Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

Journal of Molecular Biology

Volumn 245, Issue 1, 1995, Pages 43-53

  Jones, Gareth ^a   Willett, Peter ^a   Glen, Robert C ^b  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b WELLCOME RESEARCH LABORATORIES   (United Kingdom)

Author keywords

Desolvation; Genetic algorithm; Protein ligand docking

Indexed keywords

ANTIVIRUS AGENT; DIHYDROFOLATE REDUCTASE; FOLIC ACID; LIGAND; METHOTREXATE; SIALIDASE; TRIMETHOPRIM;

ALGORITHM; ARTICLE; BINDING SITE; COMPUTER PROGRAM; GENETICS; HYDROGEN BOND; MOLECULAR RECOGNITION; MOUSE; NONHUMAN; PRIORITY JOURNAL; RECEPTOR BINDING;

EID: 0028854034     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(95)80037-9     Document Type: Article

References (41)

1. Beeson, C., Nguyen, P., Shipps, G. & Dix, T. A. (1993). A comprehensive description of the free energy of an intramolecular hydrogen-bond as a function of solvation: NMR study. J Amer. Client. Soc. 115, 6803-6812.
2. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, F., Bryce, M. D., Rogers, J. R., Kennard, O., Shikanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol. Biol. 112, 535-542.
3. Blaney, J. M. & Dixon, J S. (1993). A good ligand is hard to find: automated docking methods. Perspect. Drug Disc. Design, 1, 301-319.
4. Blommers, M, Lucasius, C. B., Kateman, G. & Kaptein, R. (1992). Conformational analysis of a dinucleotide photodimer with the aid of a genetic algorithm. Biopolymers, 32, 45-52.
5. Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C. & Kraut, J (1982). Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. J Biol. Client. 257, 13650-13662.
6. Brown, R. D., Jones, G., Willett, P. & Glen, R. C. (1994). Matching two-dimensional chemical graphs using genetic algorithms. J. Cliem. Inform. Comput. Sci. 34, 63-70.
7. Champness, J. N., Stammers, D. K., Beddell, C. R. (1986). Crystallographic investigation of the cooperative interaction between trimethoprim, reduced cofactor and dihydrofolate reductase. FEBS Letters, 199, 61-67.
8. Champness, J. N., Achari, A., Ballantine, S. P., Bryant, P. K., Delves, C. J. & Stammers, D. K. (1994). The structure of Pneumocystis Carinii dihydrofolate reductase to 1.9 A resolutions. Structure, 2, 915-924.
9. 13C NMR determination of the tautomeric and ionization states of folate in its complexes with Lactobacillus casei dihydrofolate reductase. Biochemistry, 32, 6846-6854.
10. Clark, D. E., Jones, G., Willett, P., Kenny, P. W. & Glen, R. C. (1994). Pharmacophoric pattern matching in files of three-dimensional chemical structures: comparison of conformational-searching algorithms for flexible searching. J Chem. Inform. Comput. Sci. 34, 197-206.
11. Clark, M., Cramer, R. D. & Van Opdenbosch, N. (1989). Validation of the general-purpose TRIPOS 5.2 force field.Comput. Client. 10, 982-1012.
12. Cramer, C. J., Lynch, G. C., Hawkins, G. D. & Truhlar, D. G. (1993). AMSOL 3.5c User Manual, Quantum Chemical Program Exchange, Department of Chemistry, University of Indiana, Bloomington, IN.
13. Dandekar, T. & Argos, P. (1993). Folding the main chain of small proteins with the genetic algorithm. J Mol. Biol. 236, 844-861.
14. Davis, J. F., Delcamp, T. J., Prendergast, N.J., Ashford, V. A., Freisheim, J. H. & Kraut, J. (1990). Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate. Biochemistry, 29, 9467-9479.
15. Davis L. D. (1991). Editor of Handbook of Genetic Algorithms, Van Nostrand Reinhold, New York.
16. Desjarlais, R. L., Sheridan, R., Dixon, J. S., Kuntz, I. D. & Venkataraghavan, R. (1986). Docking flexible ligands to macromolecular receptors by molecular shape. J Med. Chem. 29, 2149-2153.
17. Desjarlais, R. L., Sheridan, R. P., Seibel, G. L., Dixon J. S., Kuntz, I. D. & Venkataraghavan, R. (1988). Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known threedimensional structure. J Med. Client. 31, 722-729.
18. Digby, P. G. N. & Kempton, R. A. (1987). Multivariate Analysis of Ecological Communities, pp. 112-115, Chapman and Hall, London.
