Pharmacophore-based screening and identification of novel human ligase i inhibitors with potential anticancer activity

Journal of Chemical Information and Modeling

Volumn 54, Issue 3, 2014, Pages 781-792

  Krishna, Shagun ^a   Singh, Deependra Kumar ^a   Meena, Sanjeev ^a   Datta, Dipak ^a,b   Siddiqi, Mohammad Imran ^a,b   Banerjee, Dibyendu ^a,b  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

^b ACADEMY OF SCIENTIFIC AND INNOVATIVE RESEARCH ACSIR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; DISEASES; DNA; ENZYMES; PHARMACODYNAMICS;

ANTI-TUMOR ACTIVITIES; ANTICANCER ACTIVITIES; COLON CANCER CELLS; DNA REPLICATIONS; DOUBLE STRAND BREAKS; EXPRESSION LEVELS; OKAZAKI FRAGMENTS; SMALL-MOLECULE LIBRARY;

CELLS;

ANTINEOPLASTIC AGENT; DNA; DNA LIGASE (ATP); ENZYME INHIBITOR; OKAZAKI FRAGMENTS; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

ANTAGONISTS AND INHIBITORS; CELL PROLIFERATION; CHEMISTRY; DRUG DEVELOPMENT; DRUG EFFECTS; ENZYMOLOGY; HUMAN; METABOLISM; MOLECULAR DOCKING; NEOPLASMS; TUMOR CELL LINE;

ANTINEOPLASTIC AGENTS; CELL LINE, TUMOR; CELL PROLIFERATION; DNA; DNA LIGASES; DRUG DISCOVERY; ENZYME INHIBITORS; HUMANS; MOLECULAR DOCKING SIMULATION; NEOPLASMS;

EID: 84896914708     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci5000032     Document Type: Article

References (57)

