分子对接技术筛选抗HIV-1逆转录酶活性化合物

摘要

Objective To screen the non-nucleoside compounds against HIV-1 reverse transcriptase by molecular modeling and bioactivity assay. Methods Surflex-Dock module of Tripos SYBYL software was used to simulate the binding pattern of 22 000 compounds in SPECS database with the active pocket of HIV-1 reverse transcriptase. Based on the simulation results, the interaction mode between the above compounds and the crystal structure of HIV-1 reverse transcriptase was analyzed. The compounds with higher docking scores and better binding pattern were determined by anti-HIV-1 ac tivities test in vitro. Results The virtual screening results showed that the docking conformation of 1- (4-fluorophenyl) -3- [2- (1H-indol-3-yl) ethyl] thiourea was similar to the embedded ligand in Rilpivirine crystal structure. 1- ( 4-fluorophenyl) -3- [ 2- ( 1H-indol-3-yl) ethyl] thiourea was held together with the key residue Lys101 in docking pocket of HIV-1 reverse transcriptase by hydrogen bonds, and hadπ-πstacking action together with the conservative residue Trp229 and the aromatic residue Tyr181 respectively. The bioassay in vitro results showed that when the proliferation rate of C8166 lymphocyte syncytium infected by HIV-1ⅢB arrived 50% ( EC50) , the concentration of 1- ( 4-fluorophenyl) -3- [ 2- ( 1H-indol-3-yl) ethyl] thiourea was 5.45μg/mL. Conclusion Molecule docking technology is an effective approach to reducing the screening of candidate compounds with micromolecular activity, and can be used to predict the interaction mode between the compound and the target receptor. In the study, active compound 1- (4-fluorophenyl) -3- [2- (1H-indol-3-yl) ethyl] thiourea has been screened out by molecule docking technology.%【目的】通过分子模拟和活性测试筛选非核苷类抗人类免疫缺陷病毒-1（HIV-1）逆转录酶活性化合物。【方法】采用Tripos SYBYL软件Surflex-Dock分子对接模块，模拟SPECS数据库中22000个化合物与HIV-1逆转录酶活性口袋的结合，根据模拟结果分析化合物与HIV-1逆转录酶晶体结构的相互作用模式。对于打分较高与结合模式较优的化合物，采用体外抗HIV-1活性测试方法检测其生物活性。【结果】虚拟筛选结果显示化合物1-（4-fluorophenyl）-3-[2-（1H-indol-3-yl） ethyl] thiourea对接构象与晶体结构中内嵌配体非常接近，它与HIV-1逆转录酶结合口袋重要残基Lys101形成氢键、与保守残基Trp229和芳香残基Tyr181分别形成π-π堆积作用。体外抗HIV-1活性测试结果显示其抑制HIV-1I IB病毒感染的C8166淋巴细胞合胞体形成50%时的浓度即EC50值为5.45μg/mL。【结论】分子对接技术能缩小活性化合物筛选范围，并可用于预测化合物与蛋白质的相互作用模式，本研究利用该技术筛选出活性化合物。