A general and fast scoring function for protein-ligand interactions: A simplified potential approach

Journal of Medicinal Chemistry

Volumn 42, Issue 5, 1999, Pages 791-804

  Muegge, Ingo ^a,b   Martin, Yvonne C ^a  

^a ABBOTT LABORATORIES   (United States)

^b BAYER CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; ENERGY; ENTROPY; LIGAND BINDING; MOLECULAR DYNAMICS; OXIDATION REDUCTION POTENTIAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; SOLVATION;

ALGORITHMS; DATABASES, FACTUAL; DRUG DESIGN; LIGANDS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 0033545622     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm980536j     Document Type: Article

References (53)

1. Greer, J.; Erickson, J. W.; Baldwin, J. J.; Varney, M. D. Application of the three-dimensional structures of protein target molecules in structure-based drug design. J. Med. Chem. 1994, 37, 1035-1054.
2. Martin, Y. C. Challenges and prospects for computational aids to molecular diversity. Perspect. Drug Discovery Des. 1997, 7/8, 159-172.
3. Kollman, P. Free energy calculations-applications to chemical and biological phenomena. Chem. Rev. 1993, 7, 2395-2417.
4. Lee, F. S.; Chu, Z. T.; Warshel, A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J. Comput. Chem. 1993, 14, 161-185.
5. Aqvist, J.; Medina, C.; Samuelsson, J. E. New method for predicting binding affinity in computer-aided drug design. Prot. Eng. 1994, 7, 385-391.
6. Muegge, I.; Schweins, T.; Langen, R.; Warshel, A. Electrostatic control of GTP and GDP binding in the oncoprotein p21ras. Structure 1996, 4, 475-489.
7. Sharp, K. A.; Honig, B. Electrostatic interactions in macromolecules. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301-332.
8. Williams, D. H.; Cox, J. P. L.; Doig, A. J.; Gardner, M.; Gerhard, U.; Kaye, P. T.; Lai, A. R.; Nicholls, I. A.; Salter, C. J.; Mitchell, R. C. Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution. J. Am. Chem. Soc. 1991, 113, 7020-7030.
9. Böhm, H.-J. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput.-Aided Mol. Des. 1992, 6, 593-606.
10. Böhm, H.-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 243-256.
11. Wallqvist, A.; Jernigan, R. L.; Covell, D. G. A preference-based free energy parametrization of enzyme-inhibitor binding. Application to HIV-1-protease inhibitor design. Protein Sci. 1995, 4, 1881-1903.
12. Jain, A. N. Scoring noncovalent protein-ligand interactions: A continouus differentiable function tuned to compute binding affinites. J. Comput.-Aided Mol. Des. 1996, 10, 427-440.
13. Head, R. D.; Smythe, M. L.; Oprea, T. L.; Waller, C. L.; Green, S. M.; Marshall, G. M. VALIDATE: A New method for the receptor-based prediction of binding affinites of novel ligands. J. Am. Chem. Soc. 1996, 118, 3959-3969.
14. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
15. Murray, C. W.; Auton, T. R.; Eldridge, M. D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. J. Comput.-Aided Mol. Des. 1998, 12, 503-519.
16. Böhm, H.-J. Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J. Comput.-Aided Mol. Des. 1998, 12, 309-323.
17. Kuntz, I. D. Structure-based strategies for drug design and discovery. Science 1992, 257, 1078-1082.
18. Ewing, T.; Kuntz, I. D. Critical evaluation of search algorithms for automated molecular docking and database screening. J. Comput. Chem. 1997, 18, 1175-1189.
19. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast felxible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
20. 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.
21. Welch, W.; Ruppert, J.; Jain, A. N. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 1996, 3, 449-462.
22. Dixon, J. S. Evaluation of the CASP2 docking section. Proteins: Struct., Funct., Genet., Suppl. 1997, 1, 198-204.
23. Sippl, M. J. Calculation of conformational ensembles from potentials of mean force. J. Mol. Biol. 1990, 213, 859-883.
24. Sippl, M. J.; Ortner, M.; Jaritz, M.; Lackner, P.; Flöckner, H. Helmholtz free energies of atom pair interactions in proteins. Folding Des. 1996, 1, 289-298.
25. Jones, D. T.; Taylor, W. R.; Thornton, J. M. A new approach to protein fold recognition. Nature 1992, 358, 86-89.
26. Godzik, A.; Kolinski, A.; Skolnick, J. Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 1992, 227, 227-238.
27. Ouzounis, C.; Sander, C.; Scharf, M.; Schneider, R. Prediction of protein structure by evaluation of sequence-structure fitness. J. Mol. Biol. 1993, 232, 805-825.
28. Bahar, I.; Jernigan, R. L. Interresidue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 1997, 266, 195-214.
29. Bahar, I.; Jernigan, R. L. Coordination geometry of nonbonded residues in globular proteins. Folding Des. 1996, 1, 357-370.
