OP allyl Ala OP nPent N n Gly OP Bu ABA OP iBu Ala OP nBu K1-P O O {N 2 CHA CHA Me /N-1 N 45 Phe Phe Allyl K2 ABA ABA nPent Gly Gly iBu Gly Gly iPr Phe OP iBu Ala OP Pr 50 Phe OP nBu 31. The compound of embodiment 1 wherein B is selected ABA OP Pr from the group consisting of adenine, guanine, cytosine, ABA OP E Ala Ala Bn uracil, thymine, 7-deaZaadenine, 7-deazaguanine, 7-deaza-8- Phe Phe ill azaguanine, 7-deaza-8-azaadenine, inosine, nebularine, ABA ABA Pr nitropyrrole, nitroindole, 2-aminopurine, 2-amino-6-chloro ABA ABA E purine, 2,6-diaminopurine, hypoxanthine, pseudouridine, 55 Ala Ala Pr pseudocytosine, pseudoisocytosine, 5-propynylcytosine, iso Ala OP iPr Ala OP Bn cytosine, isoguanine, 7-deazaguanine, 2-thiopyrimidine, Ala Ala nBu 6-thioguanine, 4-thiothymine, 4-thiouracil, O'-methylgua Ala Ala iBu nine, N'-methyladenine, O-methylthymine, 5,6-dihy ABA ABA nBu 60 ABA ABA iPr drothymine, 5,6-dihydrouracil, 4-methylindole, substituted Ala OP iBu triazole, and pyrazolo 3,4-Dipyrimidine. ABA OP Me 32. The compound of embodiment 1 wherein B is selected ABA OP iPr form the group consisting of adenine, guanine, cytosine, ABA ABA iBu uracil, thymine, 7-deaZaadenine, 7-deazaguanine, 7-deaza-8- 65 azaguanine, 7-deaza-8-azaadenine, aminopurine, 2-amino-6- wherein Ala represents L-alanine, Phe represents L-phe chloropurine, 2,6-diaminopurine, and 7-deazaguanine. nylalanine, Met represents L-methionine, ABA repre US 7,871,991 B2 131 132 sents (S)-2-aminobutyric acid, Pro represents L-proline, wherein: CHA represents 2-amino-3-(S)cyclohexylpropionic R’ is independently H. W., R or a protecting group: acid, Gly represents glycine; K1 or K2 amino acid carboxyl-groups are esterified as R" is independently H or alkyl of 1 to 18 carbon atoms; denoted in the ester column, wherein RandR'' are independently H, R', R, or R' wherein each cPent is cyclopentane ester; Et is ethyl ester, 3-furan-4H is Risindependently substituted with 0 to 3R groups or taken the (R) tetrahydrofuran-3-yl ester; clBut is cyclobutane together at a carbonatom, two R groups form a ring of 3 to 8 ester; shBu(S) is the (S) secButyl ester; shBu(R) is the (R) carbons and the ring may be substituted with 0 to 3 R groups; SecButyl ester; iBu is isobutyl ester; CH-cPr is methyl R is R, R, R or R, provided that when R is bound cyclopropane ester, nBu is n-butyl ester; CH-cBu is 10 methylcyclobutane ester; 3-pent is 3-pentyl ester; nPent to a heteroatom, then R is R or R': is nPentyl ester; iPr is isopropyl ester, nPr is nPropyl R" is F, Cl, Br, I, CN, N or - NO; ester; allyl is allyl ester; Me is methyl ester; Bn is Benzyl R is Y: ester, and R is R, N(R)(R), SR', S(O)R’, S(O),R, wherein A or B in parentheses denotes one stereoisomer at 15 S(O)(OR), S(O)(OR), OC(Y)R’, OC(Y)OR, phosphorus, with the least polar isomer denoted as (A) OC(Y)(N(R)(R)), SC(Y)R', SC(Y)OR', SC and the more polar as (B). (Y)(N(R')(R)), N(R)C(Y)R’, N(R)C(Y)OR, or 35. A compound of formula B, and the salts and solvates N(R)C(Y)(N(R)(R)); thereof. Riis C(Y)R’, C(Y)OR or C(Y)(N(R)(R)); R" is an alkyl of 1 to 18 carbon atoms, alkenyl of 2 to 18 carbon atoms, or alkynyl of 2 to 18 carbon atoms; (B) R is R' wherein each R is substituted with 0 to 3 R' 25 groups: W is W or W5; W is R., C(Y)R, C(Y)W, SOR, or —SOW: 30 W is carbocycle or heterocycle wherein W is indepen dently substituted with 0 to 3 R' groups; W is W independently substituted with 1, 2, or 3 A groups: 35 M2 is 0, 1 or 2: wherein: M12a is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; M12b is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12; M1a, M1 c, and M1d are independently 0 or 1; and A is: 40 M12c is 0, 1,2,3,4,5,6,7,8,9, 10, 11 or 12; wherein A is not-O-CH-P(O)(OH), or - O CH-P(O)(OEt). Yl 2 P R 36. The compound of embodiment 35 wherein m2 is 0, Y is Y. Y2 Ny2 O, Y’ is O, M12b and M12a are 1, one Y is -OR where R' Y2NR 45 is Wand the ther Y is N(H)R where R is R2 R2 2 22 af2. 2.

