Reagent-based and product-based computational approaches in library design

Current Opinion in Chemical Biology

Volumn 7, Issue 3, 2003, Pages 326-330

  Jamois, Eric A ^a  

^a ACCELRYS INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUND; REAGENT;

CHEMICAL ANALYSIS; CHEMICAL MODIFICATION; CHEMICAL PROCEDURES; CHEMICAL STRUCTURE; COMBINATORIAL LIBRARY; EXPERIMENTATION; REVIEW; STRUCTURE ANALYSIS; SYNTHESIS; TASK PERFORMANCE;

EID: 0038198874     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(03)00053-X     Document Type: Review

References (34)

1. Ghose AK, Viswanadhan VN (eds): Combinatorial Library Design and Evaluation - Principles, Software Tools and Applications in Drug Discovery. New York: Marcel Dekker; 2001.
2. Valler M.J., Green D. Diversity screening versus focused screening in drug discovery. Drug Discov. Today. 5:2000;286-293.
3. Pickett S.D., McLay I.M., Clark D.E. Enhancing the hit to lead properties of lead optimization libraries. J. Chem. Inf. Comput. Sci. 40:2000;263-272 Provides an interesting example of incorporating 'drug-likeness' in the library design process.
4. Martin E.J., Crichlow R.W. Beyond mere diversity: tailoring combinatorial libraries for drug discovery. J. Comb. Chem. 1:1999;32-45.
5. Johnson M, Maggiora GM: Concepts and Applications of Molecular Similarity. New York, NY: Wiley; 1990.
6. Snarey M., Terrett N.K., Willett P., Wilton D.J. Comparison of algorithms for dissimilarity-based compound selection. J. Mol. Graphics Mod. 15:1997;372-385.
7. Lajiness M.S. Dissimilarity-based compound selection techniques. Perspect. Drug Discovery Design. 7:1997;65-84.
8. Marengo E., Todeschini R. A new algorithm for optimal distance-based experimental design. Chemo-metrics Intell. Lab Syst. 16:1992;37-44.
9. Holliday J.D., Ranade S.S., Willett P. A fast algorithm for selecting sets of dissimilar structures from large chemical databases. Quant. Struct-Activity Relationships. 14:1995;501-506.
10. Hassan M., Bielawski J.P., Hempel J.C., Waldman M. Optimization and visualization of molecular diversity of combinatorial libraries. Mol. Divers. 2:1996;64-74.
11. Brown R.D., Martin Y.C. Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J. Chem. Inf. Comput. Sci. 36:1996;572-584.
12. Zheng W., Cho S.J., Tropsha A. Rational combinatorial library design. 1. Focus-2D: a new approach to targeted combinatorial chemical libraries. J. Chem. Inf. Comput. Sci. 38:1998;251-258.
13. Leach A.R., Green D.V.S., Hann M.M., Judd D.B., Good A.C. Where are the gaps? A rational approach to monomer acquisition and selection. J. Chem. Inf. Comput. Sci. 40:2000;1262-1269 Provides an interesting example of reagent-based design with 3D pharmacophore descriptors.
14. Gillet V.J., Willett P., Bradshaw J. The effectiveness of reactant pools for generating structurally-diverse combinatorial libraries. J. Chem. Inf. Comput. Sci. 37:1997;731-740.
15. Jamois E.J., Hassan M., Waldman M. Evaluation of reagent-based and product-based strategies in the design of combinatorial library subsets. J. Chem. Inf. Comput. Sci. 40:2000;63-70.
16. Gillet V.J., Willett P., Bradshaw J., Green D.V.S. Selecting combinatorial libraries to optimize diversity and physical properties. J. Chem. Inf. Comput. Sci. 39:1999;169-177 A reference of special interest that details how optimization can be performed against multiple objectives.
17. Reynolds C.H., Tropsha A., Pfahler L.B., Druker R., Chakravorty S., Ethiraj G., Zheng W. Diversity and coverage of structural sublibraries selected using the SAGE and SCA algorithms. J. Chem. Inf. Comput. Sci. 41:2001;1470-1477 Comparison of several compound selection algorithms and schemes.
