A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases

Journal of Combinatorial Chemistry

Volumn 1, Issue 1, 1999, Pages 55-68

  Ghose, Arup K ^a   Viswanadhan, Vellarkad N ^a   Wendoloski, John J ^a  

^a AMGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG;

ALGORITHM; ARTICLE; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG DESIGN; FACTUAL DATABASE; METHODOLOGY; PHARMACOLOGY; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; CHEMISTRY, PHARMACEUTICAL; COMBINATORIAL CHEMISTRY TECHNIQUES; DATABASES, FACTUAL; DRUG DESIGN; PHARMACEUTICAL PREPARATIONS; PHARMACOLOGY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0032600640     PISSN: 15204766     EISSN: None     Source Type: Journal    
DOI: 10.1021/cc9800071     Document Type: Article

References (17)

1. Drews, J. Genomic sciences and the medicine of tomorrow. Nature Biotechnol. 1996, 14, 1516-1518.
2. Drews, J. Sciences towards the Medicine of Tomorrow. Chimia 1996, 30, 507-510.
3. Armstrong, R. W.; Combs, A. P.; Tempest, P. A.; Brown, S. D.; Keating, T. A. Multiple-component condensation strategies for combinatorial library synthesis. Acc. Chem. Res. 1996, 29, 123-131.
4. Chaiken, I. M.; Janda, K. D. Molecular Diversity and Combinatorial Chemistry: ACS Conference Proceeding Series; American Chemical Society: Washington, DC, 1996
5. Caflisch, A.; Karplus, M. Computational combinatorial chemistry for de novo ligand design: Review and assessment. Perspect. Drug Discovery Des. 1995, 3, 51-84.
6. Ghose, A. K.; Viswanadhan, V. N.; Wendoloski, J. J. Adapting structure-based drug design in the paradigm of combinatorial chemistry and high-throughput screening: An overview and new examples with important caveats for newcomers to combinatorial library design using pharmacophore models or multiple copy simultaneous search (MCSS) fragments. In Rational Drug Design; Parrill, A., Reddy, M. R., Eds.; American Chemical Society: Washington, DC, 1998; in press.
7. Moran, E. J.; Sarshar, S.; Cargill, J. F.; Shahbaz, M. M.; Lio, A.; Mjalli, A. M. M.; Armstrong, R. W. Radio frequency tag encoded combinatorial library method for the discovery of tripeptide-substituted cinnamic acid inhibitors of the protein tyrosine phosphatase PTP1B. J. Am. Chem. Soc. 1995, 117, 10787-10788.
8. 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., Genet. 1997, 29, 32-58.
9. (a) Kuntz, I. D. Structure-Based Strategies for Drug Design and Discovery. Science 1992, 257, 1078-1082.
10. (b) Kick, E. K.; Roe, D. C.; Skillman, A. G.; Liu, G.; Ew̌ing, T. J. A.; Sun, Y.; Kuntz, I. D.; Ellman, J. A. Structure-Based Design and Combinatorial Chemistry Yield Low Nanomolar Inhibitors of Cathepsin D. Chem. Biol. 1997, 4, 297-307.
11. See also the web page www.combinatorial.com.
12. Kollman, P. Molecular-Dynamics and Free-Energy Perturbation Calculations - What Role Do They Play In Computer-Assisted Molecular Design. FASEB J. 1995, 9, A1253-A1253.
13. Head, R. D.; Smythe, M. L.; Oprea, T. I.; Waller, C. L.; Green, S. M.; Marshall, G. R. VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc. 1996, 118, 3959-3969.
14. Chose, A. K.; Crippen, G. M. Use of physicochemical parameters in distance geometry and related three-dimensional quantitative structure-activity relationships: a demonstration using Escherichia coli dihydrofolate reductase inhibitors. J. Med. Chem. 1985, 28, 333-46.
15. Ghose, A. K.; Crippen, G. M.; Revankar, G. R.; McKernan, P. A.; Smee, D. F.; Robins, R. K. Analysis of the in vitro antiviral activity of certain ribonucleosides against parainfluenza virus using a novel computer aided receptor modeling procedure. J. Med. Chem. 1989, 32, 746-756.
16. Ghose, A. K.; Logan, M. E.; Treasurywala, A. M.; Wang, H.; Wahl, R. C.; Tomczuk, B.; Gowravaram, M.; Jaeger, E. P.; Wendoloski, J. J. Determination of Pharmacophoric Geometry for Collagenase Inhibitors Using a Novel Computational Method and Its Verification Using Molecular Dynamics, NMR and X-ray Crystallography. J. Am. Chem. Soc. 1995, 117, 4671-4682.
17. Ghose, A. K.; Wendoloski, J. J. Pharmacophore Modeling: Methods, Experimental Verifications and Applications. In 3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity; Kubinyi, H., Folker, G., Martin, Y. C., Eds.; Kluwer Academic: The Netherlands, 1998.