人类丝氨酸消旋酶的同源模建及其与多肽类抑制剂的分子对接

利用同源模建和分子动力学模拟方法构建了人类丝氨酸消旋酶(hSR)的三维结构, 并利用profile-3D和procheck方法评估了模型的可靠性. 在此基础上用分子对接程序(affinity)将多肽类抑制剂A和B分别与hSR进行对接, 获得了其复合物结构的理论模型. 通过配体与受体之间相互作用能和结构分析给出了此类抑制剂与hSR的具体结合方式, 明确了hSR与此类抑制剂结合时起重要作用的氨基酸残基, 为基于人类丝氨酸消旋酶三维结构的药物设计提供重要的参考信息.     

毒蕈碱型M1受体的同源模建和分子对接

采用同源模建方法对M1受体的三维结构进行了模拟,将得到的模型分别与M受体完全激动剂乙酰胆碱和M1受体选择性激动剂占诺美林进行分子对接,形成非特异性激动和特异性激动的受体-配体复合物.用分子动力学模拟方法分别将未与小分子对接的M1受体、M1受体-乙酰且H碱复合物、M1受体-占诺美林复合物置于磷脂双膜中模拟10 ns.将模拟后的蛋白质结构与包含活性分子的测试库对接并将结果打分,以top5%富集因子(EF)作为评价依据,用占诺美林优化后的M1受体模型的EF为8.0,用乙酰胆碱优化后M1受体模型的EF为6.5,非复合物的EF为1.5.说明M1受体选择性激动剂复合物进行分子动力学模拟后得到的三维结构模型比较合理,可以作为化合物虚拟筛选的模型对新化合物进行虚拟筛选,为找到新的选择性M1受体激动剂奠定了基础.     

鲍曼不动杆菌abaI基因的克隆表达分析、同源建模及分子对接分析

高丝氨酸内脂合成酶(homoserine lactone synthase, abaI)是导致鲍曼不动杆菌生物被膜形成的关键酶之一,对其结构功能的研究有助于我们对抑制生物被膜形成有很大帮助。本研究通过Genebank查找abaI(A1S＿0109)蛋白序列,运用分子技术对其进行表达分析,应用生物分析软件ExPASy、ESPript、MEG5.0、SWISS-MODEL等对其进行结构分析,使用分子对接软件分析抑制剂的关键结合位点。结果显示,在含有pET28a-abaI重组质粒BL21菌株与野生BL21菌株相比生物被膜形成能力以及运动性显著增高。从生成生物膜被膜的定义上,BL21从不产生物被膜菌株,变成了产膜菌株。预测其结构蛋白与TofI蛋白高度相似,通过分子对接首次揭示abaI蛋白抑制剂与abaI蛋白相互作用关系。研究结果显示abaI在BL21中能够促使生物被膜的形成和增强细菌的运动,分子对接揭示了abaI蛋白的相互作用位点,为进一步研究其活性以及抑制剂提供了重要的参考信息。     

毒蕈碱型M1受体的同源模建和分子对接

采用同源模建方法对M1受体的三维结构进行了模拟, 将得到的模型分别与M受体完全激动剂乙酰胆碱和M1受体选择性激动剂占诺美林进行分子对接, 形成非特异性激动和特异性激动的受体-配体复合物. 用分子动力学模拟方法分别将未与小分子对接的M1受体、M1受体-乙酰胆碱复合物、M1受体-占诺美林复合物置于磷脂双膜中模拟10 ns. 将模拟后的蛋白质结构与包含活性分子的测试库对接并将结果打分, 以top5%富集因子(EF)作为评价依据, 用占诺美林优化后的M1受体模型的EF为8.0, 用乙酰胆碱优化后M1受体模型的EF为6.5, 非复合物的EF为1.5. 说明M1受体选择性激动剂复合物进行分子动力学模拟后得到的三维结构模型比较合理, 可以作为化合物虚拟筛选的模型对新化合物进行虚拟筛选, 为找到新的选择性M1受体激动剂奠定了基础.     