1. Lehman, I. R. DNA ligase: Structure, mechanism, and function Science 1974, 186 (4166) 790-797
2. Chen, X.; Zhong, S.; Zhu, X.; Dziegielewska, B.; Ellenberger, T.; Wilson, G. M.; MacKerellJr, A. D.; Tomkinson, A. E. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair Cancer Res. 2008, 68 (9) 3169-3177
3. Srivastava, M.; Nambiar, M.; Sharma, S.; Karki, S. S.; Goldsmith, G.; Hegde, M.; Kumar, S.; Pandey, M.; Singh, R. K.; Ray, P.; Natarajan, R.; Kelkar, M.; De, A.; Choudhary, B.; Raghavan, S. C. An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression Cell 2012, 151 (7) 1474-1487
4. Singh, D. K.; Krishna, S.; Chandra, S.; Shameem, M.; Deshmukh, A. L.; Banerjee, D. Human DNA ligases: A comprehensive new look for cancer therapy Med. Res. Rev. 2013, 10.1002/med.21298
5. Wilkinson, A.; Day, J.; Bowater, R. Bacterial DNA ligases Mol. Microbiol. 2001, 40, 1241-12481
6. + specificity of bacterial DNA ligase revealed Structure 2004, 8, 1335-1336
7. Söderhäll, S.; Lindahl, T. Mammalian deoxyribonucleic acid ligase. Isolation of an active enzyme-adenylate complex J. Biol. Chem. 1973, 248 (2) 672-675
8. Söderhäll, S. Properties of a DNA-adenylate complex formed in the reaction between mammalian DNA ligase I and DNA containing single-strand breaks Eur. J. Biochem. 1975, 51 (1) 129-36
9. Barnes, D. E.; Johnston, L. H.; Kodama, K.; Tomkinson, A. E..; Lasko, D. D.; Lindahl, T. Human DNA ligase I cDNA: Cloning and functional expression in Saccharomyces cerevisiae Proc. Natl. Acad. Sci.U.S.A. 1990, 87 (17) 6679-83
10. Wei, Y. F.; Robins, P.; Carter, K.; Caldecott, K.; Pappin, D. J.; Yu, G. L.; Wang, R. P.; Shell, B. K.; Nash, R. A.; Schar, P. Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination Mol. Cell. Biol. 1995, 15 (6) 3206-3216
11. Robins, P.; Lindahl, T. DNA ligase IV from HeLa cell nuclei J. Biol. Chem. 1996, 271 (39) 24257-61
12. Ellenberger, T.; Tomkinson, A. E. Eukaryotic DNA ligases: Structural and functional insights Annu. Rev. Biochem. 2008, 77, 313-338
13. Teo, I. A.; Arlett, C. F.; Harcourt, S. A.; Priestley, A.; Broughton, B. C. Multiple hypersensitivity to mutagens in a cell strain (46BR) derived from a patient with immuno-deficiencies Mutat. Res. 1983, 107, 371-386
14. Moser, J.; Kool, H.; Giakzidis, I.; Caldecott, K.; Mullenders, L. H.; Fousteri, M. I. Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase III alpha in a cell-cycle-specific manner Mol. Cell 2007, 27 (2) 311-323
15. Prasad, R.; Singhal, R. K.; Srivastava, D. K.; Molina, J. T.; Tomkinson, A. E.; Wilson, S. H. Specific interaction of DNA polymerase 13 and DNA ligase I in a multiprotein base excision repair complex from bovine testis J. Biol. Chem. 1996, 271, 16000-16007
16. Robertson, A. B.; Klungland, A.; Rognes, T.; Leiros, I. DNA repair in mammalian cells: Base excision repair: the long and short of it Cell. Mol. Life Sci. 2009, 66 (6) 981-993
17. Dianov, G. L. Base excision repair targets for cancer therapy Am. J. Cancer Res. 2011, 1 (7) 845-851
18. Liang, L.; Deng, L.; Nguyen, S. C.; Zhao, X.; Maulion, C. D.; Shao, C.; Tischfield, J. A. Human DNA ligases I and III, but not ligase IV, are required for microhomology-mediated end joining of DNA double-strand breaks Nucleic Acids Res. 2008, 36 (10) 3297-3310
19. Kubota, Y.; Nash, R. A.; Klungland, A.; Schar, P.; Barnes, D. E.; Lindahl, T. Reconstitution of DNA base excision-repair with purified human proteins: Interaction between DNA polymerase beta and the XRCC1 protein EMBO J. 1996, 15, 6662-6670
20. Wilson, T. E.; Grawunder, U.; Lieber, M. R. Yeast DNA ligase IV mediates non-homologous DNA end joining Nature 1997, 388 (6641) 495-498
21. Grawunder, U.; Zimmer, D.; Fugmann, S.; Schwarz, K.; Lieber, M. R. DNA ligase IV is essential for V(D)J recombination and DNA double-strand break repair in human precursor lymphocytes Mol. Cell 1998, 2 (4) 477-84
22. Chrzanowska, K. H.; Gregorek, H.; Dembowska-Baginska, B.; Kalina, M. A.; Digweed, M. Nijmegen breakage syndrome (NBS) Orphanet J. Rare Dis. 2012, 7, 13
23. Teraoka, H.; Sawai, M.; Yamamoto, K.; Tsukada, K. DNA ligase I mRNA and enzyme levels in human hematopoietic cells under dimethyl sulfoxide-induced growth-arrest and differentiation Biochem. Int. 1992, 26 (5) 963-971
24. Jessberger, R.; Schar, P.; Robins, P.; Ferrari, E.; Riwar, B.; Hubscher, U. Regulation of DNA metabolic enzymes upon induction of preB cell development and V(D)J recombination: Up-regulation of DNA polymerase delta Nucleic Acids Res. 1997, 25 (2) 289-296
25. Sun, D.; Urrabaz, R.; Nguyen, M.; Marty, J.; Stringer, S.; Cruz, E.; Medina-Gundrum, L.; Weitman, S. Elevated expression of DNA ligase I in human cancers Clin. Cancer Res. 2001, 7 (12) 4143-4148
26. Bajorath, J. Integration of virtual and high throughput screening Nat. Rev. Drug Discovery 2002, 1, 882-894
27. Swann, S. L.; Brown, S. P.; Muchmore, S. W.; Patel, H.; Merta, P.; Locklear, J.; Philip, J.; Hajduk, P. J. A unified, probabilistic framework for structure- and ligand-based virtual screening J. Med. Chem. 2010, 54, 1223-1232
