摘要
In order to analyze and explain the mechanism of the two small inhibitors （ADS-JI and ADS-J2） binding to HIV-1 gp41, a computational study is carried out to help identifying possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and characterize structures of binding complexes. The binding interactions of gp41-molecule and free energies of binding are obtained through molecular dynamics simulation and molecular mechanic/Poisson- Boitzmann surface area （ MM/PBSA ） calculation. Specific molecular interactions in the gp41-inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point tbr further refinement of small molecular gp41 inhibitors.
为分析和解释2个小分子抑制剂ADS-J1和ADS-J2与艾滋病病毒蛋白gp41的抑制机理,通过采用理论计算的方式把抑制剂和gp41蛋白疏水性空穴对接,得到了可能的结合方式,并通过采用分子动力学和MM/PBSA相结合的方法,确定蛋白质和抑制剂的具体结合方式和结合自由能,并且获得了抑制剂和蛋白的精确结合构型和相互作用力,明确了抑制剂和蛋白质之间的抑制机理.理论研究证实了相关实验的推测,并且为以后设计新型的gp41小分子抑制剂提供了良好的基础.
基金
The National Basic Research Program of China (973 Program) (No. 2007CB936300)
