Predicting fragment binding poses using a combined MCSS MM-GBSA approach

Journal of Chemical Information and Modeling

Volumn 51, Issue 5, 2011, Pages 1092-1105

  Haider, Muhammad K ^a   Bertrand, Hugues Olivier ^b   Hubbard, Roderick E ^a,c  

^a UNIVERSITY OF YORK   (United Kingdom)

^b Accelrys   (France)

^c Vernalis PLC   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; CRYSTAL STRUCTURE; FORECASTING; LIGANDS; MOLECULAR ORIENTATION; MOLECULES;

CHEMICAL OPTIMIZATIONS; HIGH-RESOLUTION STRUCTURES; IMPLICIT SOLVENTS; LOW MOLECULAR WEIGHT COMPOUNDS; MULTIPLE RECEPTORS; MULTIPLE STRUCTURES; POSITION AND ORIENTATIONS; STRUCTURE ACTIVITY RELATIONSHIPS;

BINDING ENERGY;

CELL SURFACE RECEPTOR; HEAT SHOCK PROTEIN 90; LIGAND; PROTEIN BINDING;

ALGORITHM; BINDING SITE; CHEMISTRY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; STRUCTURE ACTIVITY RELATION; SURFACE PROPERTY; THERMODYNAMICS; ARTICLE; PROTEIN BINDING;

ALGORITHMS; BINDING SITES; HSP90 HEAT-SHOCK PROTEINS; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; RECEPTORS, CELL SURFACE; STRUCTURE-ACTIVITY RELATIONSHIP; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 79960244405     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100469n     Document Type: Article

References (59)

1. Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent developments in fragment-based drug discovery. J. Med. Chem. 2008, 51, 3661-3680. (Pubitemid 351956496)
2. Erlanson, D. A.; McDowell, R. S.; O'Brien, T. Fragment-based drug discovery. J. Med. Chem. 2004, 47, 3463-3482. (Pubitemid 38822007)
3. Fischer, M.; Hubbard, R. E. Fragment-based ligand discovery. Mol. Interventions 2009, 9, 22-30.
4. Zartler, E. R.; Shapiro, M. J. Fragonomics: fragment-based drug discovery. Curr. Opin. Chem. Biol. 2005, 9, 366-370. (Pubitemid 41019682)
5. de Kloe, G. E.; Bailey, D.; Leurs, R.; deEsch, I.J. P. Transforming fragments into candidates: small becomes big in medicinal chemistry. Drug Discovery Today 2009, 14 630-646.
6. Hajduk, P. J.; Greer, J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discovery 2007, 6 211-219. (Pubitemid 46344625)
7. Goodford, P. J. A Computational-Procedure For Determining Energetically Favorable Binding-Sites On Biologically Important Macro-molecules. J. Med. Chem. 1985, 28, 849-857. (Pubitemid 15012490)
8. Miranker, A.; Karplus, M. Functionality Maps Of Binding-Sites - A Multiple Copy Simultaneous Search Method. Proteins: Struct. Funct. Genet. 1991, 11 29-34.
9. Caflisch, A.; Miranker, A.; Karplus, M. Multiple copy simultaneous search and construction of ligands in binding sites - application to inhibitors of HIV-1 aspartic proteinase. J. Med. Chem. 1993, 36 2142-2167. (Pubitemid 23241149)
10. Eisen, M. B.; Wiley, D. C.; Karplus, M.; Hubbard, R. E. HOOK: A Program for Finding Novel Molecular Architectures That Satisfy the Chemical and Steric Requirements of a Macromolecule Binding Site. Proteins: Struct. Funct. Genet. 1994, 19 199-221. (Pubitemid 24215048)
11. Caflisch, A. Computational combinatorial ligand design: Application to human alpha-thrombin. J. Comput.-Aided Mol. Des. 1996, 10 372-396. (Pubitemid 126712436)
12. Joseph-McCarthy, D.; Hogle, J. M.; Karplus, M. Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. Proteins: Struct. Funct. Bioinf. 1997, 29, 32-58. (Pubitemid 27377417)
13. Evensen, E.; Joseph-McCarthy, D.; Weiss, G.; Schreiber, S.; Karplus, M. Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. J. Comput.-Aided Mol. Des. 2007, 21 395-418. (Pubitemid 47193849)
14. Cross, S.; Cruciani, G. Molecular fields in drug discovery: getting old or reaching maturity?. Drug Discovery Today 2010, 15, 23-32.
15. Schubert, C. R.; Stultz, C. M. The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design. J. Comput.-Aided Mol. Des. 2009, 23, 475-489.
16. Allen, K. N.; Bellamacina, C. R.; Ding, X. C.; Jeffery, C. J.; Mattos, C.; Petsko, G. A.; Rnge, D. An experimental approach to mapping the binding surfaces of crystalline proteins. J. Phys. Chem. 1996, 100, 2605-2611. (Pubitemid 126793213)
17. Mattos, C.; Ringe, D. Locating and characterizing binding sites on proteins. Nat. Biotechnol. 1996, 14 595-599. (Pubitemid 26135122)
18. Joseph-McCarthy, D.; Fedorov, A. A.; Almo, S. C. Comparison of experimental and computational functional group mapping of an RNase A structure: Implications for computer-aided drug design. Protein Eng. 1996, 9, 773-780. (Pubitemid 26308525)
19. English, A. C.; Groom, C. R.; Hubbard, R. E. Experimental and computational mapping of the binding surface of a crystalline protein. Protein Eng. 2001, 14 47-59. (Pubitemid 32318937)
20. Silberstein, M.; Dennis, S.; Brown, L.; Kortvelyesi, T.; Clodfelter, K.; Vajda, S. Identification of substrate binding sites in enzymes by computational solvent mapping. J. Mol. Biol. 2003, 332, 1095-1113. (Pubitemid 37108802)
21. Majeux, N.; Scarsi, M.; Apostolakis, J.; Ehrhardt, C.; Caflisch, A. Exhaustive docking of molecular fragments with electrostatic solvation. Proteins: Struct Funct. Genet. 1999, 37 88-105. (Pubitemid 29408922)
22. Brenke, R.; Kozakov, D.; Chuang, G. Y.; Beglov, D.; Hall, D.; Landon, M. R.; Mattos, C.; Vajda, S. Fragment-based identification of druggable hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009, 25, 621-627.
23. Imai, T.; Oda, K.; Kovalenko, A.; Hirata, F.; Kidera, A. Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design. J. Am. Chem. Soc. 2009, 131 12430-12440.
24. Feig, M.; Brooks, C. L. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 2004, 14 217-224. (Pubitemid 38495800)
