基于MOE软件的虚拟仿真实验*——多奈哌齐与乙酰胆碱酯酶的分子对接

基于MOE软件设计了多奈哌齐与乙酰胆碱酯酶的分子对接虚拟仿真实验。通过分子结构预处理、分子对接以及数据分析等内容,帮助学生掌握分子对接的基本技能,深入理解立体化学结构对药物-靶分子相互作用的影响。本实验可以作为药物化学、生物化学等基础课的扩展内容,提高学生研究式学习的兴趣和能力。     

分子对接在药物虚拟筛选中的应用进展

虚拟筛选是药物设计的重要手段之一,利用小分子化合物与药物靶标间的分子对接运算,研究人员可以准确地获取两者之间的相互作用情况,从候选化合物库中快速筛选出潜在的药物或药物前体,从而加速药物开发过程。介绍了虚拟筛选与分子对接的相关原理与流程,主要综述了对药物进行虚拟筛选时所涉及的分子对接技术类型、常见的分子对接软件以及分子对接典型样例。分子对接对提高虚拟筛选的效率、降低药物开发的成本具有重要的现实意义。     

分子对接方法的应用与发展

分子对接方法加快了药物开发周期,具有快速、准确度高等优点.本文详述了分子对接方法的基本原理,及分子对接空间和能量的匹配要求和优化时的各种方法.综述了该方法在药物设计、药理分析和探测生命体系等方面的应用.     

吲哚衍生物类VEGFR-2酪氨酸激酶抑制剂的从头设计

以血管内皮生长因子受体-2(VEGFR-2)酪氨酸激酶的晶体结构为基础, 采用从头药物设计方法, 设计了一系列吲哚类化合物, 并用类药性和分子对接进行了筛选, 最后得到10个对接能量较低的化合物分子, 对具有最低结合能的化合物与VEGFR-2酪氨酸激酶的复合物进行了10 ns的分子动力学模拟, 并对其结合模式进行了分析. 这些化合物结构新颖, 可能作为抗肿瘤的先导化合物或候选药物. 本文结果为VEGFR-2酪氨酸激酶抑制剂的进一步改造、 设计及合成提供了理论基础, 并有助于开发高活性和高选择性的抗肿瘤药物.     

基于计算机模拟技术对JAK2抑制剂的定量构效关系、分子设计和分子动力学研究

本文选取了52个对Janus激酶2(JAK2)有抑制作用的小分子化合物,分别使用3D-QSAR中的CoMFA和CoMSIA方法构建了两个可靠的、具有预测能力的模型,并利用分子对接分析数据集化合物与JAK2蛋白的相互作用,表明化合物主要通过氢键和范德华作用与JAK2靶蛋白结合。根据3D-QSAR模型的分析结果,设计了40个化合物,利用构建的模型预测其抑制活性;使用软件预测了化合物的药代动力学(ADME)参数,开展分子对接模拟,最终选择化合物D01和D22与JAK2靶蛋白进行了分子动力学模拟研究,结果显示两个复合物结合构象稳定,与分子对接结果趋势一致。本研究的结果可以为JAK2抑制剂的研发提供一些新的思路,为临床开发此类药物提供理论支撑。     

人血白蛋白结合位点II的分子结合模式研究

人血白蛋白是血浆中含量最高的蛋白,是一种重要的载体蛋白,能与多种内源性和外源性物质结合。人血白蛋白主要有两个药物结合位点,位点I和位点II,其中位点II的柔性较大,对药物分子的亲和性较高。本文采用分子模拟方法,基于12种结合于位点II的小分子-人血白蛋白晶体结构,分析了相互作用能,发现12种分子的结合以疏水作用为主,静电作用为辅。进一步采用丙氨酸扫描和结合能评价,分析结合部位的关键氨基酸残基,探究结合模式的规律性,发现从位点入口到空腔内部存在静电、疏水和杂合的三层相互作用分布,共同形成了稳定的分子结合。最后采用分子对接和分子动力学模拟,预测了L-色氨酸的结合模式。研究结果有助于深入了解人血白蛋白药物位点II的小分子结合模式,为基于位点II的药物和分离配基的优化设计提供指导。     

MOE软件在分子对接教学中的应用*

主要介绍MOE软件在分子对接教学中的应用。详细介绍了MOE用于分子对接的使用流程,并分析了对接的可靠性及小分子与蛋白的连接情况,为后续药物的设计提供参考。本案例既可以用于理论教学也可以设计成计算机辅助药物设计上机实验,增强了学生的学习兴趣,降低了教学的难度,也为涉及到分子对接的大学生创新创业项目提供方法。     

计算机化学模拟—分子构象识别的新方法

简介了几种利用计算机图形技术研究化合物分子构象的新方法。重点介绍了分子力学计算方法中的系统搜索、随机搜索方法和分子动力学计算方法中的模拟淬火、模拟退火等新技术 ,为药物分子设计中受体与配体分子构象的识别提供了合理可行的方法。     

