(19) & (11) EP 2 494 993 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 05.09.2012 Bulletin 2012/36 A61K 48/00 (2006.01) A61K 47/06 (2006.01) A61K 9/127 (2006.01) C12N 15/88 (2006.01) (2006.01) (2006.01) (21) Application number: 12158867.7 C07C 279/14 C07D 213/40 C07D 233/26 (2006.01) C12N 15/11 (2006.01) (22) Date of filing: 02.05.2008 (84) Designated Contracting States: • Houston, Michael AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Sammamish, WA Washington 98074 (US) HR HU IE IS IT LI LT LU LV MC MT NL NO PL PT • Harvie, Pierrot RO SE SI SK TR Bothell, WA Washington 98011 (US) Designated Extension States: • Adami, Roger AL BA MK RS Bothell, WA Washington 98012 (US) • Fam, Renata (30) Priority: 04.05.2007 US 916131 P Kenmore, WA Washington 98028 (US) 29.06.2007 US 947282 P • Prieve, Mary 02.08.2007 US 953667 P Lake Forest Park, WA Washington 98155 (US) 14.09.2007 US 972590 P • Fosnaugh, Kathy 14.09.2007 US 972653 P Bellevue, WA Washington 98008 (US) 22.01.2008 US 22571 P • Seth, Shaguna Bothell, WA Washington 98012 (US) (62) Document number(s) of the earlier application(s) in accordance with Art. 76 EPC: (74) Representative: Srinivasan, Ravi Chandran 08747568.7 / 2 157 982 J A Kemp 14 South Square (71) Applicant: Marina Biotech, Inc. Gray’s Inn Bothell, WA 98021-7266 (US) London WC1R 5JJ (GB) (72) Inventors: Remarks: • Quay, Steven This application was filed on 09-03-2012 as a Woodinville, WA Washington 98072 (US) divisional application to the application mentioned under INID code 62. (54) Amino acid lipids and uses thereof (57) The present invention provides a compound comprising the structure shown in Formula I for use in delivering a therapeutic nucleic acid, one or more drug agents, or a biologically active agent to a cell, R3-(C=O)-Xaa-Z-R4 Formula I wherein Xaa is histidine, 1-methylhistidine, pyridylalanine, lysine, arginine, homoarginine, nor- norarginine, ornithine, homolysine, asparagine, N ethylasparagine, glutamine, 4- aminophenylalanine, and nor-arginine, or an N- methylated version thereof; R3 is independently a lipophilic tail derived from a naturally- occurring or synthetic lipid, phospholipid, glycolipid, triacylg- lycerol, glycerophospholipid, sphingolipid, ceramide, sphingomyelin, cerebroside, or ganglioside, wherein the tail may contain a steroid; or a substituted or unsubstituted C(3-22)alkyl, C(6-12)cycloalkyl, C(6-12)cycloalkyl-C(3-22)alkyl, C (3-22)alkenyl, C(3-22)alkynyl, C(3-22)alkoxy, or C(6-12)alkoxy-C(3-22)alkyl; R4 is independently a lipophilic tail derived from a naturally- occurring or synthetic lipid, phospholipid, glycolipid, triacylg- lycerol, glycerophospholipid, sphingolipid, ceramide, sphingomyelin, cerebroside, or ganglioside, wherein the tail may contain a steroid; or a substituted or unsubstituted C(3-22)alkyl, C(6-12)cycloalkyl, C(6-12)cycloalkyl-C(3-22)alkyl, C (3-22)alkenyl, C(3-22)alkynyl, C(3-22)alkoxy, or C(6-12)alkoxy-C(3-22)alkyl; wherein both R3 and R4 are lipophilic tails; and Z is NH, O, S, -CH 2S-, -CH2S(O)-, or an organic linker consisting of 1-40 atoms selected from hydrogen, carbon, oxygen, nitrogen, and sulfur atoms; EP 2 494 993 A2 Printed by Jouve, 75001 PARIS (FR) (Cont. next page) EP 2 494 993 A2 and salts thereof. 2 EP 2 494 993 A2 Description FIELD OF THE INVENTION 5 [0001] This invention relates to novel drug delivery enhancing agents including lipids that are useful for delivering various molecules to cells. This invention provides a range of compounds, compositions, formulations, methods and uses of such agents directed ultimately toward drug delivery, therapeutics, and the diagnosis and treatment of diseases and conditions, including those that respond to modulation of gene expression or activity in a subject. More specifically, this invention relates to compounds, liposomes, lamellar vesicles, emulsions, micelles, suspensions, particles, solutions 10 and other forms of delivery enhancing compositions and formulations, as well as therapeutic methods and uses for these delivery materials. BACKGROUND 15 [0002] The delivery of a therapeutic compound to a subject can be impeded by limited ability of the compound to reach a target cell or tissue, or by restricted entry or trafficking of the compound within cells. Delivery of a therapeutic material is in general restricted by membranes of cells. These barriers and restrictions to delivery can result in the need to use much higher concentrations of a compound than is desirable to achieve a result, which brings the risk of toxic effects and side effects. 