A molecular mechanics approach to modeling protein-ligand interactions: Relative binding affinities in congeneric series

Journal of Chemical Information and Modeling

Volumn 51, Issue 9, 2011, Pages 2082-2089

  Rapp, Chaya ^a   Kalyanaraman, Chakrapani ^b   Schiffmiller, Aviva ^a   Schoenbrun, Esther Leah ^a   Jacobson, Matthew P ^b  

^a YESHIVA UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CRYSTALS; FREE ENERGY; MOLECULAR MECHANICS; PROTEINS;

BINDING AFFINITIES; CONFORMATIONAL SPACE; CONGENERIC SERIES; ENERGY MINIMIZATION; FREE ENERGY PERTURBATION; GOOD CORRELATIONS; RELATIVE BINDING AFFINITY; SCORING FUNCTIONS;

LIGANDS;

LIGAND; PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN DATABASE;

DATABASES, PROTEIN; LIGANDS; MODELS, MOLECULAR; PROTEINS;

EID: 80053299829     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200033n     Document Type: Article

References (56)

1. Jorgensen, W. L. Efficient drug lead discovery and optimization Acc. Chem. Res. 2009, 42, 724-33
2. Steinbrecher, T.; Labahn, A. Towards accurate free energy calculations in ligand protein-binding studies Curr. Med. Chem. 2010, 17, 767-85
3. Pohorille, A.; Jarzynski, C.; Chipot, C. Good practices in free-energy calculations J. Phys. Chem. B 2010, 114, 10235-53
4. Singh, N.; Warshel, A. Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions Proteins 2010, 78, 1705-23
5. Ge, X.; Roux, B. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome J. Phys. Chem. B 2010, 114, 9525-39
6. Boyce, S. E.; Mobley, D. L.; Rocklin, G. J.; Graves, A. P.; Dill, K. A.; Shoichet, B. K. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site J. Mol. Biol. 2009, 394, 747-63
7. Rodinger, T.; Howell, P. L.; Pomes, R. Calculation of absolute protein-ligand binding free energy using distributed replica sampling J. Chem. Phys. 2008, 129, 155102
8. Chen, W.; Glison, M. K.; Webb, S. P.; Potter, M. J. Modeling protein-ligand binding my mining minima J. Chem. Theory Comput. 2010, 6, 3540-3557
9. Michel, J.; Essex, J. W. Prediction of protein-ligand binding affinity by free energy simulations: Assumptions, pitfalls and expectations J. Comput.-Aided Mol. Des. 2010, 24, 639-58
10. Lyne, P. D.; Lamb, M. L.; Saeh, J. C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring J. Med. Chem. 2006, 49, 4805-8 (Pubitemid 44201037)
11. Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA J. Comput. Chem. 2010, 31, 797-810
12. Guimaraes, C. R.; Cardozo, M. MM-GB/SA rescoring of docking poses in structure-based lead optimization J. Chem. Inf. Model. 2008, 48, 958-70
13. Huang, N.; Kalyanaraman, C.; Bernacki, K.; Jacobson, M. P. Molecular mechanics methods for predicting protein-ligand binding Phys. Chem. Chem. Phys. 2006, 8, 5166-77
14. Ferrari, A. M.; Degliesposti, G.; Sgobba, M.; Rastelli, G. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors Bioorg. Med. Chem. 2007, 15, 7865-77 (Pubitemid 47575902)
15. Huang, N.; Kalyanaraman, C.; Irwin, J. J.; Jacobson, M. P. Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening J. Chem. Inf. Model. 2006, 46, 243-53 (Pubitemid 43282119)
16. Foloppe, N.; Hubbard, R. Towards predictive ligand design with free-energy based computational methods? Curr. Med. Chem. 2006, 13, 3583-608 (Pubitemid 44873749)
17. Guimaraes, C. R.; Mathiowetz, A. M. Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations J. Chem. Inf. Model. 2010, 50, 547-59
18. Rapp, C. S.; Schonbrun, C.; Jacobson, M. P.; Kalyanaraman, C.; Huang, N. Automated site preparation in physics-based rescoring of receptor ligand complexes Proteins 2009, 77, 52-61
19. Nervall, M.; Hanspers, P.; Carlsson, J.; Boukharta, L.; Aqvist, J. Predicting binding modes from free energy calculations J. Med. Chem. 2008, 51, 2657-67 (Pubitemid 351620787)