19. Dixon, J. S. (1993). Flexible docking of ligands to receptor sites using genetic algorithms. In Trends in QSAR and Molecular Modelling 92 (Wermuth, C. G., ed.), pp. 412-413, ESCOM, Leiden.
20. Fountain, E. (1992). Application of genetic algorithms in the field of constitutional similarity. J. Chem. Inform. Comput. Sci. 32, 748-752.
21. Goldberg, D. E. (1989). Genetic Algorithms in Search, Optimisation and Machine Learning, Addison-Wesley, Reading, MA.
22. Goodsell, D. S. & Olson, A. J. (1990). Automated docking of substrates to proteins by simulated annealing. Proteins: Struct. Fund. Genet. 8, 195-202.
23. Groom, C. R., Thillett, J., North, A. C. T., Pictet, R. & Geddes, A. J. (1991). Trimethoprim binds in a bacterial mode to the wild-type and E30D mutant of mouse dihydofolate reductase. J Biol. Cliem. 266, 19890-19893.
24. Hirschfelder, J. O., Curtiss, C. F. & Bird, R. B. (1964). Molecular Theory of Gases and Liquids, John Wiley, New York.
25. Ho, C. M. W. & Marshall, G. R. (1990). Cavity search: an algorithm for the isolation and display of cavity like binding regions. J Comput. Aid. Mol. Des. 4, 337-354.
26. Holland, J. H. (1975). Adaptation in Natural and Artificial Systems, University of Michigan Press, Ann Arbor.
27. Judson, R. S., Jaeger, E. P., Treasurywala, A. M. & Peterson, M. L. (1993). Conformational searching methods for small molecules. II. Genetic algorithm approach. J. Comput. Chem. 14, 1407-1414.
28. Kuntz, I. D. (1992). Structure-based strategies for drug design and discovery Science, 257, 1078-1082.
29. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R. & Ferrin, T. E. (1982). A geometric approach to macromolecule-ligand interactions. J Mol. Biol. 161, 269-288.
30. Lawrence, M. C. & Davis, P. C. (1992). CLIX—a search algorithm for finding novel ligands capable of binding proteins of known 3-dimensional structure. Proteins: Struct. Fund. Genet. 12, 31-41.
31. Leach, A. R. (1994). Ligand docking to proteins with discrete side-chain flexibility. J Mol. Biol. 235, 345-356.
32. Matthews, D. A., Bolin, J. T., Burridge, J. M., Filman, D. J., Volz, K. W., Kaufman, B. T., Beddell, C. R., Champness, J. N., Stammers, D. K. & Kraut, J. (1985). Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim. J. Biol. Chem. 260, 381-391.
33. 3-hybridised oxygen atoms and its relevance to ligand-macromolecular interactions. J. Amer. Chem. Soc. 1018-1025.
34. Payne, A. W. R. & Glen, R. C. (1993). Molecular recognition using a binary genetic search algorithm. J. Mol. Graph. 11, 74-91.
35. Rinaldi, D., Rivail, J. & Rguini, N. (1993). Fast geometry optimisation in self-consistent reaction field computations on solvated molecules. J. Comput. Chem. 13, 675-680.
36. Shoichet, B. K., Stroud, R. M., Santi, D. V., Kuntz, I. D. & Perry, K. M. (1993). Structure-based discovery of inhibitors of thymidylate synthase. Science, 259, 1445-1450.
37. Smellie, A. S., Crippen, G. M. & Richards, W. G. (1991). Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads. J. Chem. Inform. Comput. Sci. 31, 386-392.
38. Stammers, D. K., Champness, J. N., Beddell, C. R., Dann J. G., Eliopoulos, E., Geddes, A. J., Ogg, D. & North, A. C. T. (1987). The structure of mouse L1210 dihydrofolate reductase-drug complexes and the construction of a model of human enzyme. FEBS Letters, 218, 178-184.
39. Stewart, J. J. P. (1992). MOPAC User Manual Version 6.0, Quantum Chemical Program Exchange, Department of Chemistry, University of Indiana, Bloomington, IN.
40. 108Leu) that exhibits enhanced affinity and altered specificity Biochemistry, 30, 6861-6866.
41. von Itzstein, M., Wu Wen-Yang, Kok G. B., Pegg, M. S., Dyson, J. C., Jin, B., Phan, T. V., Smythe, M. L., White, H. F., Oliver, S. W., Colman, P. M., Varghese, J. N., Ryan, D. M., Woods, J. M., Bethel], R. C., Hotham, V. J., Cameron, J. M. & Penn, C. R. (1993). Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature (London), 363, 418-423.