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Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

science china Chemistry 2007年第5期50卷 665-674页

作者： hu jianping1,2, chang shan1, chen weizu1 & wang cunxin1 1 college of life science and bioengineering, beijing university of technology, beijing 100022, china 2 Department of Chemistry & life sciences, Leshan Normal university, Leshan 614004, china college of life science and bioengineering Beijing University ofTechnologyBeijing 100022China Department of Chemistry & life sciences Leshan NormalUniversityLeshan 614004China

human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

关键词： molecular docking, MD simulation, HIV-1 IN, drug design

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A holistic molecular docking approach for predicting protein-protein complex structure

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science china(life sciences) 2010年第9期53卷 1152-1161页

作者： GONG XinQi LIU Bin chang shan LI Chunhua chen weizu wang cunxin college of life science and bioengineering Beijing University of TechnologyBeijing 100124China

A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure *** article explains the detailed steps and applications for CAPRI Target *** CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

关键词： protein-protein complex structure prediction binding site molecular docking CAPRI

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