In silico binding free energy predictability with 蟺-蟺 interaction energy-augmented scoring function: Benzimidazole Raf inhibitors as a case study

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• 作者：Jae Yoon Chung^a ; ^b ; Seung Joo Cho^c ; Art E. Cho^b ; ^{artcho@korea.ac.kr} ; Jung-Mi Hah^a ; ^{jhah@hanyang.ac.kr}
• 关键词：蟺&ndash ; 蟺 interaction ; Scoring function ; LMP2 calculation ; 3D-QSAR ; Ring groups ; Active site
• 刊名：Bioorganic and Medicinal Chemistry Letters
• 出版年：2012
• 期刊代码：10_0960894x
• 类别：ch
• 出版时间：1 May, 2012
• 卷：22
• 期：9
• 页码：3278-3283
• 文件大小：841 K

摘要

The ability to estimate binding affinities of ligands precisely is of paramount importance in designing drugs. Docking programs are used primarily to predict the binding mode of ligands to receptors. However, current scoring functions as used in docking programs are not reliable enough to predict binding affinities of ligands without any further calculations. In the present study, we investigate the usefulness of adding 蟺-蟺 interaction energies between ring groups of residues and ligands to the scoring function for docking. It is found that such addition helps ranking ligand activities more correctly. LMP2 calculation is used to measure 蟺-蟺 interaction energies between ring groups. The result of this simple addition shows possibility of 蟺-蟺 interaction generalization in scoring functions.