Analysis and optimization of structure-based virtual screening protocols - 2. Examination of docked ligand orientation sampling methodology: Mapping a pharmacophore for success

Journal of Molecular Graphics and Modelling

Volumn 22, Issue 1, 2003, Pages 31-40

  Good, Andrew C ^a,c   Cheney, Daniel L ^a   Sitkoff, Doree F ^a   Tokarski, John S ^a   Stouch, Terry R ^a   Bassolino, Donna A ^a   Krystek, Stanley R ^a   Li, Yi ^a   Mason, Jonathan S ^a,c   Perkins, Timothy D J ^b,d  

^a BRISTOL MYERS SQUIBB   (United States)

^b BIOCOMPATIBLES UK LTD   (United Kingdom)

^c PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^d ASTRAZENECA   (United Kingdom)

Author keywords

Chemotype enrichment tests; Ligand sampling; Pharmacophore constraints; Structure based virtual screening

Indexed keywords

ALGORITHMS; COMPUTER PROGRAMMING; SAMPLING;

LIGANDS;

VIRTUAL REALITY;

LIGAND;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; COMPUTER PROGRAM; PHARMACOPHORE; PRIORITY JOURNAL; SAMPLING; SCREENING; TECHNIQUE;

EID: 12444278563     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(03)00124-4     Document Type: Article

References (15)

1. DOCK, developed and distributed by the Kuntz group, Department of Pharmaceutical Chemistry, 512 Parnassus, University of California, San Francisco, USA. URL: http://www.cmpharm.ucsf.edu/kuntz .
2. Baxter C.A., Murray C.W., Waszkowycz B., Li J., Sykes R.A., Bone R.G.A., Perkins T.D.J., Wylie W. New approach to molecular docking and its application to virtual screening of chemical databases. J. Chem. Inf. Comput. Sci. 40:2000;254-262.
3. GOLD version 1.2, developed and distributed by the CCDC, 12 Union Road, Cambridge, CB2 1EZ, UK. URL: http://www.ccdc.cam.ac.uk/prods/gold/index.html .
4. A.C. Good, J.S. Mason, S.D. Pickett, Pharmacophore pattern application in virtual screening, library design and QSAR, in: H.J. Böhm, G. Schneider (Eds.), Virtual Screening for Bioactive Molecules: Methods and Principles in Medicinal Chemistry, vol. 10, Wiley, 2000, pp. 131-156.
5. B.E. Thomas, D. Joseph-McCarthy, J.C. Alvarez, Pharmacophore-based molecular docking, in: O.F. Guner (Ed.), Pharmacophore Perception, Development, and Use in Drug Design, International University line La Jolla, 2000, pp. 351-367.
6. 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. 14:2000;435-448.
7. Shoichet B.K., Kuntz I.D. Matching chemistry and shape in molecular docking. Prot. Eng. 6:1993;723-732.
8. Bissantz C., Folkers G., Rognan D. Protein-based virtual screening of chemical databases. Evaluation of different docking/scoring combinations. J. Med. Chem. 43:2000;4759-4767.
9. Charifson P.S., Corkery J.J., Murcko M.A., Walters W.P. Consensus scoring: a method for obtaining improved hit rates from docking databases of three dimensional structures into proteins. J. Med. Chem. 42:1999;5100-5109.
10. Weiner S.J., Kollman P.A., Case D.A., Singh C., Ghio C., Alagona G., Profeta S. Jr., Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-784.
11. GRID Version 16, Developed and Distributed by Molecular Discovery Limited, West Way House, Elms Parade, Oxford OX2 9LL, UK.
12. Connolly M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 221:1983;709-713.
13. CONCORD 4.0, distributed by Tripos Inc., 1699 South Hanley Road, Suite 303, St. Louis, MO 63144, USA. URL: http://www.tripos.com .
14. LUDI/CATALYST, Developed and Distributed by Accelrys, 9685 North Scanton Road, San Diego, CA 92121, USA. URL: http://www.accelrys.com .
15. Böhm H.J., Boehringer M., Bur D., Gmuender H., Huber W., Klaus W., Kostrewa D., Kuehne H., Luebbers T., Meunier-Keller N., Mueller F. Novel inhibitors of DNA Gyrase: 3D structure-based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J. Med. Chem. 43:2000;2664-2674.