The role of structure-based ligand design and molecular modelling in drug discovery

Pharmacy World and Science

Volumn 18, Issue 2, 1996, Pages 56-62

  Tollenaere, J P ^a,b  

^a JANSSEN RESEARCH FOUNDATION   (Belgium)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

computer graphics; databases; drug design; molecular conformation; nuclear magnetic resonance; receptors; structure activity relationship; X ray diffraction

Indexed keywords

CHEMICAL STRUCTURE; COMPUTER AIDED DESIGN; CONFORMATION; DATA BASE; DRUG ACTIVITY; DRUG DESIGN; DRUG DEVELOPMENT; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; REVIEW; STRUCTURE ACTIVITY RELATION;

COMPUTER-AIDED DESIGN; DRUG DESIGN; DRUG INFORMATION SERVICES; HUMANS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR;

EID: 0029993165     PISSN: 09281231     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF00579706     Document Type: Review

References (38)

1. Fujita T. The extrathermodynamic approach to drug design. In: Hansch C, Sammes PG, Taylor JB, Ramdsen CA, editors. Comprehensive medicinal chemistry. Vol. 4. Quantitative drug design. Oxford: Pergamon, 1990: 497-560.
2. Rekker R. The hydrophobic fragmental constant. Amsterdam: Elsevier Scientific Publishing, 1977.
3. Leo AJ. Calculating log Poct from structures. Chem Rev 1993;93:1281-1306.
4. Hansch C, Klein T, McClarin J, Langridge R, Cornell NW. A quantitative structure-activity relationship and molecular graphics analysis of hydrophobic effects in the interactions of inhibitors with alcohol dehydrogenase. J Med Chem 1986;29:615-20.
5. Tollenaere JP, Moereels H, Raymaekers LA. Structural aspects of the structure-activity relationships of neuroleptics: principles and methods. In: Arièns EJ, editor. Drug design. Vol. 10. Oxford: Academic Press, 1980: 71-118.
6. Allen FH, Davies JE. File structures and search strategies for the Cambridge Structural Database. Crystallogr Comput 1988;2:271-89.
7. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-42.
8. Wuthrich K. The development of nuclear magnetic resonance spectroscopy as a technique for protein structure determination. Acc Chem Res 1989;22:36-44.
9. Lee GM, Chen C, Marschner TM, Andersen NH. Does the solid-state structure of endothelin-1 provide insights concerning the solution-state conformational equilibrium? FEBS Lett 1994;355:140-6.
10. Leach AR. A survey of methods for searching the conformational space of small and medium-sized molecules. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. Vol. 2. Weinheim: VCH Publishers, 1991:1-55.
11. Howard AE, Kollman PA. An analysis of the current methodologies for conformational searching of complex molecules. J Med Chem 1988;31:1669-75.
12. Wilson SR, Cui W, Moskowitz JM, Schmidt KE. Applications of simulated annealing to the conformational analysis of flexible molecules. J Comput Chem 1991;12:342-9.
13. Nayeem A, Villa J, Scheraga HA. A comparative study of simulated-annealing and Monte Carlo with minimization approaches to the minimum-energy structures of polypeptides: [Met]-enkephalin. J Comput Chem 1991;12:594-605.
14. Zerner MC. Semiempirical molecular orbital methods. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. Vol. 2. Weinheim: VCH Publishers, 1991:313-65.
15. Siebel GL, Kollman PA. Molecular mechanics and the modelling of drug structures. In: Hansch C, Sammes PG, Taylor JB, Ramdsen CA, editors. Comprehensive medicinal chemistry. Vol. 4. Quantitative drug design. Oxford: Pergamon, 1990: 125-38.
16. Bowen JP, Allinger NL. Molecular mechanics: The art and science of parametrization. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. Vol. 2. Weinheim: VCH Publishers, 1991:81-97.
17. Brooks BR, Bruccoleri ER, Olafson ER, States DJ, Swaminathan S, Karplus M. CHARMm: A program for macromolecular energy minimization and dynamic calculations. J Comput Chem 1983;4:187-217.
18. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984; 106:765-84.
19. Clark M, Cramer RD III, Van Opdenbosch N. Validation of the general purpose tripos 5.2 force field. J Comput Chem 1989;10:982-1012.
20. Dinur U, Hagler AT. New approaches to empirical force fields. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. Vol. 2. Wemheim: VCH Publishers, 1991:99-164.
21. van Gunsteren WF, Berendsen HJC. Computer simulation of molecular dynamics: methodology, applications and perspectives in chemistry. Angew Chem 1990;29:992-1023.
22. Brunger AT, Karplus M. Molecular dynamics simulations with experimental restraints. Acc Chem Res 1991;24:54-61.
23. Sheridan RP, Rushmko A III, Nilakantan R, Venkataraghavan R. Searching for pharmacophores in large coordinate data bases and its use in drug design. Proc Natl Acad Sci USA 1989;86:8165-9.
24. Martin YC, Bures MG, Willet P. Searching databases of three-dimensional structures. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry. Vol 2. Weinheim: VCH Publishers, 1991:213-63.
25. Zuckermann RN, Kerr JM, Kent SBH, Moos WH. Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis. J Am Chem Soc 1992;114:10646-7.
26. Simon RJ, Kania RS, Zuckermann RN, Huebner VD, Jewell DA, Banville S, et al. Peptoids. a modular approach to drug discovery. Proc Natl Acad Sci USA 1992;89:9367-71.
27. Zuckermann RN, Martin EJ, Spellmeyer DC, Stauber GB, Shoemaker KR, Kerr JM, et al. Discovery of nanomolar ligands for 7-transmembrane G-protein coupled receptors from a diverse (N-substituted) glycine peptoid library. J Med Chem 1994;37:2678-85.
28. Felder ER. The challenge of preparing and testing combinatorial compound libraries in the fast lane, at the front end of drug development. Chimia 1994;48:531-41.
29. Liskamp RMJ. Opportunities for new libraries: unnatural biopolymer and diversomers. Angew Chem Int Ed (Engl) 1994, 33:633-6.
30. Chen JK, Schreiber SL Kombinatorische Synthese und mehrdimensionale NMR-Spektroskopie: ein Beitrag zum Verstandnis von Protein-Ligand-Wechselwirkungen. Angew Chem 1995;107:1041-58.
31. Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986;5:823-6.
32. Bohm H-J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput-Aided Mol Design 1992;6:61-78.
33. Bohm 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 Design 1994;8:243-56.
34. Leach AR, Kilvington SR. Automated molecular design: a new fragment-joining algorithm. J Comput-Aided Mol Design 1994,8:283-98.
35. Kollman P. Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
36. Loew GH, Villar HO, Alkorta I. Strategies for indirect computer-aided drug design. Pharm Res 1993;10:475-86.
37. Lam PYS, Jadhav PK, Eyermann CJ, Hodge CN, Ru Y, Bacheler LT, et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994;263:380-4.
38. Colman PM. Structure-based drug design. Curr Opin Struct Biol 1994;4:868-74.