The importance of hydration thermodynamics in fragment-to-lead optimization

ChemMedChem

Volumn 9, Issue 12, 2014, Pages 2708-2717

  Ichihara, Osamu ^a   Shimada, Yuzo ^a   Yoshidome, Daisuke ^a  

^a SCHRÖDINGER INC   (United States)

Author keywords

Druggability; Fragment based drug design; Hot spot; Hydrophobic effect; Protein hydration thermodynamics

Indexed keywords

WATER; CYCLIN DEPENDENT KINASE 2; LIGAND; PROTEIN KINASE B; SECRETASE;

ARTICLE; BINDING AFFINITY; BINDING SITE; ENTHALPY; ENTROPY; HYDRATION; LIGAND BINDING; PHYSICAL CHEMISTRY; REACTION OPTIMIZATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY; CHEMICAL PHENOMENA; CHEMISTRY; DRUG DESIGN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN TERTIARY STRUCTURE;

AMYLOID PRECURSOR PROTEIN SECRETASES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; CYCLIN-DEPENDENT KINASE 2; DRUG DESIGN; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-AKT; THERMODYNAMICS; WATER;

EID: 84915805158     PISSN: 18607179     EISSN: 18607187     Source Type: Journal    
DOI: 10.1002/cmdc.201402207     Document Type: Article

References (63)