25. Guimaraes, C. R. W.; Cardozo, M. MM-GB/SA rescoring of docking poses in structure-based lead optimization. J. Chem. Inf. Model 2008, 48, 958-970.
26. Massova, I.; Kollman, P. A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect. Drug Discovery Des. 2000, 18 113-135. (Pubitemid 30191024)
27. Michel, J.; Verdonk, M. L.; Essex, J. W. Protein-ligand binding affinity predictions by implicit solvent simulations: A tool for lead optimization?. J. Med. Chem. 2006, 49, 7427-7439. (Pubitemid 44913402)
28. Thompson, D. C.; Humblet, C.; Joseph-McCarthy, D. Investigation of MM-PBSA rescoring of docking poses. J. Chem. Inf. Model 2008, 48, 1081-1091.
29. Onufriev, A. Continuum Electrostatics Solvent Modeling with the Generalized Born Model. In Modeling Solvent Environments Applications to Simulations of Biomolecules; Feig, M., Ed.; WILEY-VCH Verlag GmbH & Co. KGaA: Weinheim, 2010; pp 127 - 165.
30. Jones, G.; Willett, P.; Glen, R, C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748. (Pubitemid 27170693)
31. Berman, H. M.; Bhat, T. N.; Bourne, P. E.; Feng, Z. K.; Gilliland, G.; Weissig, H.; Westbrook, J. The Protein Data Bank and the challenge of structural genomics. Nat. Struct. Biol. 2000, 7, 957-959.
32. Discovery Studio, 2.5; Accelrys: San Diego, CA, 2009.
33. Rone, R.; Momany, F. A.; Dygert, M. Conformational studies on vancomycin using QUANTA-CHARMM. Smith, J. a., Rivier, J. E.; Eds.; 1992; pp 299-301.
34. Warnmark, A.; Treuter, E.; Gustafsson, J. A.; Hubbard, R. E.; Brzozowski, A. M.; Pike, A. C. W. Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. J. Biol. Chem. 2002, 277, 21862-21868. (Pubitemid 34959959)
35. Kallander, L. S.; Lu, Q.; Chen, W. F.; Tomaszek, T.; Yang, G.; Tew, D.; Meek, T. D.; Hofmann, G. A.; Schulz-Pritchard, C. K.; Smith, W. W.; Janson, C. A.; Ryan, M. D.; Zhang, G. F.; Johanson, K. O.; Kirkpatrick, R. B.; Ho, T. F.; Fisher, P. W.; Mattern, M. R.; Johnson, R. K.; Hansbury, M. J.; Winkler, J. D.; Ward, K. W.; Veber, D. F.; Thompson, S. K. 4-Aryl-1,2,3-triazole: A novel template for a reversible methionine aminopeptidase 2 inhibitor, optimized to inhibit angiogenesis in vivo. J. Med. Chem. 2005, 48, 5644-5647. (Pubitemid 41298336)
36. Halgren, T. A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94.J. Comput. Chem. 1996, 17 490-519. (Pubitemid 126567067)
37. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program. J. Comput. Chem. 2009, 30 1545-1614.
38. Feig, M.; Chocholousova, J.; Tanizaki, S. Simulating nucleic acids: Towards implicit and hybrid solvation models. Biophys. J. 2005, 88 513A-513A.
39. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr; Brooks Iii, C. L. New analytical approximation to the standard molecular volume definition and its application to generalized Born calculations. J. Comput. Chem. 2003, 24, 1348-1356.
40. Sitkoff, D.; Sharp, K. A.; Honig, B. Correlating solvation free energies and surface tensions of hydrocarbon solutes. Biophys. Chem. 1994, 51, 397-409. (Pubitemid 24244015)
41. Huth, J. R.; Park, C.; Petros, A. M.; Kunzer, A. R.; Wendt, M. D.; Wang, X. L.; Lynch, C. L.; Mack, J. C.; Swift, K. M.; Judge, R. A.; Chen, J.; Richardson, P. L.; Jin, S.; Tahir, S. K.; Matayoshi, E. D.; Dorwin, S. A.; Ladror, U. S.; Severin, J. M.; Walter, K. A.; Bartley, D. M.; Fesik, S. W.; Elmore, S. W.; Hajduk, P. J. Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies. Chem. Biol. Drug Des. 2007, 70 1-12. (Pubitemid 47057425)
42. Solit, D. B.; Chiosis, G. Development and application of Hsp90 inhibitors. Drug Discovery Today 2008, 13 38-43.
43. Richter, K.; Buchner, J. hsp90: Twist and Fold. Cell 2006, 127 251-253. (Pubitemid 44572385)
44. Cozzini, P.; Kellogg, G. E.; Spyrakis, F.; Abraham, D. J.; Costantino, G.; Emerson, A.; Fanelli, F.; Gohlke, H.; Kuhn, L. A.; Morris, G. M.; Orozco, M.; Pertinhez, T. A.; Rizzi, M.; Sotriffer, C. A. Target Flexibility: An Emerging Consideration in Drug Discovery and Design. J. Med. Chem. 2008, 51, 6237-6255.
45. Kung, P. P.; Funk, L.; Meng, J.; Collins, M.; Zhou, J. Z. X.; Johnson, M. C.; Ekker, A.; Wang, J.; Mehta, P.; Yin, M. J.; Rodgers, C.; Davies, J. F.; Bayman, E.; Smeal, T.; Maegley, K. A.; Gehring, M. R. Dihydroxylphenyl amides as inhibitors of the Hsp90 molecular chaper-one. Bioorg. Med. Chem. Lett. 2008, 18 6273-6278.
