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(12) United States Patent (10) Patent No.: US 8,785.499 B2 Mackerell, Jr

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(12) United States Patent (10) Patent No.: US 8,785.499 B2 Mackerell, Jr US008785499B2 (12) United States Patent (10) Patent No.: US 8,785.499 B2 Mackerell, Jr. et al. (45) Date of Patent: Jul. 22, 2014 (54) TARGETING NAD BIOSYNTHESIS IN Medicinal Chemistry Letters 18, 2008, pp. 3932-3937, cited BACTERAL PATHOGENS in ISR. A. K. Halve et al. “N/C-4 substituted azetidin-2-ones: Synthesis and (75) Inventors: Alexander Mackerell, Jr., Baltimore, preliminary evaluation as new class of antimicrobial agents.” MD (US); Hong Zhang, Dallas, TX Bioorganic & Medicinal Chemistry Letters 17, 2007, pp. 341-345, (US); Andrei Osterman, San Diego, CA cited in IRS. P. V. Desai et al. “Identification of Novel Parasitic Cysteine Protease (US); Rohit Kolhatkar, Loves Park, IL Inhibitors. Using Virtual Screening. 1. The ChemBridge Datebase.” (US) Journal of Medicinal Chemistry 2004, No. 47, pp. 6609-6615, cited (73) Assignees: University of Maryland, Baltimore, in ISR. H.J. Yoon et al..."Crystal Structure of Nicotinic Acid Mononucleotide Baltimore, MD (US); The Board of Adenylyltransferase from Pseudomonas aeruginosa in its Apo and Regents of the University of Texas Substrate-complexed Forms Reveals a Fully Open Conformation.” System, Austin, TX (US); Journal of Medicinal Chemistry, 2005, No. 351, pp. 258-265. Sanford-Burnham Medical Research S. Lu et al. “Structure of nicotinic acid mononucleotide Institute, La Jolla, CA (US) adenylyltransferase from Bacillus anthracis,” Structural Biology and Crystalization Communications, 2008, No. 64, pp. 893-898. (*) Notice: Subject to any disclaimer, the term of this H. Zhang et al. "Crystal Structures of E. coli Nicotinate patent is extended or adjusted under 35 Mononucleotide Adenylyltransferase and its Complex with U.S.C. 154(b) by 228 days. Deamido-NAD.” Structure, Vo. 10, Jan. 2002, pp. 69-79. A. M. Olland et al. “Identification, Characterization, and Crystal (21) Appl. No.: 13/383,340 Structure of Bacillus subtilis Nicotinic Acid Mononucleotide Adenylyltransferase.” The Journal of Biological Chemistry, vol. 277. (22) PCT Filed: Jul. 12, 2010 No. 5, Feb. 1, 2002, pp. 3698-3707. S. Han et al. “Crystal Structure of Nicotinic Mononucleotide (86). PCT No.: PCT/US2O10/041708 Adenylyltransferase from Staphyloccocus aureus: Structural Basis S371 (c)(1), for NaAD Interaction in Functional Dimer,” Journal of Mol. Biol., 2006, No. 360, pp. 814-825. (2), (4) Date: Apr. 10, 2012 V. C. Sershon et al. "Kinetic and X-Ray Structural Evidence for Negative Cooperativity in Substrate Binding to Nicotinate (87) PCT Pub. No.: WO2011/006158 Mononucleotide Adenylyltransferase (NMAT) from Bacillus PCT Pub. Date: Jan. 13, 2011 anthracis,” Journal of Mol. Biol. 2009, No. 385, pp. 867-888. International Search Report of PCT/US2010/041708, date of mailing (65) Prior Publication Data Mar. 28, 2011. Written Opinion of PCT/US2010/041708, date of mailing Mar. 28, US 2012/O190708 A1 Jul. 26, 2012 2011. L. Sorcietal. “Targeting NAD Biosynthesis in Bacterial Pathogens: Related U.S. Application Data Structure-Based Development of Inhibitors of Nicotinate Mononucleotide Adenylyltransferase NadD.” Chemistry & Biology (60) Provisional application No. 61/224,504, filed on Jul. 16, Aug. 28, 2009, pp. 849-861. 10, 2009. L. Sorci et al. “Targeting Nad Biosynthesis in Bacterial Pathogens: Structure-Based Development of Inhibitors of Nicotinate (51) Int. Cl. Mononucleotide Adenylyltransferase NadD.” Chemistry & Biology A6 IK3I/65 (2006.01) 16, Aug. 28, 2009, Supplemental Data. (52) U.S. Cl. USPC ............................ 514/615: 514/614:564/151 * cited by examiner (58) Field of Classification Search USPC ................................... 564/151; 514/614, 615 Primary Examiner — Shailendra Kumar See application file for complete search history. (74) Attorney, Agent, or Firm — Westerman, Hattori, Daniels & Adrian, LLP (56) References Cited (57) ABSTRACT U.S. PATENT DOCUMENTS The emergence of multidrug-resistant pathogens necessitates 2007/0037752 A1* 2/2007 Ansorge et al. ................. 