1. M. Chaplin, Nat. Rev. Mol. Cell Biol. 2006, 7, 861-866.
2. G. M. Whitesides, P. Snyder, D. Moustakas, K. Mirica in Physical Biology: From Atoms to Medicine (Ed.: A. H. Zewail), Imperial College Press, London, 2008, pp. 189-216.
3. T. S. Olsson, M. A. Williams, W. R. Pitt, J. E. Ladbury, J. Mol. Biol. 2008, 384, 1002-1017.
4. G. M. Whitesides, V. M. Krishnamurthy, Q. Rev. Biophys. 2005, 38, 385-395
5. D. Chandler, Nature 2005, 437, 640-647
6. N. T. Southall, K. A. Dill, A. Haymet, J. Phys. Chem. B 2002, 106, 521-533
7. P. L. Privalov, S. J. Gill, Adv. Protein Chem. 1988, 39, 191-234
8. B. Breiten, M. R. Lockett, W. Sherman, S. Fujita, M. Al-Sayah, H. Lange, C. M. Bowers, A. Heroux, G. Krilov, G. M. Whitesides, J. Am. Chem. Soc. 2013, 135, 15579-15584
9. P. W. Snyder, J. Mecinovic, D. T. Moustakas, S. W. Thomas III, M. Harder, E. T. Mack, M. R. Lockett, A. Heroux, W. Sherman, G. M. Whitesides, Proc. Natl. Acad. Sci. USA 2011, 108, 17889-17894
10. M. R. Lockett, H. Lange, B. Breiten, A. Heroux, W. Sherman, D. Rappoport, P. O. Yau, P. W. Snyder, G. M. Whitesides, Angew. Chem. Int. Ed. 2013, 52, 7714-7717
11. Angew. Chem. 2013, 125, 7868-7871.
12. J. Michel, J. Tirado-Rives, W. L. Jorgensen, J. Am. Chem. Soc. 2009, 131, 15403-15411.
13. T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga, Proc. Natl. Acad. Sci. USA 1987, 84, 3086-3090
14. M. K. Gilson, K. A. Sharp, B. H. Honig, J. Comput. Chem. 1988, 9, 327-335.
15. M. Wojciechowski, B. Lesyng, J. Phys. Chem. B 2004, 108, 18368-18376.
16. B. Kuhn, P. A. Kollman, J. Med. Chem. 2000, 43, 3786-3791.
17. M. Sgobba, F. Caporuscio, A. Anighoro, C. Portioli, G. Rastelli, Eur. J. Med. Chem. 2012, 58, 431-440
18. T. Hou, J. Wang, Y. Li, W. Wang, J. Comput. Chem. 2011, 32, 866.
19. K. A. Sharp, A. Nicholls, R. F. Fine, B. Honig, Science 1991, 252, 106-109.
20. C. R. Guimaries, A. M. Mathiowetz, J. Chem. Inf. Model. 2010, 50, 547-559.
21. H. Yu, S. W. Rick, J. Am. Chem. Soc. 2009, 131, 6608-6613.
22. T. Young, R. Abel, B. Kim, B. J. Berne, R. A. Friesner, Proc. Natl. Acad. Sci. USA 2007, 104, 808-813
23. R. Abel, T. Young, R. Farid, B. J. Berne, R. A. Friesner, J. Am. Chem. Soc. 2008, 130, 2817-2831.
24. L. Wang, Y. Deng, J. L. Knight, Y. Wu, B. Kim, W. Sherman, J. C. Shelley, T. Lin, R. Abel, J. Chem. Theory Comput. 2013, 9, 1282-1293.
25. Y. Yang, F. C. Lightstone, S. E. Wong, Expert Opin. Drug Discovery 2013, 1-11.
26. L. Wang, B. Berne, R. Friesner, Proc. Natl. Acad. Sci. USA 2011, 108, 1326-1330.
27. R. M. A. Knegtel, D. D. Robinson, Mol. Inf. 2011, 30, 950-959
28. F. Shah, J. Gut, J. Legac, D. Shivakumar, W. Sherman, P. J. Rosenthal, M. A. Avery, J. Chem. Inf. Model. 2012, 52, 696-710
29. T. Beuming, Y. Che, R. Abel, B. Kim, V. Shanmugasundaram, W. Sherman, Proteins 2012, 80, 871-883.
30. T. Lazaridis, J. Phys. Chem. B 1998, 102, 3531-3541.
31. D. D. Robinson, W. Sherman, R. Farid, ChemMedChem 2010, 5, 618-627
32. C. Higgs, T. Beuming, W. Sherman, ACS Med. Chem. Lett. 2010, 1, 160-164.
33. M. Congreve, G. Chessari, D. Tisi, A. J. Woodhead, J. Med. Chem. 2008, 51, 3661-3680
34. C. W. Murray, M. L. Verdonk, D. C. Rees, Trends Pharmacol. Sci. 2012, 33, 224-232.
35. G. G. Ferenczy, G. M. Keseru, J. Chem. Inf. Model. 2012, 52, 1039-1045.
36. N. Amin, E. Chiarparin, J. Coyle, G. Williams, FRAGMENTS III-Third RSC-BMSC Fragment-Based Drug Discovery Meeting, Stevenage (UK), 2011.
37. M. Orita, K. Ohno, M. Warizaya, Y. Amano, T. Niimi, Methods Enzymol. 2011, 493, 383-419.
38. A. G. Coyne, D. E. Scott, C. Abell, Curr. Opin. Chem. Biol. 2010, 14, 299-307.
39. C. W. Murray, T. L. Blundell, Curr. Opin. Struct. Biol. 2010, 20, 497-507.
40. F. C. Bernstein, T. F. Koetzle, G. J. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi, Eur. J. Biochem. 1977, 80, 319-324.
41. G. M. Sastry, M. Adzhigirey, T. Day, R. Annabhimoju, W. Sherman, J. Comput.-Aided Mol. Des. 2013, 27, 221-234.
42. W. L. Jorgensen, J. D. Madura, Mol. Phys. 1985, 56, 1381-1392.
43. G. G. Ferenczy, G. M. Keseru, J. Med. Chem. 2013, 56, 2478-2486.
44. V. M. Krishnamurthy, B. R. Bohall, V. Semetey, G. M. Whitesides, J. Am. Chem. Soc. 2006, 128, 5802
45. R. Talhout, A. Villa, A. E. Mark, J. B. Engberts, J. Am. Chem. Soc. 2003, 125, 10570-10579
46. A. T. Fenley, H. S. Muddana, M. K. Gilson, Proc. Natl. Acad. Sci. USA 2012, 109, 20006-20011
47. C. H. Reynolds, M. K. Holloway, ACS Med. Chem. Lett. 2011, 2, 433-437
48. C. Bissantz, B. Kuhn, M. Stahl, J. Med. Chem. 2010, 53, 5061-5084.
49. P. Setny, R. Baron, J. A. McCammon, J. Chem. Theory Comput. 2010, 6, 2866-2871
50. R. Baron, P. Setny, J. A. McCammon, J. Am. Chem. Soc. 2010, 132, 12091-12097.
51. P. J. Hajduk, J. R. Huth, S. W. Fesik, J. Med. Chem. 2005, 48, 2518-2525.
52. E. Leipinsh, G. Otting, Nat. Biotechnol. 1997, 15, 264-268
53. C. Mattos, C. R. Bellamacina, E. Peisach, A. Pereira, D. Vitkup, G. A. Petsko, D. Ringe, J. Mol. Biol. 2006, 357, 1471-1482.
54. R. Brenke, D. Kozakov, G. Y. Chuang, D. Beglov, D. Hall, M. R. Landon, C. Mattos, S. Vajda, Bioinformatics 2009, 25, 621-627
55. M. R. Landon, D. R. Lancia, J. Yu, S. C. Thiel, S. Vajda, J. Med. Chem. 2007, 50, 1231-1240
56. K. W. Lexa, H. A. Carlson, J. Am. Chem. Soc. 2011, 133, 200-202
57. A. Bakan, N. Nevins, A. S. Lakdawala, I. Bahar, J. Chem. Theory Comput. 2012, 8, 2435-2447
58. O. Guvench, A. D. MacKerell, Jr., PLoS Comput. Biol. 2009, 5, e1000435.
59. F. N. Edfeldt, R. H. Folmer, A. L. Breeze, Drug Discovery Today 2011, 16, 284-287.
60. A. C. Cheng, R. G. Coleman, K. T. Smyth, Q. Cao, P. Soulard, D. R. Caffrey, A. C. Salzberg, E. S. Huang, Nat. Biotechnol. 2007, 25, 71-75.
61. M. K. Haider, H. O. Bertrand, R. E. Hubbard, J. Chem. Inf. Model. 2011, 51, 1092-1105.
62. J. L. Kulp III, J. L. Kulp, Jr., D. L. Pompliano, F. Guarnieri, J. Am. Chem. Soc. 2011, 133, 10740-10743.
63. Y. Alexeev, M. P. Mazanetz, O. Ichihara, D. G. Fedorov, Curr. Top. Med. Chem. 2012, 12, 2013-2033.