Y' is independently O, S, N(R), N(O)(R), N(OR), N(O) (OR), or N(N(R)(R)); 50 Yl R. R. Y1 Y is independently a bond, O, N(R), N(O)(R), N(OR), N(O)(OR), N(N(R)(R)). —S(O) , or —S(O). S R. (O) ; and when Yi joins two phosphorous atoms Y can Y2 afe 2 Y4),2 YMid2 also be C(R)(R): R’ is independently H. R. R. W., a protecting group, or 55 the formula: 37. The compound of embodiment 36 wherein the terminal R'

60 of R is selected from the group of esters in Table 100. Yl R. R. Yl 38. The compound of embodiment 36 wherein the terminal R' R; of R is a C1-C8 normal, secondary, tertiary or cyclic alky Y2 af2c 2 2 lene, alkynylene or alkenylene. afe Y). Y1 Mid 65 39. The compound of embodiment 36 wherein the terminal R' of R is a heterocycle containing 5 to 6 ring atoms and 1 or 2 N, O and/or Satoms in the ring. US 7,871,991 B2 133 134 40. The compound of embodiment 1 having the formula XX: 53. The compound of embodiment 1 for use in antiretroviral or antihepadinaviral treatment. (XX) 54. A method of preparing the compound of embodiment 1 according to the Examples or Schemes. NH2 55. Use of a compound of embodiment 1 for preparing a medicament for treating HIV or a HIV associated disorder. 56. A method of therapy for treating HIV or HIV-associated X O { 2 O HN N- N N disorders with the compound of embodiment 1. O o 57. A method of treating disorders associated with HIV, said method comprising administering to an individual infected F with, or at risk for HIV infection, a pharmaceutical compo 15 sition which comprises a therapeutically effective amount of the compound of any of embodiments 1-28. 58. A compound of Table Y, provided the compound is not 41. The compound of embodiment 1 having the formula XXX:

556-E.6 NH2 (XXX) N O NH2 O 2 N 25 w N Ho- / N EtO n N 1 N-1 O N -/ O ( HO N2 HN) O O N 2 po1'N1 N 30

F or its ethyl diester.

42. A pharmaceutical composition comprising a pharmaceu 35 EXAMPLES AND EXEMPLARY tical excipient and an antivirally-effective amount of the com EMBODIMENTS pound of embodiment 1. Examples 43. The pharmaceutical composition of embodiment 32 that further comprises a second active ingredient. 40

44. A combination comprising the compound of embodiment O 1 and one or more antivirally active ingredients. BZO F 45. The combination of embodiment 44 wherein one or more Br 45 of the active ingredients is selected from Table 98. Bzó 46. The combination of embodiment 45 wherein one of the active ingredients is selected from the group consisting of Truvada, Viread, Emtriva, d4T, Sustiva, or Amprenavir anti viral compounds. 2-deoxy-2-fluoro-3,5-di-O-benzoyl--D-arabinofura 50 nosylbromide (2) 47. The combination of embodiment 44 wherein one or more of the active ingredients is selected from Table 99. Tannet al., JOC 1985, 50, p3644 48. The combination of embodiment 47 wherein one of the active ingredients is selected from the group consisting of 55 Howell et al. JOC 1988, 53, p85 Truvada, Viread, Emtriva, d4T, Sustiva, or Amprenavir anti To a solution of 1 (120g, 258 mmol), commercially avail viral compounds. able from Davos or CMS chemicals, in CHCl (1 L) was 49. The combination of embodiment 46 for use in medical added 33% HBr/Acetic acid (80 mL). The mixture was stirred therapy. 60 at room temperature for 16 h, cooled with ice-water, and 50. The combination of embodiment 48 for use in medical slowly neutralized over 1-2 h with NaHCO, (150 g/1.5 L therapy. solution). The CHCl2 phase was separated and concentrated under reduced pressure. The residue was dissolved in ethyl 51. The pharmaceutical composition of embodiment 42 for acetate and washed with NaHCO until no acid was present. use in medical therapy. 65 The organic phase was dried over MgSO filtered and con 52. The pharmaceutical composition of embodiment 43 for centrated under reduced pressure to give product2 as a yellow use in medical therapy oil (~115 g). US 7,871,991 B2 135 136

OMe

N n O O {/ eN HO F

10 HG

2-deoxy-2-fluoro-3,5-di-O-benzoyl-B-D-arabinofura 15 2-deoxy-2-fluoro-5-carboxy-f-D-arabinofuranosyl nosyl-9H-6-chloropurine (3) 6-methoxyadenine (5)

Ma et al., J. Med. Chem. 1997, 40, 2750 Moss et al. J. Chem. Soc. 1963, p1149 A mixture of Pt/C (10%, 15 g (20-30% mol equiv.) as a Marquez et al., J. Med. Chem. 1990,33,978 water slurry) and NaHCO, (1.5g, 17.94 mmol) in HO (500 Hildebrand et al., J. Org. Chem. 1992, 57, 1808 mL) was stirred at 65° C. under H for 0.5 h. The reaction mixture was then allowed to cool, placed under a vacuum and Kazimierczuk et al. JACS 1984, 106,6379 flushed with N several times to completely remove all H. To a suspension of NaH (14 g. 60%) in ACETONITRILE 25 Compound 4 (5.1 g, 17.94 mmol) was then added at room (900 mL), 6-chloropurine (52.6 g) was added in 3 portions. temperature. The reaction mixture was stirred at 65°C. under The mixture was stirred at room temperature for 1.5 h. A O. (balloon) until the reaction was complete by LC-MS (typi cally 24-72 h). The mixture was cooled to room temperature solution of 2 (258 mmol) in ACETONITRILE (300 mL) was and filtered. The Pt/C was washed with HO extensively. The added dropwise. The resulting mixture was stirred at room combined filtrates were concentrated to ~30 mL, and acidi temperature for 16 h. The reaction was quenched with Acetic 30 fied (pH4) by the addition of HCl (4N) at 0°C. A black solid acid (3.5 mL), filtered and concentrated under reduced pres precipitated out which was collected by filtration. The crude sure. The residue was partitioned between CHC1 and water. product was dissolved in a minimum amount of Methanol and The organic phase was dried over MgSO filtered and con filtered through a pad of silica gel (eluting with Methanol). centrated. The residue was treated with CH2Cl and then The filtrate was concentrated and crystallized from water to EtOH (~ 1:2 overall) to precipitate out the desired product3 as 35 give compound 5 (2.5 g) as an off-white Solid. a yellowish solid (83 g. 65% from 1). OMe

