Abstract
A system of virtual screening of organic molecule databases is designed, which permits preprocessing of databases, molecular docking to a three-dimensional model of receptor, and post-processing of the results obtained. Using this screening system, it is possible to reproduce positions of the known ligands in the glutamate sites of the NMDA and AMPA receptors and in the glycine site of the NMDA receptor, to substantially enrich the database with potentially active compounds, and to distinguish between the agonistic and antagonistic character of the action of these compounds in the case of docking to the open and closed forms of the binding sites. Based on the results of screening of a database of low-molecular-weight organic compounds (total of 135,000 structures) using models of the open and closed forms of the glutamate and glycine sites of the NMDA receptor and of the glutamate site of the AMPA receptor, focused libraries of potential agonists and antagonists of these sites were designed.
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References
M. L. Connolly, J. Appl. Crystallogr., 1983, 16, 548.
T. J. A. Ewing and I. D. Kuntz, J. Comput. Chem., 1997, 18, 1175.
R. L. DesJarlais and J. S. Dixon, J. Comput.-Aided Molec. Design, 1994, 8, 231.
D. A. Gschwend, W. Sirawaraporn, D. V. Santi, and I. D. Kuntz, Proteins, 1997, 29, 59.
L. R. Hoffman, I. D. Kuntz, and J. M. White, J. Virol., 1997, 71, 8808.
R. Li, X. Chen, B. Gong, P. M. Selzer, Z. Li, E. Davidson, G. Kurzban, R. E. Miller, E. O. Nuzum, J. H. McKerrow, R. J. Fletterick, S. A. Gillmor, C. S. Craik, I. D. Kuntz, F. E. Cohen, and G. L. Kenyon, Bioorg. Med. Chem., 1996, 4, 1421.
B. K. Shoichet, R. M. Stroud, D. V. Santi, I. D. Kuntz, and K. M. Perry, Science, 1993, 259, 1445.
C. Bissantz, G. Folkers, and D. Rognan, J. Med. Chem., 2000, 43, 4759.
S. Gruneberg, M. T. Stubbs, and G. Klebe, J. Med. Chem., 2002, 45, 3588.
B. B. Waszkowycz, T. D. J. Perkins, R. A. Sykes, and J. Li, IBM Systems J., 2001, 40, 360.
T. Langer and E. M. Krovat, Curr. Opin. Drug Discov. Devel., 2003, 6, 370.
O. Schwardt, H. Kolb, and B. Ernst, Curr. Top. Med. Chem., 2003, 3, 1.
R. D. Cramer III, D. E. Patterson, and J. D. Bunce, J. Am. Chem. Soc., 1988, 110, 5959.
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, and N. S. Zefirov, Dokl. Akad. Nauk, 2002, 382, 550 [Dokl. Chem., 2002 (Engl. Transl.)].
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, N. S. Zefirov, and S. O. Bachurin, J. Med. Chem., 2002, 45, 3836; 5608.
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, and N. S. Zefirov, Dokl. Akad. Nauk, 2002, 382, 840 [Dokl. Chem., 2002 (Engl. Transl.)].
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, and N. S. Zefirov, J. Med. Chem., 2003, 46, 1609.
N. Armstrong and E. Gouaux, Neuron, 2000, 28. 165.
Sybyl 6.7.2, Tripos Assoc., St. Louis (MO).
W. D. Ihlenfeldt, Y. Takahashi, H. Abe, and S. Sasaki, J. Chem. Inf. Comp. Sci., 1994, 34, 109.
R. Wang, Y. Gao, and L. Lai, Pers. Dr. Discov. Des., 2000, 19, 47.
R. Wang, Y. Gao, and L. Lai, J. Mol. Model., 2000, 6, 498.
C. A. Lipinski, F. Lombardo, B. W. Dominy, and P. J. Feeney, Adv. Drug Delivery Rev., 1997, 23, 23.
Quantum Chemistry Program Exchange (QCPE), Creative Arts Bldg. 181 Indiana University, Bloomington (IN 47405).
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, and N. S. Zefirov, Dokl. Akad. Nauk, 2003, 389, 123 [Dokl. Chem., 2003 (Engl. Transl.)].
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Tikhonova, I.G., Baskin, I.I., Palyulin, V.A. et al. Virtual screening of organic molecule databases. Design of focused libraries of potential ligands of NMDA and AMPA receptors. Russian Chemical Bulletin 53, 1335–1344 (2004). https://doi.org/10.1023/B:RUCB.0000042297.38213.6e
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DOI: https://doi.org/10.1023/B:RUCB.0000042297.38213.6e