联用多步骤虚拟筛选方法发现具有新母核的GABAA受体正性变构调节剂  

Identification of Novel GABAA Receptor Positive Allosteric Modulators with Novel Scaffolds via Multistep Virtual Screening

作　　者：孔维恺忻 廉靖靖 彭超 朱杰 郑钰琳 黄巍然 张博文 段桂芳 马琳[2] 彭晓东[2] 马维宁[7] 朱素杰 黄卓[1,8] Weikaixin Kong;Jingjing Lian;Chao Peng;Jie Zhu;Yulin Zheng;Weiran Huang;Bowen Zhang;Guifang Duan;Lin Ma;Xiaodong Peng;Weining Ma;Sujie Zhu;Zhuo Huang(Department of Molecular and Cellular Pharmacology,School of Pharmaceutical Sciences,Peking University Health Science Center,Beijing 100191,China;School of Basic Medical Science,Ningxia Medical University,Yinchuan 750004,China;Institute for Molecular Medicine Finland(FIMM),University of Helsinki,Helsinki 00250,Finland;Institute Sanqu Technology(Hangzhou)Co.,Ltd.,Hangzhou 310012,China;Institute of Translational Medicine,The Affiliated Hospital of Qingdao University,Qingdao 266023,Shandong Province,China;ComMedX(Computational Medicine Beijing Co.,Ltd.),Beijing 100094,China;Department of Neurosurgery,Shengjing Hospital affiliated to China Medical University,Shenyang 110022,China;State Key Laboratory of Natural and Biomimetic Drugs,Peking University Health Science Center,Beijing 100191,China.)

机构地区：[1]北京大学医学部药学院分子与细胞药理学系,北京100191 [2]宁夏医科大学基础医学院,宁夏750004 [3]赫尔辛基大学分子医学研究所,芬兰赫尔辛基002504 [4]三驱科技(杭州)有限公司,杭州310012 [5]青岛大学附属医院转化医学研究所,山东青岛266023 [6]康迈迪森(北京)医药科技有限公司,北京100094 [7]中国医科大学附属盛京医院神经外科,沈阳110022 [8]北京大学医学部天然药物与仿生药物国家重点实验室,北京100191

出　　处：《物理化学学报》2024年第1期22-23,共2页Acta Physico-Chimica Sinica

基　　金：国家自然科学基金(81903539,32000674,82271498);北京大学肿瘤医院科学基金(JC202304);中国脑科学与类脑智能技术国家计划(2021ZD0202102);山东省高等学校青创团队计划(2022KJ145);宁夏回族自治区重点研发计划(2022BEG02042)资助。

摘　　要：GABAA受体主要介导哺乳动物中枢神经系统的抑制性信号传递,是镇静催眠药的关键靶点。在寻找具有新母核的镇静催眠药的过程中,计算机辅助药物设计(CADD)方法显示出巨大的优势。在这项研究中,首先,我们通过机器学习模型、分子对接模型和分子力学广义玻恩比表面积(MMGBSA)方法筛选了来自于商业数据库中的41112种化合物。经过筛选,我们得到了16个化合物,然后我们通过全细胞膜片钳电生理学实验验证了4个结构新颖的化合物确实为有效的GABAA受体正性变构调节剂。其中,化合物GPR120在细胞水平和动物水平都得到了实验验证。在重组表达α1β2γ2型受体的皮层神经元中,在10和50µmol∙L^(−1)浓度下,GPR120可将GABA EC3-10电流分别增强71.5%和163.8%。通过全分解贡献分析和点突变实验,我们发现GPR120与GABAA受体结合的关键位点是H102,与阳性药物地西泮相似。为了进一步验证GPR120在动物水平上的功能,我们进行了运动活动测试和翻正反射消失(LORR)实验。GPR120对小鼠的运动活动有抑制作用,6 h后可恢复,说明GPR120是一种中度镇静剂。在戊巴比妥钠(PB)诱导的翻正反射消失实验中,与生理盐水组相比,GPR120(20 mg∙kg^(−1))可显著缩短开始LORR的时间并延长LORR的持续时间。综上所述,通过联用多种虚拟筛选方法,我们发现了GPR120是一种具有新型母核的中度强度镇静剂。The GABAA receptor mainly mediates inhibitory signal transmission in mammalian central nervous systems and is the key target of sedative-hypnotics.However,the long-term use of sedativehypnotics often leads to drug resistance,necessitating the development of novel sedative-hypnotics.This development can be achieved with novel scaffolds designed via the computer-aided drug design methods to obtain significant advantages.In this study,robust virtual screening models were established by identifying effective positive allosteric modulators of the GABAA receptor from ChEMBL and BindingDB databases.These compounds combined with randomly extracted negative compounds were firstly applied for a 10-fold cross validation and grid search to establish machine learning models which were subsequently evaluated in an independent test set.In this step,4 machine learning methods and 6 fingerprints were used to establish 24 models.In the test set,the CDK_LR model performed the best(MCC=0.751)and was used for subsequent virtual screening.Two effective molecular docking models were also established based on conformation 6D6T and 6D6U,wherein the root mean square deviation(RMSD)values of redocking experiments were 1.141 and 1.505Å(1Å=0.1 nm),respectively.During the virtual screening,41112 compounds from a commercial database were scanned by machine learning,molecular docking,and molecular mechanics-generalized Born surface area models.After the screening,16 hits were obtained,4 of which were structurally novel positive hits verified by whole-cell patch-clamp electrophysiology experiments.The compound GPR120 was verified experimentally at both the cell and animal levels.In cortical neurons recombinantly expressingα1β2γ2-type receptors,at 10 and 50µmol∙L^(−1),GPR120 could potentiate GABA EC3-10 current by 71.5%and 163.8%,respectively.Total decomposition contribution analysis and point mutation experiment showed that the key binding site between GPR120 and the GABAA receptor is H102,similar to that of the positive drug Diazepam.

关 键 词：机器学习 离子通道 分子对接 虚拟筛选 GABAA受体 

分 类 号：O641[理学—物理化学]