40 N n

2 Bo 'Su-o O N N EtO F 45 i HG 50 (2R3'S,4'R,5R)-6-Methoxy-9-tetrahydro 4-iodo-3- fluoro-5-(diethoxyphosphinyl)methoxy-2-furanyl 2-deoxy-2-fluoro-B-D-arabinofuranosyl-6-methoxy purine (6) adenine (4) 55 Zemlicka et al., J. Amer: Chem. Soc. 1972, 94, p3213 To a suspension of 3 (83 g, 167 mmol) in Methanol (1 L) at To a solution of 5 (22g, 73.77 mmol) in DMF (400 mL), 0° C., NaOMe (25% wit, 76 mL) was added. The mixture was DMF dineopenty1 acetal (150 mL, 538 mmol) and methane stirred at room temperature for 2 h, and then quenched with sulfonic acid (9.5 mL, 146.6 mmol) were added. The reaction Acetic acid (-11 mL, pH=7). The mixture was concentrated mixture was stirred at 80-93°C. (internal temperature) for 30 60 min, then cooled to room temperature and concentrated under under reduced pressure and the resultant residue partitioned reduced pressure. The residue was partitioned between ethyl between hexane and water (approximately 500 mL hexane acetate and water. The organic phase was separated and and 300 mL water). The aqueous layer was separated and the washed with NaHCO, followed by brine, dried over MgSO, organic layer mixed with water once again (approximately filtered and concentrated under reduced pressure. The residue 300 mL). The water fractions were combined and concen 65 and diethyl (hydroxymethyl)phosphonate (33 mL, 225 trated under reduced pressure to -100 mL. The product, 4. mmol) were dissolved in CHCl (250 mL) and cooled down precipitated out and was collected by filtration (42 g, 88%). to -40° C. US 7,871,991 B2 137 138 A solution of iodine monobromide (30.5 g, 1.1 mol) in (2R,5R)-9-(3-fluoro-2,5-dihydro-5-phospho CHCl (100 mL) was added dropwise. The mixture was nomethoxy-2-furanyl)adenine di Sodium salt (8) stirred at -20 to -5° C. for 6 h. The reaction was then quenched with NaHCO and NaSO. The organic phase A solution of compound 7 (2.3 g, 5.7 mmol) in methanol (6 was separated and the water phase was extracted with 5 CHC1. The combined organic phases were washed with mL) was mixed with ammonium hydroxide (28-30%) (60 brine, dried over MgSO, filtered and concentrated under mL). The resultant mixture was stirred at 120° C. for 4 h. reduced pressure. The residue was purified by silica gel chro cooled, and then concentrated under reduced pressure. The matography to give product 6 (6 g. 15.3%). residue was dried under vacuum for 12 h. The residue was 10 dissolved in DMF (40 mL) and bromotrimethylsilane (3.5 Alternative Procedure for the Preparation of 6 mL) was added. The mixture was stirred at room temperature A solution of 5 (2.0 g. 6.7 mmol) in THF (45 mL) was for 16 h, and then concentrated under reduced pressure. The treated with triphenyl phosphine (2.3 g, 8.7 mmol) under N. residue was dissolved in aqueous NaHCO, (2.3 g in 100 mL Diisopropyl azodicarboxylate (1.8 g., 8.7 mmol) was added of water). The solution was evaporated and the residue was slowly. The resultant mixture was stirred at room temperature 15 purified on C-18 (40 um) column, eluting with water. The for 1 h and then concentrated under reduced pressure to aqueous fractions were freeze dried to give di-sodium salt 8 dryness. The residue was dissolved in CHCl (20 ml), and (1.22g, 57%). then treated with diethyl(hydroxymethyl)phosphonate (4.5 g. 27 mmol). The mixture was cooled to -60° C. and then a cold solution of iodine monobromide 2 g, 9.6 mmol) in CHCl, (10 ml) was added. The reaction mixture was warmed to -10° C. and then kept at -10°C. for 1 h. The reaction mixture was diluted with CHCl2, washed with saturated aqueous NaHCO, and then with aqueous sodium thiosulfate. The organic phase was separated, dried over MgSO, and concen 25 trated under reduced pressure to dryness. The reaction mix ture was purified by silica gel chromatography (eluting with 25% ethyl acetate in CHCl2, then switching to 3% methanol in CHCl) to afford product 6 (0.9 g, 33%). 30

OMe

N n Example of Monoamidate Preparation (52) 35 Disodium salt 8 (25 mg, 0.066 mmol), (S)-Ala-O-cyclobu O 2 tylester hydrochloride (24 mg, 2 eq., 0.133 mmol) and phenol EtO 7'Su- {N N (31 mg, 0.333 mmol) were mixed in anhydrous pyridine (1 mL). Triethylamine (111 uL, 0.799 mmol) was added and the resultant mixture was stirred at 60° C. under nitrogen. In a separate flask, 2-Aldrithiol (122 mg, 0.466 mmol) and triph 40 enylphosphine (103 mg, 0.466 mmol) were dissolved in anhydrous pyridine (0.5 mL) and the resulting yellow solu tion was stirred for 15-20 min. The solution was then added to (2R,5R)-6-Methoxy-9-3-fluoro-2,5-dihydro-5- the solution of 8 in one portion. The combined mixture was (diethoxyphosphinyl)methoxy-2-furanylpurine (7) stirred at 60° C. under nitrogen for 16 h to give a clear yellow 45 to light brown solution. The mixture was then concentrated To a solution of compound 6 (6g, 11.3 mmol) inacetic acid under reduced pressure. The resultant oil was dissolved in (2.5 mL) and methanol (50 mL), NaClO (10-13%) (50 mL) CH2Cl and purified by silica gel chromatography (eluting was added dropwise. The reaction mixture was then stirred with a linear gradient of 0 to 5% MeOH in CHCl) to give an for 0.5 h and concentrated under reduced pressure. The resi oil. The resulting oil was dissolved in acetonitrile and water due was treated with ethyl acetate and then filtered to remove 50 and purified by preparative HPLC (linear gradient, 5-95% solids. The filtrate was concentrated and the residue was acetonitrile in water). Pure fractions were combined and purified by silica gel chromatography to give product 7 (4.g. freeze-dried to give mono amidate 52 as a white powder. 88%). 55 NH2 NH2 O S N n N n / ) s ( N O 2 f O ( . 2) 60 O HN N- N N NaO 7'Su- N N NaO