20 [0003] One strategy for delivery is to improve transport of a compound into cells using lipid or polymeric carrier molecules. These materials can take advantage of mechanisms that exist for selective entry into a cell, while still excluding exogenous molecules such as nucleic acids and proteins. For example, a cationic lipid may interact with a drug agent and provide contact with a cell membrane. Lipid molecules can also be organized into liposomes or particles as carriers for drug agents. Liposomal drug carriers can protect a drug molecule from degradation while improving its uptake by 25 cells. Also, liposomal drug carriers can encapsulate or bind certain compounds by electrostatic and other interactions, and may interact with negatively charged cell membranes to initiate transport across a membrane. [0004] The understanding of regulatory RNA and the development of RNA interference (RNAi), RNAi therapy, RNA drugs, antisense therapy, and gene therapy, among others, has increased the need for effective means of introducing active nucleic acid agents into cells. In general, nucleic acids are stable for only limited times in cells or plasma. However, 30 nucleic acid-based agents can be stabilized in compositions and formulations which may then be dispersed for cellular delivery. [0005] This disclosure provides compounds, compositions, methods and uses for improving systemic and local delivery of drugs and biologically active molecules. Among other things, this application provides novel compounds and compo- sitions for making and using delivery structures and carriers which increase the efficiency of delivery of biologically active 35 molecules. BRIEF SUMMARY [0006] This disclosure provides novel compounds, compositions and formulations for intracellular and in vivo delivery 40 of drug agents for use, ultimately, as a therapeutic. The compounds and compositions of this disclosure are useful for delivery of drug agents to selected cells, tissues, organs or compartments in order to alter a disease state or a phenotype. [0007] In some aspects, this disclosure provides compounds, compositions and methods to deliver RNA structures to cells to produce the response of RNA interference, antisense effects, or the regulation of genomic expression. [0008] This invention provides a range of amino acid lipids which are lipophilic compounds for use in delivery and 45 administration of drug agents and in drug delivery systems. The amino acid lipids of this disclosure are molecules containing an amino acid residue and one or more lipophilic tails. [0009] In some aspects, this invention provides a range of amino acid lipid compounds as shown in Formula I: R3-(C=O)-Xaa-Z-R4 Formula I 50 wherein Xaa is any D- or L-amino acid residue having the formula -NRN-CR1R2-(C=O)-, or a peptide of n = 2-20 amino acid residues having the formula - N 1 2 {NR -CR R -(C=O)}n-, wherein 55 R1 is independently, for each occurrence, a non-hydrogen, substituted or unsubstituted side chain of an amino acid; R2 is independently, for each occurrence, hydrogen, or an organic group consisting of carbon, oxygen, nitrogen, sulfur, and hydrogen atoms, and having from 1 to 20 carbon atoms, or C (1-5)alkyl, cycloalkyl, cycloalkylalkyl, C(3-5)alkenyl, C (3-5)alkynyl, C(1-5)alkanoyl, C(1-5)alkanoyloxy, C(1-5)alkoxy, C(1-5)alkoxy-C(1-5)alkyl, C(1-5)alkoxy-C(1-5)alkoxy, C 3 EP 2 494 993 A2 (1-5)alkyl-amino-C(1-5)alkyl-, C(1-5)dialkyl-amino-C(1-5)alkyl-, nitro-C(1-5)alkyl, cyano-C(1-5)alkyl, aryl-C(1-5)alkyl, 4- biphenyl-C(1-5)alkyl, carboxyl, or hydroxyl, RN is independently, for each occurrence, hydrogen, or an organic group consisting of carbon, oxygen, nitrogen, sulfur, and hydrogen atoms, and having from 1 to 20 carbon atoms, or C (1-5)alkyl, cycloalkyl, cycloalkylalkyl, C(3-5)alkenyl, C 5 (3-5)alkynyl, C(1-5)alkanoyl, C(1-5)alkanoyloxy, C(1-5)alkoxy, C(1-5)alkoxy-C(1-5)alkyl, C(1-5)alkoxy-C(1-5)alkoxy, C (1-5)alkyl-amino-C(1-5)alkyl-, C(1-5)dialkyl-amino-C(1-5)alkyl-, nitro-C(1-5)alkyl, cyano-C(1-5)alkyl, aryl-C(1-5)alkyl, 4- biphenyl-C(1-5)alkyl, carboxyl, or hydroxyl, R3 is independently a lipophilic tail derived from a naturally- occurring or synthetic lipid, phospholipid, glycolipid, triacylg- lycerol, glycerophospholipid, sphingolipid, ceramide, sphingomyelin, cerebroside, or ganglioside, wherein the tail may 10 contain a steroid; or a substituted or unsubstituted C(3-22)alkyl, C(6-12)cycloalkyl, C(6-12)cycloalkyl-C(3-22)alkyl, C (3-22)alkenyl, C(3-22)alkynyl, C(3-22)alkoxy, or C(6-12)alkoxy-C(3-22)alkyl; R4 is independently a lipophilic tail derived from a naturally- occurring or synthetic lipid, phospholipid, glycolipid, triacylg- lycerol, glycerophospholipid, sphingolipid, ceramide, sphingomyelin, cerebroside, or ganglioside, wherein the tail may contain a steroid; or a substituted or unsubstituted C(3-22)alkyl, C(6-12)cycloalkyl, C(6-12)cycloalkyl-C(3-22)alkyl, C 15 (3-22)alkenyl, C(3-22)alkynyl, C(3-22)alkoxy, or C(6-12)alkoxy-C(3-22)alkyl; wherein either one of R3 and R4 is a lipophilic tail as defined above and the other is an amino acid terminal group, or both R 3 and R 4 are lipophilic tails; the amino acid terminal group being hydrogen, hydroxyl, amino, or an organic protective group; Z is NH, O, S, -CH 2S-, -CH2S(O)-, or an organic linker consisting of 1-40 atoms selected from hydrogen, carbon, oxygen, 20 nitrogen, and sulfur atoms; and salts thereof.