20. Kalyanaraman, C.; Bernacki, K.; Jacobson, M. P. Virtual screening against highly charged active sites: Identifying substrates of alpha-beta barrel enzymes Biochemistry 2005, 44, 2059-71 (Pubitemid 40223633)
21. Graves, A. P.; Shivakumar, D. M.; Boyce, S. E.; Jacobson, M. P.; Case, D. A.; Shoichet, B. K. Rescoring docking hit lists for model cavity sites: Predictions and experimental testing J. Mol. Biol. 2008, 377, 914-34
22. Taufer, M.; Armen, R.; Chen, J.; Teller, P.; Brooks, C. Computational multiscale modeling in protein-ligand docking IEEE Eng. Med. Biol. Mag. 2009, 28, 58-69
23. Jiao, D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Calculation of protein-ligand binding free energy by using a polarizable potential Proc. Natl. Acad. Sci. U S A 2008, 105, 6290-5 (Pubitemid 351758339)
24. Kaminski, G. A.; Ponomarev, S. Y.; Liu, A. B. Polarizable simulations with second order interaction model-force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations J. Chem. Theory Comput. 2009, 5, 2935-2943
25. Friesner, R. A. Modeling polarization in proteins and protein-ligand complexes: Methods and preliminary results Adv. Protein Chem. 2005, 72, 79-104
26. Ha, S.; Andreani, R.; Robbins, A.; Muegge, I. Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors J. Comput.-Aided Mol. Des. 2000, 14, 435-48 (Pubitemid 30386819)
27. Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L., III. Assessing scoring functions for protein-ligand interactions J. Med. Chem. 2004, 47, 3032-47 (Pubitemid 38702700)
28. Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R. Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 2006, 49, 534-53 (Pubitemid 43157487)
29. Prime, V2.2.108; Schrodinger LLC: New York, 2007.
30. Jacobson, M. P.; Kaminski, G. A.; Friesner, R. A.; Rapp, C. S. Force field validation using protein side chain prediction J. Phys. Chem. B 2002, 106, 11673-11680 (Pubitemid 35361141)
31. Andrec, M.; Harano, Y.; Jacobson, M. P.; Friesner, R. A.; Levy, R. M. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction J. Struct. Funct. Genomics 2002, 2, 103-11 (Pubitemid 34975806)
32. Jacobson, M. P.; Pincus, D. L.; Rapp, C. S.; Day, T. J.; Honig, B.; Shaw, D. E.; Friesner, R. A. A hierarchical approach to all-atom protein loop prediction Proteins 2004, 55, 351-67 (Pubitemid 38437493)
33. Felts, A. K.; Gallicchio, E.; Chekmarev, D.; Paris, K. A.; Friesner, R. A.; Levy, R. M. Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling J. Chem. Theory Comput. 2008, 4, 855-868
34. Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding J. Am. Chem. Soc. 2008, 130, 2817-31 (Pubitemid 351416242)
35. Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 808-13 (Pubitemid 46154692)
36. Oslob, J. D.; Romanowski, M. J.; Allen, D. A.; Baskaran, S.; Bui, M.; Elling, R. A.; Flanagan, W. M.; Fung, A. D.; Hanan, E. J.; Harris, S.; Heumann, S. A.; Hoch, U.; Jacobs, J. W.; Lam, J.; Lawrence, C. E.; McDowell, R. S.; Nannini, M. A.; Shen, W.; Silverman, J. A.; Sopko, M. M.; Tangonan, B. T.; Teague, J.; Yoburn, J. C.; Yu, C. H.; Zhong, M.; Zimmerman, K. M.; OBrien, T.; Lew, W. Discovery of a potent and selective aurora kinase inhibitor Bioorg. Med. Chem. Lett. 2008, 18, 4880-4
37. Duplantier, A. J.; Becker, S. L.; Bohanon, M. J.; Borzilleri, K. A.; Chrunyk, B. A.; Downs, J. T.; Hu, L. Y.; El-Kattan, A.; James, L. C.; Liu, S.; Lu, J.; Maklad, N.; Mansour, M. N.; Mente, S.; Piotrowski, M. A.; Sakya, S. M.; Sheehan, S.; Steyn, S. J.; Strick, C. A.; Williams, V. A.; Zhang, L. Discovery, SAR, and pharmacokinetics of a novel 3-hydroxyquinolin-2(1H)-one series of potent D-amino acid oxidase (DAAO) inhibitors J. Med. Chem. 2009, 52, 3576-85