5'-羟基-2,2',4,4',5-五溴二苯醚与人血清白蛋白结合特征研究

在模拟生理环境下,通过稳态荧光光谱、时间分辨荧光光谱、傅立叶变换红外光谱和三维荧光光谱等方法研究了5'-羟基-2,2',4,4',5-五溴二苯醚(5'-OH-BDE-99)与人血清白蛋白的结合特征,并结合分子对接与分子动力学模拟技术对其作用机制进行了分析。荧光光谱实验、非辐射能量转移理论及动力学模拟研究表明,5'-OH-BDE-99能使HSA发生猝灭作用,且猝灭机制为静态猝灭。傅立叶变换红外光谱、三维荧光光谱及动力学模拟研究表明,5'-OH-BDE-99可诱导HSA构象和周围环境发生变化。此外,分子对接和热力学方法研究表明,二者间的主要作用力为疏水作用力。     

遗传算法在计算机辅助药物分子设计中的应用

作为一种重要的启发式优化算法,遗传算法在计算机辅助药物分子设计中得到了广泛的应用.本文介绍了遗传算法的基本概念以及工作原理,同时结合作者科研组的工作,就遗传算法在定量构效关系、构象分析、药效团模拟、分子对接以及虚拟组合化学等方面的应用做了系统的阐述。     

分子对接和动力学模拟提高嗜热蛋白酶PhpI的活力

通过分子对接和动力学模拟对嗜热蛋白酶的分子进行改造, 确定蛋白酶PH1704(PhpI)定点突变残基, 并通过分子生物学实验进行验证. 突变体K43C的蛋白酶活力提高了5.8倍. 分子动力学模拟结果表明, 经过8 ns的动力学模拟后, K43C突变体二级结构由野生型的S2片层(F11-E12-D13)变成环状结构. E12和K43均是活性位点的重要残基, 这种变化将导致活性位点的柔性增强, 有利于催化反应的发生.     

含磷嘧啶类CDK9抑制剂的分子对接、3D-QSAR和分子动力学模拟

选取64个具有潜力的含磷嘧啶类细胞周期依赖性蛋白激酶(CDK9)小分子抑制剂,采用分子对接方法研究了该类小分子与CDK9的结合作用,结果表明,分子构象、氢键形成、疏水性和氨基酸残基Cys106在此类抑制剂与CDK9的结合过程中具有重要作用.在配体叠合的基础上,运用比较分子力场分析(Co MFA)、比较分子相似性指数分析(Co MSIA)和Topomer Co MFA(T-COMFA)研究了分子结构与抑制活性的关系,发现由训练集立体场、静电场和疏水场组合的Co MSIA模型为最优模型,其内部交叉验证相关系数(Q2=0.557)、非交叉验证相关系数(R2=0.959)和外部预测相关系数(r2=0.863)具有统计学意义,该模型的三维等值线图直观显示了化合物的活性与其三维结构的关系.根据这些结果设计了10个具有新结构的含磷嘧啶类化合物,分子对接和分子动力学模拟结果表明,新化合物和CDK9的结合模式与原化合物64相同,自由能分析从理论上证明了新化合物64d的CDK9抑制活性优于化合物64,并且显示含磷基团与残基Asp109的静电场能在化合物与CDK9作用过程中有重要作用.     

A molecular docking study of potential inhibitors and repurposed drugs against SARS-CoV-2 main protease enzyme

COVID-19 has affected millions of people. Although many drugs are in use to combat disease, there is not any sufficient treatment yet. Having critical role in propagation of the novel coronavirus (SARS-CoV-2) works Main Protease up into a significant drug target. We have performed a molecular docking study to define possible inhibitor candidates against SARS-CoV-2 Main Protease enzyme. Besides docking Remdesivir, Ribavirin, Chloroquine and 28 other antiviral inhibitors (totally 31 inhibitors) to Main Protease enzyme, we have also performed a molecular docking study of 2177 ligands, which are used against Main Protease for the first time by using molecular docking program Autodock4. All ligands were successfully docked into Main Protease enzyme binding site. Among all ligands, EY16 coded ligand which previously used as EBNA1-DNA binding blocker candidate showed the best score for Main Protease with a binding free energy of −10.83 ​kcal/mol which was also lower than re-docking score of N3 ligand (−10.72 ​kcal/mol) contained in crystal structure of Main Protease. After analyzing the docking modes and docking scores we have found that our ligands have better binding free energy values than the inhibitors in use of treatment. We believe that further studies such as molecular dynamics or Molecular Mechanic Poisson Boltzmann Surface Area studies can make contribution that is more exhaustive to the docking results.     