65 US 7,871,991 B2 139 140 Example of Bisamidate Preparation (17) 50% methanol in acetonitrile, was used to elute isomer B, 57. Disodium salt 8 (12 mg, 0.032 mmol) and (S)-Ala-O-n-Pr out from the column in 8 mins. Removed all solvent and then ester hydrochloride (32 mg, 6 eq., 0.192 mmol) were mixed in re-dissolved in acetonitrile and water. Freeze-dried the anhydrous pyridine (1 mL). Triethylamine (53 uL, 0.384 samples (Mass—348 mg). mmol) was added and the resultant mixture was stirred at 60° C. under nitrogen. In a separate flask, 2'-Aldrithiol (59 mg, 0.224 mmol) and triphenylphosphine (49 mg, 0.224 mmol) O NH2 were dissolved in anhydrous pyridine (0.5 mL) and the result w N ing yellow solution was stirred for 15-20 min. The solution EtO n N was then added to the solution of 8 in one portion. The 10 combined mixture was stirred at 60° C. under nitrogen for 16 HN,'...} O (N 4.2 h to give a clear yellow to light brown solution. The mixture /N1 O was then concentrated under reduced pressure. The resultant PhO oil was dissolved in CH2Cl and purified by silica gel chro matography (eluting with a linear gradient of 0 to 5% MeOH 15 in CH2Cl2) to give an oil. The resulting oil was dissolved in F acetonitrile and water and purified by preparative HPLC (lin eargradient, 5-95% acetonitrile in water). Purefractions were combined and freeze-dried to give bis amidate as a white Example 11b powder. 1H NMR (CDC13) 8.39 (s, 1H) 8.12 (s, 1H) 6.82 (m, 1H) 5.96-5.81 (m, 4H) 4.03-3.79 (m, 10H) 3.49 (s, 1H) 3.2 (m, 2H) 1.96-1.69 (m. 10H) 1.26 (m, 4H) 0.91 (m, 12H)31P NMR (CDC13) 20.37 (s, 1P) MS (M+1) 614 25 Example 12b 1H NMR (CDC13) 8.39 (s, 1H) 8.13 (s, 1H) . 727-7.11 (m, 5H) 6.82 (s, 1H) 5.97-5.77 (m, 4H) 4.14-3.79 (m, 6H) 30 3.64 (t, 1H) 2.00-1.88 (bm, 4H) 1.31 (dd, 3H) 0.91 (m, 6H)31PNMR (CDC13). 20.12(s, 0.5P) 19.76(s, 0.5P)MS (M+1) 535 Example 13b 35 'HNMR (CDC1): 8.39 (s.1H), 8.13 (s, 1H), 6.81 (m. 1H), Example of Monoamidate Preparation (69) 5.95 (m. 1H), 5.81 (s, 1H), 4.98 (m, 2H), 3.90 (m, 2H), 3.37 Compound 8 (1.5g, 4 mmol) was mixed with ethylalanine (m. 1H), 3.19 (m. 1H), 1.71 (m, 4H), 1.25 (m, 12H), 0.90 (m, ester HCl salt (1.23g, 8 mmol) and phenol (1.88 g. 20 mmol). 6H) Anhydrous pyridine (35 mL) was added followed by TEA 40 Mass Spectrum (m/e): (M+H)" 586.3 (6.7 mL, 48 mmol). The mixture was stirred at 60° C. under nitrogen for 15-20 min, 2'-Aldrithiol (7.3 g) was mixed in a Example 14 separate flask with triphenylphosphine (6.2 g) in anhydrous pyridine (5 mL) and the resultant mixture was stirred for 'HNMR (CDC1): 8.38 (s, 1H), 8.12 (s, 1H), 6.80 (m. 1H), 10-15 minto give a clear light yellow solution. The solution 45 5.93 (m. 1H), 5.79 (s, 1H), 4.02 (m, 6H), 3.42 (m, 1H), 3.21 was then added to the above mixture and stirred overnight at (m. 1H), 1.65 (m, 4H), 1.35 (m, 8H), 0.92 (m, 12H) 60° C. The mixture was concentrated under reduced pressure Mass Spectrum (m/e): (M+H)' 614.3 to remove pyridine. The resultant residue was dissolved in ethyl acetate and washed with saturated sodium bicarbonate Example 15 solution (2x) and then with saturated sodium chloride solu 50 tion. The organic layer was dried over sodium sulfate, filtered 'HNMR (CDC1): 8.38 (s, 1H), 8.12 (s, 1H), 6.80 (m. 1H), and then concentrated under reduced pressure. The resultant 5.93 (m, 2H), 5.80 (s, 1H), 3.91 (m, 6H), 3.42 (m, 1H), 3.30 oil was dissolved in dichloromethane and loaded onto a dry (m. 1H), 1.91 (m, 2H), 1.40 (m, 6H), 0.90 (m, 12H) CombiFlash column, 40 g, eluting with a linear gradient of Mass Spectrum (m/e): (M+H)" 586.3 0-5% methanol in dichloromethane over 10 min and then 5% 55 Example 16 methanol in dichloromethane for 7-10 min. Fractions con taining the desired product were combined and concentrated 'HNMR (CDC1): 8.37 (s, 1H),8.17 (s, 1H), 6.80 (m 1H), under reduced pressure to give a foam. The foam was dis 6.18 (s, 1H), 5.93 (m, 1H), 5.79 (s.1H), 4.02 (m, 6H), 3.46 (m, solved in acetonitrile and purified by prep HPLC to give 69 1H), 3.37 (m. 1H), 1.61 (m, 4H), 1.32 (m. 10H), 0.92 (m, 6H) (0.95g). 60 Mass Spectrum (m/e): (M+H)' 614.3 Dissolved 69 (950 mg) in small amount of acetonitrile and let stand at room temperature overnight. Collected solid by Example 17 filtration and washed with small amount of acetonitrile. Solid was GS-327.625. Filtrate was reduced under vacuum and then H NMR (CDOD): 8.29 (s, 1H), 8.25 (s, 1H), 6.84 (m loaded onto Chiralpak AS-H column equilibrated in Buffer A, 65 1H), 6.00 (s, 1H), 5.96 (m. 1H), 4.04 (m, 8H), 1.66 (m, 4H), 2% ethanol in acetonitrile. Isomer A, 59, was eluted out with 1.38 (m, 6H), 0.98 (m, 6H) Buffer A at 10 mL/min for 17 mins. After which Buffer B, Mass Spectrum (m/e): (M+H)" 558.3