趋化因子CCR2的同源模建,分子对接和3D-QSAR研究

趋化因子CCR2参与炎症反应、免疫移植排斥和肿瘤的发生,已成为新的研究热点。本文以CCR5的晶体结构为模板,同源模建CCR2的结构,并用CCR2小分子抑制剂与其进行分子对接以得到小分子的最优构象。在对接叠合的基础上建立了QSAR模型,采用比较分子场分析(Co MFA)以及比较分子相似性分析(Co MSIA)研究得到Co MFA和Co MSIA模型最佳评价参数分别为q2=0.743,r2=0.968和q2=0.68,r2=0.978。3D-QSAR模型的等势图分析表明,改造配体R3基团可提高化合物活性。所建模型稳定性好、预测性强,对基于CCR2的小分子抑制剂的设计、优化和改造提供了参考。     

α1A-肾上腺素受体的同源模建及其对接研究

以β2肾上腺素受体(β2-AR)为模板,采用同源模建和分子动力学模拟构建了人类α1A-肾上腺素受体(α1A-AR)的三维结构模型,并利用PROCHECK,PROSA和WHAT-IF评估了模型的合理性.所得的结构采用分子对接程序Flexidock与激动剂去甲肾上腺素和拮抗剂西罗多辛分别进行对接,结果表明,2种配基具有相似...     

乙型肝炎病毒表面抗原三维结构的同源模建及功能预测

结合生物信息学方法及分子模拟手段, 通过同源模建方法构建了乙型肝炎病毒表面抗原(HBsAg)Pres12的三维空间结构, 并结合生物实验在分子水平上探讨了乙型肝炎病毒表面抗原Pres12作为抗乙型肝炎病毒重要靶标的机理. 研究结果表明, HBsAg三维空间结构是由构型性的Pres1和线性的Pres2组成, 此结构由疏水氨基酸形成3个α-螺旋结构及Loop结构域, 并且N端由Pres1中残基构成了一个开裂, 形成了HBsAg可能的活性部位. 静电势分析结果证实, N端可能的活性部位具有较大的静电势分布, 因而具有与受体细胞蛋白相互作用的能力, 这为HBV病毒抑制剂药物分子的设计提供了有益帮助.     

同源模建和分子对接研究HDAC1/HDAC8的选择性

组蛋白去乙酰化酶(HDACs)是近年来治疗肿瘤的重要靶标之一.由于HDACs包含多种亚型,且各亚型的生理功能存在一定的差异,其选择性抑制剂的开发已成为当前的研发热点.我们通过同源模建的HDAC1结构,与已有的HDAC8晶体结构的活性位点进行比较分析,探讨了对两者选择性有重要影响的残基,为基于受体的选择性抑制剂研究提供重要信息.同时选择了52个HDAC抑制剂,分别建立了HDAC1、HDAC8的活性值与对接打分值的线性回归模型.所建的HDAC1和HDAC8的线性构效关系模型的非交叉验证系数R2分别为0.82和0.80,表明具有一定的统计学意义.利用所建模型对已设计合成的化合物进行了预测,预测结果对HDAC1、HDAC8选择性抑制剂的优化改造提供了一定的指导意义.     

大麻素受体CB1三维结构的同源模建及其对接研究

大麻素CB1受体属于G蛋白偶联受体. 以牛视紫红质的晶体结构为模板, 利用同源模建法对CB1受体的三维结构进行了模拟, 并采用分子动力学方法对模型进行了修正和优化. 在此基础上, 分析了活性位点的组成和结构, 研究了拮抗剂利莫那班与CB1受体的对接, 明确了CB1受体与利莫那班结合时起重要作用的氨基酸残基. 发现利莫那班与CB1受体残基Lys192形成氢键相互作用是CB1受体拮抗剂的重要分子作用基础.     