28. Zhong, S.; Chen, X.; Zhu, X.; Dziegielewska, B.; Bachman, K. E.; Ellenberger, T.; Ballin, J. D.; Wilson, G. M.; Tomkinson, A. E.; MacKerell, A. D., Jr. Identification and validation of human DNA ligase inhibitors using computer-aided drug design J. Med. Chem. 2008, 51 (15) 4553-4562
29. Sybyl, version 7.1; Tripos, Inc.: St. Louis, MO, 2005.
30. Gasteiger, J.; MarioMarsili, M. Iterative partial equalization of orbital electronegativity- a rapid access to atomic charges Tetrahedron 1980, 36, 3219-3228
31. Jones, G.; Willet, P. GASP: Genetic Algorithm Superimposition Program. In Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line: La Jolla, CA, 2000; pp 85-106.
32. Patel, Y.; Gillet, J. V.; Bravi, G.; Leach, R. A. A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP J. Comput.-Aided Mol. Des. 2002, 16 (8-9) 653-681
33. Olah, M.; Mracec, M.; Ostopovici, L.; Rad, R.; Bora, A.; Hadaruga, N.; Olah, I.; Banda, M.; Simon, Z.; Oprea, T. I. WOMBAT: World of molecular bioactivity Chemoinf. Drug Discovery 2004, 1, 223-239
34. Tomkinson, A. E.; Chen, X.; Dziegielewska, B.; Mackerell, A. D.; Zhong, S.; Gerald, M.; Wilson, G. M. Compounds That Inhibit Human DNA Ligases and Methods of Treating Cancer. U.S. Patent Application 12/576,410, filed October 9, 2009.
35. Sun, D.; Urrabaz, R. Development of non-electrophoretic assay method for DNA ligases and its application to screening of chemical inhibitors of DNA ligase I J. Biochem. Biophys. Methods 2004, 59 (1) 49-59
36. +-dependent DNA ligase is selectively inhibited by glycosylamines compared with human DNA ligase I Nucleic Acids Res. 2005, 33 (22) 7090-7101
37. Yang, W. S.; Huang, P.; Plunkett, W.; Becker, F. F.; Chan, Y. J. Dual mode of inhibition of purified DNA ligase I from human cells by 9-beta-D-arabinofuranosyl-2-fluoroadenine triphosphate J. Biol. Chem. 1992, 267 (4) 2345-2349
38. Montecucco, A.; Fontana, M.; Focher, F.; Lestingi, M.; Spadari, S.; Ciarrocchi, G. Specific inhibition of human DNA ligase adenylation by a distamycinderivative possessing antitumor activity Nucleic Acid Res. 1991, 19 (5) 1067-1072
39. Ciarrocchi, G.; Lestingi, M.; Fontana, M.; Spadari, S.; Montecucco, A. Correlation between anthracycline structure and human DNA ligase inhibition Biochem. J. 1991, 279, 141-146
40. Ciarrocchi, G.; MacPhee, G. D.; Deady, W. L.; Tilley, L. Specific inhibition of the eubacterial DNA ligase by arylamino compounds Antimicrob. Agents Chemother. 1999, 43 (11) 2766-2772
41. Kumar, A.; Siddiqi, M. I. Virtual screening against Mycobacterium tuberculosis dihydrofolate reductase: Suggested workflow for compound prioritization using structure interaction fingerprints J. Chem. Inf. Model. 2008, 27 (4) 476-488
42. Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line: La Jolla, CA, 2000; Vol. 2.
43. UNITY, Sybyl, version 7.1; Tripos, Inc.; St. Louis, MO, 2004.
44. Lipinski, C. A. Lead-and drug-like compounds: The rule-of-five revolution Drug Discovery Today: Technol. 2004, 1 (4) 337-341
45. Pascal, J. M.; OBrien, P. J.; Tomkinson, A. E.; Ellenberger, T. Human DNA ligase I completely encircles and partially unwinds nicked DNA Nature 2004, 25; 432 (7016) 473-478
46. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 1996, 261 (3) 470-489
47. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 2000, 33 (12) 889-897
48. Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A.PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 2000, 35, W522-5
49. Barakat, K. H.; Jordheim, L. P.; Perez-Pineiro, R.; Wishart, D.; Dumontet, C.; Tuszynski, J. A. Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction PloS One 2012, 7 (12) e51329
50. Wang, T.; Tomic, S.; Gabdoulline, R. R.; Wade, R. C. How optimal are the binding energetics of barnase and barstar? Biophys. J. 2004, 87 (3) 1618-1630
51. Pérez, C.; Pastor, M.; Ortiz, A. R.; Gago, F. Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design J. Med. Chem. 1998, 41 (6) 836-852
52. Chen, X.; Pascal, J.; Vijayakumar, S.; Wilson, G. M.; Ellenberger, T.; Tomkinson, A. E. Human DNA ligases I, III and IV-Purification and new specific assays for these enzymes Methods Enzymol. 2006, 409, 39-52
53. Brown, D. A.; Kharkar, P. S.; Parrington, I.; Maarten, R. EA; Dutta, A. K.. Structurally constrained hybrid derivatives containing octahydrobenzo [g or f] quinoline moieties for dopamine D2 and D3 receptors: Binding characterization at D2/D3 receptors and elucidation of a pharmacophore model J. Med. Chem. 2008, 51 (24) 7806-7819
54. Moitessier, N.; Henry, C.; Maigret, B.; Chapleur, Y. Combining pharmacophore search, automated docking, and molecular dynamics simulations as a novel strategy for flexible docking. Proof of concept: Docking of arginine-glycine-aspartic acid-like compounds into the vβ3 binding site J. Med. Chem. 2004, 47 (17) 4178-4187
55. Hurst, T. Flexible 3D searching: The directed tweak technique J. Chem. Inf. Comput. Sci. 1994, 34 (1) 190-196
56. Foyes Principles of Medicinal Chemistry; Lemke, T. L.; Williams, D. A., Eds.; Lippincott Williams & Wilkins: Philadelphia, PA, 2008.
57. Schneider, G.; Böhm, H. J. Virtual screening and fast automated docking methods Drug Discovery Today 2002, 7 (1) 64-70