US 7,871,991 B2 145 146 Example 54 ment is described herein. By way of example and not limita tion, the point of attachment is selected from those depicted in "H NMR (CDOD): 8.24 (m, 2H), 6.85 (m, 1H), 6.01 (m, the schemes and examples. 2H), 4.43 (m, 2H), 4.09 (m, 5H), 1.38 (m, 3H) 1.23 (m, 3H) Mass Spectrum (m/e): (M+H)" 513.2 TABLE 1.1 1 Example 55 O ki- O O B "H NMR for mixture of diastereomers at phosphorus (300 10 /N-1 MHz, CDOD ref. solv.resid.3.30 ppm): (ppm)=8.22-8.27 K2 (m. 2H), 7.09-7.34 (m, 5H), 6.84 (brs, 1H), 5.93-6.02 (m, 2H), 5.00-5.14 (m. 1H), 4.01-4.26 (m,2H)3.89-3.94 (m, 1H), F 1.50-1.88 (m, 8H), 1.23, (br t, 3H, J=6.8). 'P NMR for mixture of diastereomers at phosphorus (121 MHz, "H 2 decoupled): (ppm)=23.56, 22.27 (-60:40 ratio). 15 NH2 N n Example 102 O ( N By way of example and not limitation, embodiments of the ki- O O N 4. invention are named below in tabular format (Table Y). These K2 embodiments are of the general formula “MBF3” /N-1 so MBF3: ScK1K2 F Each embodiment of MBF3, is depicted as a substituted 25 nucleus (Sc). Sc is described in Table 1.1 below. Sc is also described by any formula presented herein that bears at least TABLE 2.0.1 one K1 or K2 wherein each is a point of covalent attachment to Sc. For those embodiments described in Table Y, Sc is a nucleus designated by a number and each Substituent is des 30 ignated in order by number. Table 1.1 are a schedule of nuclei used in forming the embodiments of Table Y. Each nucleus (Sc) is given a number designation from Table 1.1 and this designation appears first in each embodiment name as num bers 1 to 2. Similarly, Tables 20.1 to 20.37 list the selected 35 Substituent groups by number designation, and are under stood to be attached to Sc at K1 or K2 as listed. It is under stood that K1 and K2 do not represent atoms, but only points of connection to the parent scaffold Sc. Accordingly, a com pound of the formula MBF3 includes compounds having Sc 40 groups based on compounds according to Table Y below. In all cases the compounds of the formula MBF3 have groups K1 and K2 on nucleus Sc., and the corresponding groups Kl and K2 are listed, as set forth in the Tables below. Accordingly, each named embodiment of Table Y is 45 depicted by a number designating the nucleus from Table 1.1, followed by a number designating each Substituent group K1. followed by the designation of substituent K2, as incorpo rated from Tables 20.1 to 20.37. In graphical tabular form, each embodiment of Table Y appears as a name having the 50 Syntax:

Each Sc group is shown having various Substituents K1 or K2. Each group K1 and K2 as listed in Table Y, is a substitu 55 ent, as listed, of the Sc nucleus listed in Table Y. K1 and K2, it should be understood, do not represent groups or atoms but are simply connectivity designations. The site of the covalent bond to the nucleus (Sc) is designated as K1 and K2 of formula MBF3. Embodiments of K1 and K2 in Tables 20.1 to 60 20.37 are designated as numbers 1 to 247. For example there are 2 Sc entries in Table 1.1 and these entries for Sc are numbered 1 to 2. Each is designated as the Sc identifier (ie. 1 to 2). In any event, entries of Tables 20.1 to 20.37 always begin with a number, and are independently selected from 65 Tables 20.1 to 20.37 and are each thus independently desig nated as numbers 1 to 247. Selection of the point of attach US 7,871,991 B2 147 148

TABLE 20.1-continued TABLE 20.3-continued

17 CH O c r 'N-1- CH c1. NCH, O 10

18 TABLE 20.2

15 c r ON 1-N-CH3 19 10 CH3

cr"CH3 c-inO 25 11 CH c N TABLE 20.4 r CH 30 O CH3 c. On 1 N-CH3 TABLE 20.3 O 35 12 21 CH CH3 c ( O CH3 40 O N O CH3 13 CH 22 CH CH c. 45 ( O N CH O 14 CH 50 c TABLE 20.5 23

15 55 CH3 c 1. O NR O 24 60 16 <- O r NH 65 O 25 US 7,871,991 B2 149 150

TABLE 20.5-continued TABLE 20.6-continued HC c O NR4 O 10 26 HC TABLE 20.7 O 34 c. NR 15 W3