18. Brown R.D., Hassan M., Waldman M. Combinatorial library design for diversity, cost efficiency, and drug-like character. J. Mol. Graphics Mod. 18:2000;427-437 A reference of special interest with optimization against multiple objectives. More specific to the Cerius2 software suite.
19. Gillet V.J., Khatib W., Willett P., Fleming P.J., Green D.V.S. Combinatorial library design using a multiobjective genetic algorithm. J. Chem. Inf. Comput. Sci. 42:2002;375-385 A reference of special interest that details how one may deal with potentially conflicting design objectives and how to explore choices for a compromise solution.
20. Lewell X.Q., Judd D.B., Watson S.P., Hann M.M. RECAP-retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci. 38:1998;511-522.
21. Langer T., Hoffmann R.D. New principal components derived parameters describing molecular diversity of heteroaromatic residues. Quant. Struct-Act Relat. 17:1998;211-223.
22. Brown R.D. Descriptors for diversity analysis. Perspect. Drug Discov. Des. 7:1997;31-49.
23. Leach A.R., Bradshaw J., Green D.V.S., Hann M.M. Implementation of a system for reagent selection and library enumeration, profiling, and design. J. Chem. Inf. Comput. Sci. 39:1999;1161-1172 Illustrates how library design tools can be integrated with other computational and cheminformatics components and deployed to chemists.
24. Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 23:1997;3-25.
25. Eagan W.J., Merz K.M., Baldwin J.J. Prediction of drug absorption using multivariate statistics. J. Med. Chem. 43:2000;3867-3877.
26. Darvas F., Dorman G., Papp A. Diversity measures for enhancing ADME admissibility of combinatorial libraries. J. Chem. Inf. Comput. Sci. 40:2000;314-322 Illustrates how early ADME considerations in library design can improve success rate from in vitro hits to in vivo leads.
27. McGregor M.J., Muskal S.M. Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J. Chem. Inf. Comput. Sci. 39:1999;569-574.
28. McGregor M.J., Muskal S.M. Pharmacophore fingerprinting. 2. Application to primary library design. J. Chem. Inf. Comput. Sci. 40:2000;117-125.
29. Agrafiotis D.K., Lobanov V.S. Ultrafast algorithm for designing focused combinatorial arrays. J. Chem. Inf. Comput. Sci. 40:2000;1030-1038 Interesting example of fast design of focused libraries using partial enumeration.
30. Lobanov V.S., Agrafiotis D.K. Stochastic similarity selections from large combinatorial libraries. J. Chem. Inf. Comput. Sci. 40:2000;460-470 Provides some interesting conclusions on the quality of results that can be obtained with minimal sampling against extremely large virtual libraries.
31. Sheridan R.P., SanFeliciano S.G., Kearsley S.K. Designing targeted libraries with genetic algorithms. J. Comput-Aided Mol. Design. 18:2000;320-334 Provides an elegant approach to the optimization of subsets from extremely large virtual libraries using a genetic algorithm with 2D or 3D objective functions.
32. Downs G.M., Barnard J.M. Techniques for generating descriptive fingerprints in combinatorial libraries. J. Chem. Inf. Comput. Sci. 37:1997;59-61.
33. Barnard J.M., Downs G.M., Scholley-Pfab A., Brown R.D. Use of Markush structure analysis techniques for descriptor generation and clustering of large combinatorial libraries. J. Mol. Graphics Mod. 18:2000;452-463.
34. 2, Version 4.8, Molecular Simulations Inc., 9685 Scranton Road, San Diego, CA 92121, USA On World Wide Web URL: http://www.accelrys.com/cerius2/c2libx.html.