46. Selinsky, B. S.; Gupta, K.; Sharkey, C. T.; Loll, P. J. Structural analysis of NSAID binding by prostaglandin H-2 synthase: Time-dependent and time-independent inhibitors elicit identical enzyme conformations. Biochemistry 2001, 40 5172-5180. (Pubitemid 32373999)
47. Hajduk, P. J.; Boyd, S.; Nettesheim, D.; Nienaber, V.; Severin, J.; Smith, R.; Davidson, D.; Rockway, T.; Fesik, S. W. Identification of novel inhibitors of urokinase via NMR-based screening. J. Med. Chem. 2000, 43, 3862-3866.
48. Rasmussen, H. B.; Branner, S.; Wiberg, F. C.; Wagtmann, N. Crystal structure of human dipeptidyl peptidase IV/CD26 in complex with a substrate analog. Nat. Struct. Biol. 2003, 10 19-25. (Pubitemid 36034172)
49. Fedorov, R.; Hartmann, E.; Ghosh, D. K.; Schlichting, I. Structural basis for the specificity of the nitric-oxide synthase inhibitors W1400 and N-omega-propyl-L-Arg for the inducible and neuronal isoforms. J. Biol. Chem. 2003, 278, 45818-45825. (Pubitemid 37432727)
50. Meyer, E. A.; Furler, M.; Diederich, F.; Brenk, R.; Klebe, G. Synthesis and In Vitro Evaluation of 2-Aminoquinazolin-4(3H)-one-Based Inhibitors for tRNA-Guanine Transglycosylase (TGT). Helv. Chim. Acta 2004, 87 1333-1356. (Pubitemid 38924109)
51. Hartshorn, M. J.; Murray, C. W.; Cleasby, A.; Frederickson, M.; Tickle, I. J.; Jhoti, H. Fragment-based lead discovery using X-ray crystallography. J. Med. Chem. 2005, 48, 403-413. (Pubitemid 40139783)
52. Wu, Q.; Gee, C. L.; Lin, F.; Tyndall, J. D.; Martin, J. L.; Grunewald, G. L.; McLeish, M. J. Structural, mutagenic, and kinetic analysis of the binding of substrates and inhibitors of human pheny-lethanolamine N-methyltransferase. J. Med. Chem. 2005, 48, 7243-7252. (Pubitemid 41743638)
53. Howard, N.; Abell, C.; Blakemore, W.; Chessari, G.; Congreve, M.; Howard, S.; Jhoti, H.; Murray, C. W.; Seavers, L. C. A.; van Montfort, R. L. M. Application of fragment screening and fragment linking to the discovery of novel thrombin inhibitors. J. Med. Chem. 2006, 49, 1346-1355. (Pubitemid 43271886)
54. Murray, C. W.; Callaghan, O.; Chessari, G.; Cleasby, A.; Congreve, M.; Frederickson, M.; Hartshorn, M. J.; McMenamin, R.; Patel, S.; Wallis, N. Application of fragment screening by X-ray crystallography to beta-secretase. J. Med. Chem. 2007, 50, 1116-1123. (Pubitemid 46496312)
55. Soldano, K. L.; Jivan, A.; Nicchitta, C. V.; Gewirth, D. T. Structure of the N-terminal domain of GRP94 - Basis for ligand specificity and regulation. J. Biol. Chem. 2003, 278, 48330-48338. (Pubitemid 37523288)
56. Barril, X.; Beswick, M. C.; Collier, A.; Drysdale, M. J.; Dymock, B. W.; Fink, A.; Grant, K.; Howes, R.; Jordan, A. M.; Massey, A.; Surgenor, A.; Wayne, J.; Workman, P.; Wright, L. 4-amino derivatives of the Hsp90 inhibitor CCT018159. Bioorg. Med. Chem. Lett. 2006, 16 2543-2548.
57. Brough, P. A.; Barril, X.; Borgognoni, J.; Chene, P.; Davies, N. G. M.; Davis, B.; Drysdale, M. J.; Dymock, B.; Eccles, S. A.; Garcia-Echeverria, C.; Fromont, C.; Hayes, A.; Hubbard, R.E.; Jordan, A.M.; Jensen, M. R.; Massey A.; Merrett, A.; Padfield, A.; Parsons, R.; Radimerski, T.; Raynaud, F. I.; Robertson, A.; Roughley, S. D.; Schoepfer, J.; Simmonite, H.; Sharp, S. Y.; Surgenor, A.; Valenti, M.; Walls, S.; Webb, P.; Wood, M.; Workman, P.; Wright, L. Combining Hit Identification Strategies: Fragment-Based and in Silico Approaches to Orally Active 2-Aminothieno 2,3-d pyrimidine Inhibitors of the Hsp90 Molecular Chaperone. J. Med. Chem. 2009, 52, 4794-4809.
58. Gopalsamy, A.; Shi, M. X.; Golas, J.; Vogan, E.; Jacob, J.; Johnson, M.; Lee, F.; Nilakantan, R.; Petersen, R.; Svenson, K.; Chopra, R.; Tam, M. S.; Wen, Y. X.; Ellingboe, J.; Andt, K.; Boschelli, F. Discovery of benzisoxazoles as potent inhibitors of chaperone heat shock protein 90. J. Med. Chem. 2008, 51, 373-375. (Pubitemid 351252261)
59. Barker, J. J.; Barker, O.; Boggio, R.; Chauhan, V.; Cheng, R. K. Y.; Corden, V.; Courtney, S. M.; Edwards, N.; Falque, V. M.; Fusar, F.; Gardiner, M.; Hamelin, E. M. N.; Hesterkamp, T.; Ichihara, O.; Jones, R. S.; Mather, O.; Mercurio, C.; Minucci, S.; Montalbetti, C.; Muller, A.; Patel, D.; Phillips, B. G.; Varasi, M.; Whittaker, M.; Winkler, D.; Yarnold, C. J. Fragment-based Identification of Hsp90 Inhibitors. ChemMedChem 2009, 4, 963-966.