O O

27 c- Yw3 H3C O 35 c-s-sO W3 O O 25 c- NR5 28 O H3C 36

O c. NCH, 30 c O

29 37 H3C 35 O c-N-N-O CH3 c., n R O 40 38 30 H3C c O c N-1\ch, 45 O OOO 39

50 TABLE 20.6 O 31 H3C 40 55 c O On 1 N-CH3

O

32 HC 60 41 c O CH O Y O O CH 65 33 US 7,871,991 B2 151 152

TABLE 20.8 TABLE 20.9-continued

52 R4 42 On c W3

O 53 10 43

O S4

15

44

55

45 56

25

57 RI 46 30

O n O W3

O

35 RI 47 TABLE 2010 O 58 c. NR5 cry On 1 N-CH3 O 40

RI 48 59

O 45 c. NR4 c rCH3 O CH 60 RI 49 (< N O 50 -N-> c NR H O O

55 TABLE 2011 TABLE 20.9 CH3 61

50 O n O ch W3 cr Yw3 60 H O H O CH 62 51 O O cr NR5 65 c NR5 H O H O US 7,871,991 B2 153 154

TABLE 2.0.11-continued TABLE 20.13-continued CH 63 HC 73

O ch'sH O c NR5 64 H O 10 H3C 74

O 65 15 c NR4 H O

H3C 75 66 c O NR H O

76 25 HC 67 c O NH H O 30 H3C 77 68

O 35 c NCH, H O

HC 78 TABLE 2012 40 O CH CH3 69 N1 ( ON-1-N-CH3 H O

H O 45 H3C 79 CH3 70 O c O CH N-1\ch, H O H O NCH 50

CH3 CH3 71 TABLE 2014 ( N CH3 H3C 55 H O ( ON-1-N-CH3

H O TABLE 2013 60 72 H3C 81 c O CH3 65 N H O CH3 US 7,871,991 B2 155 156

TABLE 2.0.14-continued TABLE 2016 91 82 O n N W3 N H c 92 Dr. 10

TABLE 20.15

W3 83 15 95 ch O Yw3 H O 84 W3 84 O n O RI ch NR5 25 H O 85 W3 85 N O 30 ch NR4 H H O 86

W3 86 35

O ch NR 87 H O 40 R5 87

O ch Yw3 98 45 H O

R5 88

O ch NR5 50 H O TABLE 20.17 RIRIRIR1R4R4R4R4 99 R5 89 O 55 cr Yw3 O W3 OOOOOOOOO ch NR4 H O 100 N R5 60 R5 90 c ~'s R3 O

O 101 ch NR O H O 65 cr NR4 R3 O US 7,871,991 B2 157 158

TABLE 2.0.17-continued TABLE 2.0.19-continued CH3 112 102 ch's

113 10 103

15 114

104

115

105

25 116

106

30

117

TABLE 2.0.18 35

107

TABLE 20.2O 40 c--- 118 CH 108 (< N On 113 cr"CH 45 R3 O CH 119 CH 109 c Nulls (< O CH3 50 N Y r^-> R3 O CH3 R3 O CH CH 120

TABLE 20.19 55 CH3 110

O n c W3 TABLE 20.21 R3 O 60 121 CH 111 c O NR5 65 R 3 O US 7,871,991 B2 159 160

TABLE 2.0.21-continued TABLE 2.0.22-continued

H3C 131 HC 122 5 CH3

O c NR5 (< N N CH3 R3 O O 10 H3C 123 TABLE 20.23 O c N R4 15 132 R3 O

HC 124 R3 O O c NR 133 R3 O () n R5 H3C 125 25 R3 O O c NH 134 R3 O () 30 n R4 HC 126 R3 O

O 135 c NCH, 35 R3 O () n RI

H3C 127 R3 O

40 O N1 CH"3 136

R3 O

HC 128 45 R3 O

137 ( N-1aCH () R3 O n R5 50 R31. O

TABLE 20.22 138

H3C 129 55 () n R4 R31. O ( N ON 1-3

R3 O 139 60 130 () n RI

R3 O 65 crR3 O CH3 US 7,871,991 B2 161 162

TABLE 20.24 TABLE 20.25-continued 140 ( 152 H On W3 153 R3 O (< R3 141 10

O ( W3 154 n R5 o1 R31. O 155 142 15 o1

O 156 n R4 1 R4 O R3 O 2O 157 143 R () O n R 158 25 1.1 H 144 159 1. R3 O O n W3 30 R3 O TABLE 20.26 145 160 O n RS 35 (< -W R31. O H 146 (< Rs 161 40 N1 () n R4

R3 O ( R4 162 147 45 N1

O n R 163 R3 O R 50

H TABLE 20.25 164 148 ( 1 H

(< W3 55 H

149 3 165 R5 N1 R 60 150 H

R4 166 -W 151 ( N 65 US 7,871,991 B2 163 164

TABLE 2.0.26-continued TABLE 20.28 HC 18O ( 167 5 O Y R5 c- o1 R SeNo

R3 O 181 4 168 10 c- -RS CH N1 O O CH R 15 O 182 169 c- Ra CH3 ( N1 RI o1 No CH

183

c Y 170 R H c-is-N-No1 No CH R3 184 25 171 c- o1 RaNo (< N1 R3

30 185 O TABLE 20.27 c- Ra o1 No c O 172 35 1. Ra us 3 O O W TABLE 20.29 O 173 O 186

1. R or, O 40 c- 1No us W3 174 O 187

O O R4 45 c-1als R5 175 O 188

RI 50 cr-ls R4 176 O 189 crO O H cr-1. 177 55 s O 190 R O O C H3 cr-1s, 178 O 191 C H3 60 us R1. O or -n, CH3 O1-YYa 179 O 192 -lu 65 or -n. 1such3 US 7,871,991 B2 165 166

TABLE 2.0.29-continued TABLE 20.31-continued

O CH 193 O 205 c.--N- c- s--- CH3 O 10 TABLE 20.30 c - *s-s-s HC 194 H3C 1No J 15 c - rusNo O O D O 195

CH or -n. 3 TABLE 20.32 CH3 208 196 O rCH3 CH &- rullsNo O or -n. 3 25 CH O CH 209 CH3 rulls 197 c - No O CH or -n. CH 30 O CH3 210

198 o1 R O CH3

O 211 or -n, 35

c-s-s-s-sCH 3 199 40 212 c - rusNo O O O

45 O 213 TABLE 20.31 O c - rulNo O Ra us W3 cr- No o1 50 O cr- RaNo us o1 R5 TABLE 20.33 O 214 55 O us W3 cr- RaNo ls O1 R4 c --> o1 O 215 O 60 ls R5 c - RaNo uso1 RI c - O1 O 216 O 204

