Constructing virtual combinatorial fragment libraries based upon MDL Drug Data Report database

Science in China, Series B: Chemistry

Volumn 50, Issue 3, 2007, Pages 364-371

  Zhang, Min ^a   Sheng, Chunquan ^a   Xu, Hui ^a   Song, Yunlong ^a   Zhang, Wannian ^a  

^a SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Drug design; Drug molecule; Fragment; Molecular database; Statistical analysis

Indexed keywords

DATABASE SYSTEMS; DRUG PRODUCTS; STRUCTURAL ANALYSIS;

DRUG DESIGN; DRUG MOLECULE; MOLECULAR DATABASE; SIDE CHAIN FRAGMENTS; STRUCTURAL FEATURES;

DIGITAL LIBRARIES;

EID: 34250901063     PISSN: 10069291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-007-0056-2     Document Type: Article

References (23)

1. Lipinski C A, Lombardo F, Dominy B W, Feenoy P J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Delivery Rev, 1997, 23(1): 3-25
2. Hornig M, Klamt A. COSMO frag: a novel tool for high-throughput ADME property prediction and similarity screening based on quantum chemistry. J Chem Inf Model, 2005, 45(5): 1169-1177
3. Refsgaard H H, Jensen B F, Brockhoff P B, Padkjaer S B, Guldbrandt M, Christensen M S. In silico prediction of membrane permeability from calculated molecular parameters. J Med Chem, 2005, 48(3): 805-811
4. Muskal S M, Jha S K, Kishore M P, Tyagi P. A simple and readily integratable approach to toxicity prediction. J Chem Inf Comput Sci, 2003, 43(5): 1673-1678
5. Mazzatorta P, Vracko M, Jezierska A, Benfenati E. Modeling toxicity by using supervised kohonen neural networks. J Chem Inf Comput Sci, 2003, 43(2): 485-492
6. Stenberg P, Norinder U, Luthman K, Artursson P. Experimental and computational screening models for the prediction of intestinal drug absorption. J Med Chem, 2001, 44(12): 1927-1937
7. Egan W J, Merz K M Jr, Baldwin J J. Prediction of drug absorption using multivariate statistics. J Med Chem, 2000, 43(21): 3867-3877
8. Darvas F, Dorman G, Papp A. Diversity measures for enhancing ADME admissibility of combinatorial libraries. J Chem Inf Comput Sci, 2000, 40(2): 314-322
9. Muller K R, Ratseh G, Sonnenburg S, Mika S, Grimm M, Heinrich N. Classifying "drug-likeness" with Kernel-based learning methods. J Chem Inf Model, 2005, 45(2): 249-253
10. Ertl P. Cheminformatics analysis of organic substituents: identification of the most common substituents, calculation of substituent properties, and automatic identification of drug-like bioisosteric groups. J Chem Inf Comput Sci, 2003, 43(2): 374-380
11. Sheridan R P, Shpungin J. Calculating similarities between biological activities in the MDL Drug Data Report database. J Chem Inf Comput Sci, 2004, 44(2): 727-740
12. Sheridan R P. The most common chemical replacements in drug-like compounds. J Chem Inf Comput Sci, 2002, 42(1): 103-108
13. Bemis G W, Murcko M A. The properties of known drugs. 1. Molecular frameworks. J Med Chem, 1996, 39(15): 2887-2893
14. Bemis G W, Murcko M A. Properties of known drugs. 2. Side chains. J Med Chem, 1999, 42(25): 5095-5099
15. Lewell X Q, Jones A C, Bruce C L, Harper G, Jones M M, McLay I M, Bradshaw J. Drug rings database with web interface. A tool for identifying alternative chemical rings in lead discovery programs. J Med Chem, 2003, 46(15): 3257-3274
16. Chen G, Zheng S, Luo X, Shen J, Zhu W, Liu H, Gui C, Zhang J, Zheng M, Puah C M, Chen K, Jiang H. Focused combinatorial library design based on structural diversity, druglikeness and binding affinity score. J Comb Chem, 2005, 7(3): 398-406
17. Wright T, Gillet V J, Green D V, Pickett S D. Optimizing the size and configuration of combinatorial libraries. J Chem Inf Coraput Sci, 2003, 43(2): 381-390
18. Douguet D, Munier-Lehmann H, Labesse G, Pochet S. LEA3D: a computer-aided ligand design for structure-based drug design. J Med Chem, 2005, 48(7): 2457-2468
19. MDDR. Licensed by Molecular Design, Ltd., San Leandro, CA 20 CMC. Available from MDL Information Systems, Inc., San Leandro, CA
20. ACD. Available Chemical Directory, MDL Information Services, San Leandro, CA
21. Xu J. GMA: a generic match algorithm for structural homomorphism, isomorphism, and maximal common substructure match and Its applications. J Chem Inf Comput Sci, 1996, 36(1): 25-34
22. Wang T, Zhou J. 3DFS: a new 3D flexible searching system for use in drug design. J Chem Inf Comput Sci, 1998, 38(1): 71-77
23. Zhang WN, Zhang M, Sheng C Q. InterD2: The Interactive New Drug Design system (in Chinese). Version 1.0. Reg. No. 2005SR04084: Second Military Medical University, 2005