Study on the binding mode of the integrase with DNA via steered molecular dynamics simulation.
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. In the current work, a model for the active site of IN and viral DNA was built by combining experimental data with the results of steered molecular dynamics simulation. The model was then taken into a series automatic molecular docking calculations with two groups of inhibitors. According to the results of molecular docking, the inhibitors of the second group share a similar binding model with those of the first group, though they have no common scaffold. The newly built model of the IN-DNA complex is helpful for our subsequent research on the design of IN inhibitors.
Wang
Cun Xin
CX
College of Life Science and Bioengineering, Beijing University of Technology, China. cxwang@bjut.edu.cn
Liu
Ming
M
Li
Ping
P
Cong
Xiao Jing
XJ
Tan
Jian Jun
JJ
Chen
Wei Zu
WZ
D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D019427:HIV Integrase / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055672:Static Electricity
D004247:DNA; D019427:HIV Integrase