65 ls R4 & o1 RaNo lso1 H c - o1 US 7,871,991 B2 167 168

TABLE 20.33-continued TABLE 20.35-continued

O 217 5 229 c 1No ls O1 RI 5 o1 s's O O 218 c.- ls o1 H 10 (< o1 RSe O YR4 230

O 219 O

ls CH3 Se c ---- 15 (< o1 R O NR 231 O 220 O

232 c.,1nls,1Ne, 2O (< Ra On 221 SSw H O

233 c-O 25 Ra O c re H O TABLE 20.34 234 222 O rCH3 30 c - R 'N c.- ls O H r O O CH 223 c 235 Y Ria O n c- ! O -- CH N R1 H O O CH3 224 40 c-s-s-k.1No O CH3 TABLE 20.36

O 225 236 Ra O c n w c ------45 R3 O CH3 237 Ra O O 226 ( N1 n R5

R O c.--1No O 50 l, 238 O 227 C Rio O c- ls 55 R3rise O 239 c Ra O NR 60 R3 O TABLE 20.35 21 240 228

c- s's 65 ( O NX 2 O R US 7,871,991 B2 169 170

TABLE 20.36-continued Lengthy table referenced here 241 USO787,1991-20110118-TOOOO1 21 5 ( Please refer to the end of the specification for access instructions. -S-X.N

10 EXEMPLARY EMBODIMENTS

21 242 15 NH2

2O Ri 'Su-o O N R

243 F

C 25 Example R1 R2 Ester MW O 55 Ala OP cPent S46.5 S4 Ala OCHCF E S12.36 53 Ala OP 3-furan- S48.47 4H TABLE 20.37 30 52 Ala OP cBut S32.47 50 Phe(B) OP E 582.53 56 Phe(A) OP E 582.53 244 57 Ala(B) OP E SO6.43 (< 51 Phe OP sBucS) 610.58 O N 58 Phe OP cBu 608.57 --R2 35 49 Phe OCHCF iBu 616.51 2 59 Ala(A) OP E SO6.43 48 Phe OP sBu(R) 610.58 60 Ala(B) OP CH-cPr S32.47 61 Ala(A) OP CH-cPr S32.47 62 Phe(B) OP nBu 610.58 40 63 Phe(A) OP nBu 610.58 47 Phe OP CH-cPr 608.57 46 Phe OP CH2cBu 622.59 245 45 Ala OP 3-pent 548.51 (< N 64 ABA(B) OP E S2O46 O 65 ABA(A) OP E S2O46 --R 44 Ala OP CH-cBu 546.5 2 45 43 Met OP E 566.55 42 Pro OP Bn 594.54 66 Phe(B) OP iBu 610.58 67 Phe(A) OP iBu 610.58 41 Phe OP iPr 596.56 40 Phe OP Pr 596.56 50 79 Ala OP CH-cPr S32.47 68 Phe OP E 582.53 246 69 Ala OP E SO6.43 N 70 ABA OP nPent S62.54 O 39 Phe Phe Pr 709.71 --R 38 Phe Phe E 681.66 2 55 37 Ala Ala E 529.47 71 CHA OP Me 574.55 36 Gly OP iPr SO6.43 35 ABA OP nBu 548.51 34 Phe OP allyl 594.54 33 Ala OP nPent 548.51 60 32 Gly OP iBu S2O46 72 ABA OP iBu 548.51 247 73 Ala OP nBu 534.48 31 CHA CHA Me 665.7 O 30 Phe Phe Allyl 705.68 29 ABA ABA nPent 641.68 28 Gly Gly iBu 55752 65 27 Gly Gly iPr 529.47 26 Phe OP iBu 610.58 US 7,871,991 B2 171 172 wherein Ala represents L-alanine, Phe represents L-phe -continued nylalanine, Met represents L-methionine, ABA repre sents (S)-2-aminobutyric acid, Pro represents L-proline, NH2 CHA represents 2-amino-3-(S)cyclohexylpropionic N 5 acid, Gly represents glycine; W NN K1 or K2 amino acid carboxyl groups are esterified as O ( e denoted in the ester column, wherein | N % cPent is cyclopentane ester; Et is ethyl ester, 3-furan-4H is Ri 'Su-o O the (R) tetrahydrofuran-3-yl ester; clBut is cyclobutane R 10 ester; shBu(S) is the (S) secButyl ester; shBu(R) is the (R) o SecButyl ester; iBu is isobutyl ester; CH-cPr is methyl F cyclopropane ester, nBu is n-butyl ester; CH-cBu is methylcyclobutane ester; 3-pent is 3-pentyl ester; nPent Example R1 R2 Ester MW is nPentyl ester; iPr is isopropyl ester, nPr is nPropyl 15 ester; allyl is allyl ester; Me is methyl ester; Bn is Benzyl 25 Ala OPh Pr S2O46 24 Phe OPh nBu 610.58 ester; and 23 ABA OPh Pr 534.48 wherein A or B in parentheses denotes one stereoisomer at 22 ABA OPh Et S2O46 phosphorus, with the least polar isomer denoted as (A) 21 Ala Ala Bn 653.61 and the more polar as (B). S. SR R s: 20 All literature and patent citations above are hereby 18 ABA ABA Et 55752 expressly incorporated by reference at the locations of their 17 Ala Ala Pr 55752 citation. Specifically cited sections or pages of the above cited 74 Ala OPh iPr S2O46 works are incorporated by reference with specificity. The f i. Si, invention has been described in detail sufficient to allow one 15 Ala Ala iBu 585.57 25 of ordinary skill in the art to make and use the subject matter 14 ABA ABA nBu 6.13.63 of the following Embodiments. It is apparent that certain 13b ABA ABA iPr 585.57 modifications of the methods and compositions of the follow 12b77 ABAAla OPh MeBu 534.48SO6.43 ing Embodiments can be made within the scope and spirit of 78 ABA OPh iPr 534.48 the invention. 11b ABA ABA iBu 6.13.63 30 In the embodiments hereinbelow, the subscript and super Scripts of a given variable are distinct. For example, R is distinct from R.