514/18 the search for new antibiotics acting on previously unex 2009/0312363 A1 12/2009 Bradner et al. plored targets. Nicotinate mononucleotide adenylyltrans ferase of the NadD family, an essential enzyme of NAD FOREIGN PATENT DOCUMENTS biosynthesis in most bacteria, was selected as a target for structure-based inhibitor development. To this end, the inven WO 2008091349 A1 T 2008 tors have identified small molecule compounds that inhibit bacterial target enzymes by interacting with a novel inhibi OTHER PUBLICATIONS tory binding site on the enzyme while having no effect on Sorcietal, Chemistry and Biology, 2009, 16(8), 849-861.* functionally equivalent human enzymes. J. Finn et al. “Identification of novel inhibitors of methionyl tRNA synthetase (MetRS) by virtual screening.” Bioorganic & 6 Claims, 18 Drawing Sheets U.S. Patent Jul. 22, 2014 Sheet 1 of 18 US 8,785.499 B2 Figure l Primary screen on as 1,000,000 in silico compound fibrary: top compounds were selected based on normalized vidWattractive energy Secondary screen (A) on top 20,000 cmpds against muttiple protein against multiple protein conformations from crystallography Conformations from MD siniations Top 500 cmpds from (A) and (B) were subjected to chemical clustering with finai : 29 (529) 40 12 active cmpds against both E. coli and B. anthracis Nadds were identified and 3 selected for further study inhibitor-bahladd crystal structures d U.S. Patent Jul. 22, 2014 Sheet 2 of 18 US 8,785.499 B2 Figure 2 8 M W WW W ------ W---- W--W--W W -W W WX MW W-8 W 25 - capa class 1 & A Cripd CiaSS. 3. OO - empch class 15 +- . WMXWWSM.888 & baMad D O 25 50 75 OO 25 50 75 200 eciad) U.S. Patent Jul. 22, 2014 Sheet 3 of 18 US 8,785.499 B2 . U.S. Patent Jul. 22, 2014 Sheet 4 of 18 US 8,785.499 B2 Figure 4 ecado inhibition 0.8 c; X. 0.8 ------, IC50 13 +/- 2 M 0.2 baNad) inhibition IC50 16+/- 4 M 0 1 2 3 4 50 SO, 0 80 SO M U.S. Patent Jul. 22, 2014 Sheet 5 of 18 US 8,785.499 B2 Figure 5 A E In 2.5 s one 5 are O O -- 30 a 60 3 - OO ce B E 100 O 9. 2. 50 e s -0.03 0.00 0.03 0.06 0.09 1/NaMN (uM") U.S. Patent Jul. 22, 2014 Sheet 6 of 18 US 8,785.499 B2 Figure 6 A / N 3. U.S. Patent Jul. 22, 2014 Sheet 7 of 18 US 8,785.499 B2 F.igure 7 U.S. Patent Jul. 22, 2014 Sheet 8 of 18 US 8,785.499 B2 Figure 8 U.S. Patent Jul. 22, 2014 Sheet 9 of 18 US 8,785.499 B2 Figure 9 U.S. Patent Jul. 22, 2014 Sheet 10 of 18 US 8,785.499 B2 Figure O U.S. Patent Jul. 22, 2014 Sheet 11 of 18 US 8,785.499 B2 Figure 11 A cir'sh O C B Ors 103 IC50=33M 105 ICsoX200 Mre, 9 t "r's C 04 ICso=25M Bror C. H O C 113 IC50=170M / or " BrorH 9 "10 f 101 IC50=O 4M C 115 IC50=122uM cr's 2 Cso as 25pily --S. Cl R H 111 IC50=30puM C lazy... Cso : 3-33ity. " O 0. baMadd d ecado 3. 8 8 9. S 4. 0. 82 , 8 s S8 8 2. 48 s 8 U.S. Patent Jul. 22, 2014 Sheet 12 of 18 US 8,785.499 B2 Figure 12 U.S. Patent Jul. 22, 2014 Sheet 13 of 18 US 8,785.499 B2 Figure 13 U.S. Patent Jul. 22, 2014 Sheet 14 of 18 US 8,785.499 B2 U.S. Patent Jul. 22, 2014 Sheet 15 of 18 US 8,785.499 B2 Figure 15 Scheme 1 HN NH ONN84- ),N-NH O o sea- S. O HN1 O O "C) C -y NH C CS-a 1. 1021 a) benzene-1,4-dicarbaldehyde, ethanol, reflux Figure 16 Scheme 2 A. O NH2 e-Na1O ames A. O : O-1 H.b oaR^- o 2 3 4. O o, O 2N ^n HN OH OH x X -N-1 " x .. "2 case O -- 0 O O O O "Cc C C "Cc 6 7 8 a) water. b) succinic anhydride, DMF, 70°C. c) HBTU, DIPEA, DMF. d) TFACHCl e) Ethanol, 1N NaOH. U.S. Patent Jul. 22, 2014 Sheet 16 of 18 US 8,785.499 B2 Figure 17 Scheme 3 OH HN N OH O2 oS-K)-ONN 4C - powers, " O o " -e-, O )- O HNO O "C N10 C NH a- (-y C 102.2 8 102.3 a) napthalene-l-carbaldehyde, ethanol, reflux. b)benzene-1,4-dicarbaldehyde, ethanol, reflux U.S. Patent Jul. 22, 2014 Sheet 17 of 18 US 8,785.499 B2 Figure 18 KS is as: S S is S S SS is 3S is sis iss: ississ $issa's U.S. Patent Jul. 22, 2014 Sheet 18 of 18 US 8,785.499 B2 Figure I s 3 & US 8,785,499 B2 1. 2 TARGETING NAD BOSYNTHESIS IN NadD converts NaMN, the first intermediate shared by the BACTERAL PATHOGENS most common de novo and Salvage/recycling routes, to nico tinic acid adenine dinucleotide (NaAD). Therefore, this STATEMENT REGARDING FEDERALLY enzyme should be indispensable in all bacterial species that SPONSORED RESEARCH ORDEVELOPMENT 5 utilize one or both of these routes for NAD biosynthesis. This is consistent with gene essentiality data for a number of This invention was made with the support of the U.S. bacterial species (as reviewed in 3, 16). For example, the government under Grant Number AI059146 from the nadD gene was shown to be essential for Survival in Staphy National Institute of Health (NIH). The U.S. government has lococcus aureus and Streptococcus pneumoniae that are fully certain rights in this invention.
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