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation

Developing chemicals that inhibit checkpoint kinase 1 (Chk1) is a promising adjuvant therapeutic to improve the efficacy and selectivity of DNA-targeting agents. Reliable prediction of binding-free energy and binding affinity of Chk1 inhibitors can provide a guide for rational drug design. In this study, multiple docking strategies and Prime/Molecular Mechanics Generalized Born Surface Area (Prime/MM-GBSA) calculation were applied to predict the binding mode and free energy for a series of benzoisoquinolinones as Chk1 inhibitors. Reliable docking results were obtained using induced-fit docking and quantum mechanics/molecular mechanics (QM/MM) docking, which showed superior performance on both ligand binding pose and docking score accuracy to the rigid-receptor docking. Then, the Prime/MM-GBSA method based on the docking complex was used to predict the binding-free energy. The combined use of QM/MM docking and Prime/MM-GBSA method could give a high correlation between the predicted binding-free energy and experimentally determined pIC(50) . The molecular docking combined with Prime/MM-GBSA simulation can not only be used to rapidly and accurately predict the binding-free energy of novel Chk1 inhibitors but also provide a novel strategy for lead discovery and optimization targeting Chk1.     

Exploring a model of a chemokine receptor/ligand complex in an explicit membrane environment by molecular dynamics simulation: the human CCR1 receptor

The seven transmembrane helices G-protein-coupled receptors (GPCRs) form one of the largest superfamilies of signaling proteins found in humans. Homology modeling, molecular docking, and molecular dynamics (MD) simulation were carried out to construct a reliable model for CCR1 as one of the GPCRs and to explore the structural features and the binding mechanism of BX471 as one of the most potent CCR1 inhibitors. In this study, BX471 has been docked into the active site of the CCR1 protein. After docking, one 20 ns MD simulation was performed on the CCR1-ligand complex to explore effects of the presence of lipid membrane in the vicinity of the CCR1-ligand complex. At the end of the MD simulation, a change in the position and orientation of the ligand in the binding site was observed. This important observation indicated that the application of MD simulation after docking of ligands is useful. Explorative runs of molecular dynamics simulation on the receptor-ligand complex revealed that except for Phe85, Phe112, Tyr113, and Ile259, the rest of the residues in the active site determined by docking are changed. The results obtained are in good agreement with most of the experimental data reported by others. Our results show that molecular modeling and rational drug design for chemokine targets is a possible approach.     

Design,synthesis and MAO inhibitory activity of 2-(arylmethylidene)-2,3-dihydro-1-benzofuran-3-one derivatives

A series of 2-(arylmethylidene)-2,3-dihydro-1-benzofuran-3-one derivatives(aurones, 1–20) were synthesized and screened for their inhibitory activity against h MAO. Seventeen compounds(1–5, 7–17,19) were found to be selective towards h MAO-B, while two were non-selective(6 and 20) and one(18)selective towards h MAO-A. Compound 17(Ki = 0.10 0.01 mmol/L) was found to be equally potent and selective towards h MAO-B, when compared with the standard drug Selegiline(Ki = 0.12 0.01 mmol/L).Nature and position of substitution in aryl ring at 2nd position of benzofuranone influences h MAO-B inhibitory potency, while their structural bulkiness influences selectivity between h MAO-A and h MAO-B.Molecular docking simulation was also carried out to understand the interaction of inhibitor with the enzyme at molecular level, and we found the docking results were in good agreement with the experimental values. Comparison of the activity profile of the aurones with their corresponding flavones reported earlier by our group revealed that there exists no difference in potency as well as selectivity.     

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

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.     

Binding conformation of 2-oxoamide inhibitors to group IVA cytosolic phospholipase A2 determined by molecular docking combined with molecular dynamics

The group IVA cytosolic phospholipase A(2) (GIVA cPLA(2)) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA(2) inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA(2) active site through a combination of molecular docking calculations and molecular dynamics simulations. Recently, the location of the 2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA(2) was determined using a combination of deuterium exchange mass spectrometry followed by molecular dynamics simulations. After the optimization of the AX007-GIVA cPLA(2) complex using the docking algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors have been docked in the enzyme active site. The calculated binding affinity presents a good statistical correlation with the experimental inhibitory activity (r(2) = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the design of new compounds with improved inhibitory activity against GIVA cPLA(2).     

噻吩并嘧啶类FLT3抑制剂结合模式预测与分析

FLT3(FMS样酪氨酸酶III)是酪氨酸激酶受体(RTKIII)成员之一,其异常超表达或突变与急性髓细胞白血病(AML)呈现非常大的相关性,成为治疗AML的重要靶位点。本文采用不同的方法对FLT3活性位点进行了预测,利用分子对接、分子动力学以及药效团分析研究了新型嘧啶类化合物与FLT3的相互作用与结合模式。分子对接得到的结合模式与分子动力学模拟得到的结果一致,结合药效团分析表明该嘧啶类化合物主要通过疏水相互作用和氢键与FLT3激活位点结合,从而起到抑制作用。本研究对以FLT3为靶点的嘧啶类抑制剂的开发提供了理论和实验依据。