LENGTHY TABLES The patent contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US0787 1991 B2). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

The invention claimed is: resents L-proline, CHA represents 2-amino-3-(S) 1. A compound of formula MBFI, or a pharmaceutically 45 cyclohexylpropionic acid, and Gly represents gly acceptable salt or ester thereof, cine; and K1 or K2 amino acid carboxyl groups are esterified as denoted in the ester column, wherein, cBent is 50 cyclopentane ester, Et is ethyl ester, 3-furan-4H MBFI is the (R) tetrahydrofuran-3-yl ester, cBut is NH2 cyclobutane ester, shBu(S) is the (S) secButyl N n N ester, shBu(R) is the (R) secButyl ester, iBu is O s isobutyl ester, CH-cPr is methylcyclopropane ( e 55 ester, nBu is n-butyl ester, CH-cBu is methylcy K1-P N % clobutane ester, 3-pent is 3-pentyl ester, nPent is K2 nPentyl ester, iPr is isopropyl ester, nPr is nPro A re pyl ester, allyl is allyl ester, Me is methyl ester, F 60 and Bn is Benzyl ester. 2. A pharmaceutical composition comprising an effective wherein, amount of the compound of claim 1, or the pharmaceutically K1 and K2 are independently selected from Table 100, acceptable salt or ester thereof, and a pharmaceutical excipi wherein Ala represents L-alanine, Phe represents 65 ent. L-phenylalanine, Met represents L-methionine, 3. The pharmaceutical composition of claim 2, which fur ABA represents (S)-2-aminobutyric acid, Pro rep ther comprises a second active ingredient. US 7,871,991 B2 173 174 4. A combination comprising the compound of claim 1, or the pharmaceutically acceptable salt or ester thereof, and one or more antiviral active ingredients. 5. The combination of claim 4, wherein the one or more active ingredients are selected from Table 99, 5 EtO ... N SN

TABLE 99 Abacavir sulfate PhO Abacavir sulfateflamivudine Adefovir dipivoxil 10 o Amprenavir Atazanavir Sulfate F Delavirdine mesilate Dideoxycytidine; Zalcitabine Dideoxyinosine; Didanosine 11. A compound having the formula XXX, or a pharma Efavirenz ceutically acceptable salt thereof, Emtricitabine Fosamprenavir calcium Foscarnet sodium Indinavir Sulfate (XXX) O NH Lamivudine 2 Lamivudine Zidovudine 2O w Lopinavir EtO v Lopinavirritonavir O y NN. Nelfinavir mesilate Nevirapine HN ( 2 Ritonavir Saquinavir mesilate 25 PhO /'N1 v -O N Stavudine Tenofovir disoproxil fumarate? emitricitabine Tipranavir Zidovudine: Azidothymidine. F

30 6. The combination of claim 4, wherein the one or more 12. A pharmaceutical composition comprising an effective active ingredients are selected from the group consisting of amount of the compound of claim 11, or the pharmaceutically tenofovir disoproxil fumarate/emtricitabine, tenofovir diso acceptable salt thereof, and a pharmaceutical excipient. proxil fumarate, emitricitabine, d4T, efavirenz, amprenavir, 13. The pharmaceutical composition of claim 12, which abacavir Sulfate, abacavir Sulfate/lamivudine, atazanavir Sul is further comprises a second active ingredient. fate, lamivudine, lamivudine/zidovudine and lopinavir/ 14. A combination comprising the compound of claim 11, ritonavir. or the pharmaceutically acceptable salt thereof, and one or 7. A method of treating HIV in an individual in need more antiviral active ingredients. thereof, comprising administering to the individual a thera 15. The combination of claim 14, wherein the one or more peutically effective amount of the compound of 1, or the 40 active ingredients are selected from Table 99, pharmaceutically acceptable salt or ester thereof. 8. A prophylactic method of reducing a risk of HIV infec TABLE 99 tion in a patient that may be exposed to HIV, comprising Abacavir sulfate administering to the patient a therapeutically effective Abacavir sulfateflamivudine 45 Adefovir dipivoxil amount of the compound of 1, or the pharmaceutically Amprenavir acceptable salt or ester thereof. Atazanavir Sulfate 9. A compound having the formula XX, or a pharmaceuti Delavirdine mesilate Dideoxycytidine; Zalcitabine cally acceptable salt thereof, Dideoxyinosine; Didanosine 50 Efavirenz Emtricitabine (XX) Fosamprenavir calcium Foscarnet Sodium Indinavir Sulfate Lamivudine Lamivudine Zidovudine 55 Lopinavir Lopinavirritonavir Nelfinavir mesilate Nevirapine Ritonavir Saquinavir mesilate 60 Stavudine Tenofovir disoproxil fumarate? emitricitabine Tipranavir Zidovudine: Azidothymidine.

65 16. The combination of claim 14, wherein the one or more 10. A compound having the following structure, or a phar active ingredients are selected from the group consisting of maceutically acceptable salt thereof, tenofovir disoproxil fumarate/emtricitabine, tenofovir diso US 7,871,991 B2 175 176 proxil fumarate, emitricitabine, d4T, efavirenz, amprenavir, 18. A prophylactic method of reducing a risk of HIV infec abacavir Sulfate, abacavir Sulfate/lamivudine, atazanavir Sul- tion in a patient that may be exposed to HIV, comprising fate, lamivudine, lamivudine/zidovudine and lopinavir/ administering to the patient a therapeutically effective ritonavir. amount of the compound of 11, or the pharmaceutically 17. A method of treating HIV in an individual in need 5 acceptable salt thereof. thereof, comprising administering to the individual a thera peutically effective amount of the compound of 11, or the pharmaceutically acceptable salt thereof. k . . . .