Evaluation of various inverse docking schemes in multiple targets identification

作者: Liu Hui-fang , Shen Qing , Zhang Jian , Fu Wei

DOI: 10.1016/J.JMGM.2010.09.004

关键词:

摘要: The lack of accurate and efficient methods for target identification has been the bottleneck in drug discovery. In recent years, inverse docking applied as an method identification, several specific strategies have employed academic industrial researches. However, effectiveness these multiple targets is unclear. this study, five schemes were evaluated to find out most effective approach identification. A database containing a highly qualified dataset that composed 1714 entries from 1594 known covering 18 biochemical functions was collected testing pool docking. engines including GOLD, FlexX, Tarfisdock two in-house search TarSearch-X TarSearch-M by eight systems dataset. results show validation among schemes, GOLD also acceptable. Moreover, will be helpful predicting undesirable effects drugs, such toxicity.

参考文章(29)
Yataro Daigo, Toyomasa Katagiri, Yusuke Nakamura, Chie Suzuki, Takefumi Kikuchi, Identification of COX17 as a therapeutic target for non-small cell lung cancer Cancer Research. ,vol. 63, pp. 7038- 7041 ,(2003)
P. Bernard, C. Dufresne-Favetta, P. Favetta, Q.-T. Do, F. Himbert, S. Zubrzycki, T. Scior, C. Lugnier, Application of Drug Repositioning Strategy to TOFISOPAM Current Medicinal Chemistry. ,vol. 15, pp. 3196- 3203 ,(2008) , 10.2174/092986708786848488
Gaia V Paolini, Richard H B Shapland, Willem P van Hoorn, Jonathan S Mason, Andrew L Hopkins, Global mapping of pharmacological space Nature Biotechnology. ,vol. 24, pp. 805- 815 ,(2006) , 10.1038/NBT1228
Sonya M. Khersonsky, Da-Woon Jung, Tae-Wook Kang, Daniel P. Walsh, Ho-Sang Moon, Hakryul Jo, Eric M. Jacobson, Vivekananda Shetty, Thomas A. Neubert, Young-Tae Chang, Facilitated Forward Chemical Genetics Using a Tagged Triazine Library and Zebrafish Embryo Screening Journal of the American Chemical Society. ,vol. 125, pp. 11804- 11805 ,(2003) , 10.1021/JA035334D
David N. Howbrook, Anne M. van der Valk, Meg C. O'Shaughnessy, Dipak K. Sarker, Simon C. Baker, Andrew W. Lloyd, Developments in microarray technologies. Drug Discovery Today. ,vol. 8, pp. 642- 651 ,(2003) , 10.1016/S1359-6446(03)02773-9
Andrea Cavalli, Maria Laura Bolognesi, Anna Minarini, Michela Rosini, Vincenzo Tumiatti, Maurizio Recanatini, Carlo Melchiorre, Multi-Target-Directed Ligands To Combat Neurodegenerative Diseases Journal of Medicinal Chemistry. ,vol. 51, pp. 347- 372 ,(2008) , 10.1021/JM7009364
Holger Claussen, Marcus Gastreich, Volker Apelt, Jonathan Greene, Sally Hindle, Christian Lemmen, The FlexX database docking environment--rational extraction of receptor based pharmacophores. Current Drug Discovery Technologies. ,vol. 1, pp. 49- 60 ,(2004) , 10.2174/1570163043484815
Mahesh Kulharia, Roger S. Goody, Richard M. Jackson, Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein-Ligand Binding Affinity Journal of Chemical Information and Modeling. ,vol. 48, pp. 1990- 1998 ,(2008) , 10.1021/CI800125K
Jens Sadowski, Johann Gasteiger, Gerhard Klebe, Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures Journal of Chemical Information and Computer Sciences. ,vol. 34, pp. 1000- 1008 ,(1994) , 10.1021/CI00020A039
C. Ezerzer, M. Dolgin, J. Skovorodnikova, N. Harris, Chemokine receptor-derived peptides as multi-target drug leads for the treatment of inflammatory diseases. Peptides. ,vol. 30, pp. 1296- 1305 ,(2009) , 10.1016/J.PEPTIDES.2009.03.016