30. DeWitte, R. S.; Shakhnovich, E. I. SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 1996, 118, 11733-11744.
31. Verkhivker, G.; Appelt, K.; Freer, S. T.; Villafranca, J. E. Empirical free eenrgy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995, 8, 677-691.
32. Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge based scoring function to predict protein-ligand interactions. Poster presented at the 12th European QSAR Symposium in Copenhagen, Denmark, September 22-27, 1998.
33. Muegge, I.; Ermler, U.; Fritzsch, G.; Knapp, E. W. Free energy of cofactors at the quinone-QA site of the photosynthetic reaction center of Rhodobacter spheroides calculated by minimizing the statistical error. J. Phys. Chem. 1995, 99, 17917-17925.
34. Apostolakis, J.; Muegge, I.; Ermler, U.; Fritzsch, G.; Knapp, E. W. Free energy computations on the shift of the special pair redox potential - mutants of the reaction center of Rhodobacter spheroides. J. Am. Chem. Soc. 1996, 118, 3743-3752.
35. Muegge, I.; Apostolakis, J.; Ermler, U.; Fritzsch, G.; Lubitz, W.; Knapp, E. W. Shift of special pair redox potential: electrostatic energy computations of mutants of the reaction center of Rhodobacter spheroides. Biochemistry 1996, 35, 8359-8370.
36. Muegge, I.; Tao, H.; Warshel, A. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. Protein Eng. 1997, 10, 1363-1372.
37. Muegge, I.; Qi, X. P.; Wand, A. J.; Chu, Z. T.; Warshel, A. The reorganization energy of cytochrome c revisited. J. Phys. Chem. B 1997, 101, 825-836.
38. Muegge, I.; Schweins, T.; Warshel, A. Electrostatic contributions to protein-protein binding affinities: Application to rap/raf-interaction. Proteins: Struct., Funct., Genet. 1998, 30, 407-423.
39. Martin, Y. C.; Lin, C. T.; Wu, J. Application of CoMFA to the design and structural optimization of D1 dopaminaergic agonists. In 3D QSAR in Drug Design. Theory Methods and Applications; Kubinyi, H. Ed.; ESCOM: Leiden, 1993; pp 643-660.
40. Martin, Y. C.; Lin, C. T.; Hetti, C.; DeLazzer, J. PLS analysis of distance matrixes detects nonlinear relationships between biological potency and molecular properties. J. Med. Chem. 1995, 38, 3009-3015.
41. Martin, Y. C.; Lin, C. T. Three-dimensional quantitative structure-activity relationships: D2 dopamine agonists as an example. In The Practice of Medical Chemistry; Wermuth, C. G., Ed.; Academic Press: London, 1996; pp 459-483.
42. Kim, K. H.; Martin, Y. C.; Brooks, C. Quantitative structure activity relationship of 5-lipoxygenase inhibitors - inhibitory potency of triazinone analogues in a broken cell. Quant. Struct. Act. Relat. 1996, 15, 491-497.
43. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Jr., E. F. M.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem. 1977, 80, 319-324.
44. Warshel, A.; Papazyan, A.; Muegge, I. Microscopic and semi-macroscopic redox calculations: What can and cannot be learned from continuum methods. J. Biol. Inorg. Chem. 1997, 2, 143-152.
45. Sippl, M. J. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comput.-Aided Mol. Des. 1993, 7, 473-501.
46. Searle, M. S.; Williams, D. H. The cost of conformational order: Entropy changes in molecular associations. J. Am. Chem. Soc. 1992, 114, 10690-10697.
47. Searle, M. S.; Williams, D. H.; Gerhard, U. Partitioning of free energy contributions in the estimate of binding constants: Residual motions and consequences for amide-amide hydrogen bond strengths. J. Am. Chem. Soc. 1992, 114, 10697-10704.
48. Hendlich, M.; Rippmann, F.; Barnickel, G. BALI: Automatic-assignment of bond and atom types for protein ligands in the Brookhaven Protein Databank. J. Chem. Inf. Comput. Sci. 1996, 37, 774-778.
49. Muegge, I.; Martin, Y. C.; Hajduk, P. J.; Fesik, S. W. Evaluation of PMF-scoring in docking weak ligands to the FK506 binding protein, submitted.
50. Holloway, M. K.; Wai, J. M.; Halgren, T. A.; Fitzgerald, P. M. D.; Vacca, J. P.; Dorsey, B. D.; Levin, R. B.; Thompson, W. J.; Chen, L. J.; deSolms, S. J.; Gaffin, N.; Ghosh, A. K.; Giuliani, E. A.; Graham, S. L.; Guare, J. P.; Hungate, R. W.; Lyle, T. A.; Sanders, W. M.; Tucker, T. J.; Wiggins, M.; Wiscount, C. M.; Woltersdorf, O. W.; Young, S. D.; Darke, P. L.; Zugay, J. A. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J. Med. Chem. 1995, 38, 305-317.
51. Astley, T.; Birch, G. G.; Drew, M. G. B.; Rodger, P. M.; Wilden, G. R. H. Effect of available volumes on radial distribution functions. J. Comput. Chem. 1998, 19, 363-367.
52. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857.
53. McQuarrie, D. A. Statistical Mechanics; Harper Collins Publishers: New York, 1976.