3D-Databases

The first task was the aeation of large 3D chemical structure databases. By devising so-called fast Automatic 3D model builder, software such as the CORINA [27, 28] and CONCORD [29, 30] programs resulted in a boom in 3D database development (see Section 2.9 in this book and Chapter II, Section 7.1 in the Handbook). A subsequent step was the development of fast... 

D database searching. As each conformation is generated an appropriate bit is set in the binary key. At me, the binary key appropriate to the pharmacophore is set up and compared with the keys in the database. 

A flow chart showing the various phases leading to the final compound is reproduced ii Figure 12.35. The first step was a 3D database search of a subset of the Cambridge Structura Database. The pharmacophore for this search comprised two hydrophobic groups and i... 

H-J 1998. Prediction of Binding Constants of Protein Ligands A Fast Method for the aritisation of Hits Obtained from De Novo Design or 3D Database Search Programs. Journal of nputer-Aided Molecular Design 12 309-323. 

S Kahn, H Savoj, P Sprague and S Teig 1994, Chemical Function Queries for 3D Database ch. Journal of Chemical Information and Computer Science 34 1297-1308. 

S Wang, DW Zaharevitz, R Sharma, VE Marquez, NE Lewm, L Du, PM Blumberg, GWA Milne. The discovery of novel, stnicturally diverse protein kinase C agonists through computer 3D-database pharmacophore search. I Med Chem 37 4479-4489, 1994. 

Today, 3D databases, which provide the means for storing and searching for 3D information of compounds, are proven to be useful tools in drug discovery programs. This is well exemplified with the recent discovery of novel nonpeptide HIV-1 protease inhibitors using pharmacophore searches of the National Cancer Institute 3D structural database [13-15]. 

This method represents the most common and traditional application of computational tools to rational drug design. From a list of molecules of known activity, one can establish a 3D-pharmacophore hypothesis that is then transformed into a 3D-search query. This query is then used to search a 3D database for structures that fit the hypothesis within a certain tolerance. If the yield of active molecules is significant, then the query can be used to predict activities on novel compounds. In our situation, the enantiophore is built from the superposition of a list of sample molecules, which are all well separated on a given CSR Hence, the common features of this series of molecules can become a good enantiophore hypothesis for the enantiores-olution on this CSR... 

These first-created enantiophores are rudimentary, but may serve as useful guidelines for a further design of more sophisticated and efficient search queries in consideration of possible alternative modes of binding and conformational changes in the CSP receptor structure. Undoubtedly, this query optimization will soon take advantage of the backgrounds of our new 3D-database project called CHIR-SOURCE. 

Martin YC. 3D database searching in drug design. J Med Chem 1992 35 2145-54. 

Bcl-2 is one of the many factors that control apoptosis, and overexpression of Bcl-2 has been observed in many different cancers. A homology model of Bcl-2 was derived from the NMR 3D structure of the Bcl-XL complex with a Bak BH3 peptide. This model served to search the NCI 3D database of 206,876 organic compounds for potential Bcl-2 inhibitors, which bind to the Bak BH3 binding site of Bcl-2. Full conformational flexibility of the ligands was taken into account in the program DOCK. Thirty-five potential inhibitors were tested, and seven of them had IC50 values from 1.6 to W.OpM. One of... 

Iwata Y, Arisawa M, Hamada R, Kita Y, Mizutani MY, Tomioka N, Itai A, Miyamoto S. Discovery of novel aldose reductase inhibitors using a protein structure-based approach 3D-database search followed by design and synthesis. J Med Chem 2001 44 1718-28. 

P. W., Hoffman, R. Catalyst pharmacophore models and their utility as queries for searching 3D databases. In Computer-Assisted Lead Finding and Optimization - Current Tools for Medicinal Chemistry, Van de Waterbeemd, H., Testa, B Folkers, G. (eds.),VHCA, Basel, 1990,... 

J. H. van Drie, Strategies for the determination of pharmacophoric 3D database queries,... 

Oshiro C, Bradley EK, Eksterowicz J, Evensen E, Lamb ML, et al. 2004. Performance of 3D-database molecular docking studies into homology models. J Med Chem 47(3) 764-767. 

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