38. Grunewald, G. L.; Seim, M. R.; Regier, R. C.; Martin, J. L.; Gee, C. L.; Drinkwater, N.; Criscione, K. R. Comparison of the binding of 3-fluoromethyl-7-sulfonyl-1,2,3,4-tetrahydroisoquinolines with their isosteric sulfonamides to the active site of phenylethanolamine N-methyltransferase J. Med. Chem. 2006, 49, 5424-33 (Pubitemid 44373175)
39. Farmer, L. J.; Bemis, G.; Britt, S. D.; Cochran, J.; Connors, M.; Harrington, E. M.; Hoock, T.; Markland, W.; Nanthakumar, S.; Taslimi, P.; Ter Haar, E.; Wang, J.; Zhaveri, D.; Salituro, F. G. Discovery and SAR of novel 4-thiazolyl-2-phenylaminopyrimidines as potent inhibitors of spleen tyrosine kinase (SYK) Bioorg. Med. Chem. Lett. 2008, 18, 6231-5
40. Grey, R.; Pierce, A. C.; Bemis, G. W.; Jacobs, M. D.; Moody, C. S.; Jajoo, R.; Mohal, N.; Green, J. Structure-based design of 3-aryl-6-amino- triazolo[4,3-b]pyridazine inhibitors of Pim-1 kinase Bioorg. Med. Chem. Lett. 2009, 19, 3019-22
41. Krystof, V.; Cankar, P.; Frysova, I.; Slouka, J.; Kontopidis, G.; Dzubak, P.; Hajduch, M.; Srovnal, J.; de Azevedo, W. F., Jr.; Orsag, M.; Paprskarova, M.; Rolcik, J.; Latr, A.; Fischer, P. M.; Strnad, M. 4-Arylazo-3,5-diamino-1H- pyrazole CDK inhibitors: SAR study, crystal structure in complex with CDK2, selectivity, and cellular effects J. Med. Chem. 2006, 49, 6500-9 (Pubitemid 44657444)
42. Yan, S.; Larson, G.; Wu, J. Z.; Appleby, T.; Ding, Y.; Hamatake, R.; Hong, Z.; Yao, N. Novel thiazolones as HCV NS5B polymerase allosteric inhibitors: Further designs, SAR, and X-ray complex structure Bioorg. Med. Chem. Lett. 2007, 17, 63-7 (Pubitemid 44959988)
43. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242 (Pubitemid 30047768)
44. Maestro; Schrodinger LLC: New York, 2007.
45. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 (Pubitemid 26399746)
46. Yu, Z.; Jacobson, M. P.; Friesner, R. A. What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules J. Comput. Chem. 2006, 27, 72-89
47. Zhang, L. Y.; Gallicchio, E.; Friesner, R. A.; Levy, R. M. Solvent models for protein-ligand binding: Comparison of implicit solvent Poisson and surface generalized born models with explicit solvent simulations J. Comput. Chem. 2001, 22, 591-607 (Pubitemid 32382606)
48. Zhu, K.; Shirts, M. R.; Friesner, R. A.; Jacobson, M. P. Multiscale optimization of a truncated Newton minimization algorithm and application to proteins and protein-ligand complexes J. Chem. Theory Comput. 2007, 3, 640-648
49. Wei, H. Y.; Tsai, K. C.; Lin, T. H. Modeling ligand-receptor interaction for some MHC class IIHLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques J. Chem. Inf. Model. 2005, 45, 1343-1351
50. Ali, A.; Reddy, G. S.; Cao, H.; Anjum, S. G.; Nalam, M. N.; Schiffer, C. A.; Rana, T. M. Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands J. Med. Chem. 2006, 49, 7342-56 (Pubitemid 44913395)
51. Nazare, M.; Essrich, M.; Will, D. W.; Matter, H.; Ritter, K.; Urmann, M.; Bauer, A.; Schreuder, H.; Czech, J.; Lorenz, M.; Laux, V.; Wehner, V. Novel factor Xa inhibitors based on a 2-carboxyindole scaffold: SAR of P4 substituents in combination with a neutral P1 ligand Bioorg. Med. Chem. Lett. 2004, 14, 4197-201 (Pubitemid 38916934)
52. Nazare, M.; Will, D. W.; Matter, H.; Schreuder, H.; Ritter, K.; Urmann, M.; Essrich, M.; Bauer, A.; Wagner, M.; Czech, J.; Lorenz, M.; Laux, V.; Wehner, V. Probing the subpockets of factor Xa reveals two binding modes for inhibitors based on a 2-carboxyindole scaffold: A study combining structure-activity relationship and X-ray crystallography J. Med. Chem. 2005, 48, 4511-25 (Pubitemid 40993413)
53. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes J. Med. Chem. 2006, 49, 6177-96 (Pubitemid 44595196)
54. Maestro, V 9.1.107; Schrodinger LLC: New York, 2007.
55. Community Structure-Activity Resource (CSAR). http://www.csardock.org/.
56. Zhou, H. X.; Gilson, M. K. Theory of free energy and entropy in noncovalent binding Chem. Rev. 2009, 109, 4092-107