MMP-26的同源模建及S_1'结合袋的结构特点

以基质金属蛋白酶-12(MMP-12)的晶体结构为模板,采用同源模建方法构建了基质金属蛋白酶-26(MMP-26)的三维结构,并阐明了其S1'结合袋的结构特点,MMP-26中His233残基插入S1'结合袋,限制了S1'结合袋的深度,符合中袋MMPs的特点,因此MMP-26属于中袋MMPs.在此基础上,研究了抑制剂GM6001与MMP-26的相互作用模式,发现GM6001中异羟肟酸结构的羰基氧和羟基氧与催化锌离子发生双齿配位,符合异羟肟酸类MMPs抑制剂的配位特点.     

Furcatin 水解酶的三维结构模建和与furcatin 的对接研究

利用同源模建和动力学模拟方法，模建了furcatin水解酶（FH）的三维结构．并在这基础上，分析了活性位点的组成和结构．研究了furcatin与FH的对接．结果表明，Ser84，Arg146，Thr189，Thr234和Gly372在复合物的形成过程中起重要的作用．其中，Ser84，Argl46和Thr189是在FH的活性口袋的二糖部分的亚单位一1中重要的氨基酸，Thr234和Gly372是亚单位-2中重要的氨基酸．     

Identification of novel Plasmodium falciparum PI4KB inhibitors as potential anti-malarial drugs: Homology modeling,molecular docking and molecular dynamics simulations

The current study was set to discover selective Plasmodium falciparum phosphatidylinositol-4-OH kinase type III beta (pfPI4KB) inhibitors as potential antimalarial agents using combined structure-based and ligand-based drug discovery approach. A comparative model of pfPI4KB was first constructed and validated using molecular docking techniques. Performance of Autodock4.2 and Vina4 software in predicting the inhibitor-PI4KB binding mode and energy was assessed based on two Test Sets: Test Set I contained five ligands with resolved crystal structures with PI4KB, while Test Set II considered eleven compounds with known IC50 value towards PI4KB. The outperformance of Autodock as compared to Vina was reported, giving a correlation coefficient (R²) value of 0.87 and 0.90 for Test Set I and Test Set II, respectively. Pharmacophore-based screening was then conducted to identify drug-like molecules from ZINC database with physicochemical similarity to two potent pfPI4KB inhibitors –namely cpa and cpb. For each query inhibitor, the best 1000 hits in terms of TanimotoCombo scores were selected and subjected to molecular docking and molecular dynamics (MD) calculations. Binding energy was then estimated using molecular mechanics–generalized Born surface area (MM-GBSA) approach over 50 ns MD simulations of the inhibitor-pfPI4KB complexes. According to the calculated MM-GBSA binding energies, ZINC78988474 and ZINC20564116 were identified as potent pfPI4KB inhibitors with binding energies better than those of cpa and cpb, with ΔG_binding ≥ −34.56 kcal/mol. The inhibitor-pfPI4KB interaction and stability were examined over 50 ns MD simulation; as well the selectivity of the identified inhibitors towards pfPI4KB over PI4KB was reported.     

Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies

The homology modeling technique has been used to construct the structure of enterovirus 71 (EV 71) capsid protein VP1. The protein is consisted of 297 amino acid residues and treated as the target. The amino acid sequence identity between the target protein and sequences of template proteins 1EAH, 1PIV, and 1D4M searched from NCBI protein BLAST and WorkBench protein tools were 38, 37, and 36%, respectively. Based on these template structures, the protein model was constructed by using the InsightII/Homology program. The protein model was briefly refined by energy minimization and molecular dynamics (MD) simulation steps. The protein model was validated using some web available servers such as ERRAT, PROCHECK, PROVE, and PROSA2003. However, an inconsistency between the docking scores and the measured activity was observed for a series of EV 71 VP1 inhibitors synthesized by Shia et al. (J Med Chem 2002, 45, 1644) and docked into the binding pocket of the protein model using the DOCK 4.0.2 program. The protein model with an EV 71 VP1 inhibitor docked and engulfed was then refined further by some MD simulation steps in the presence of water molecules. The docking scores obtained for these inhibitors after such a MD refinement were well correlated with the activities. The structure-activity relationships for the ligand-protein model system was also analyzed using the GRID-VOLSURF programs and the corresponding noncrossvalidated and crossvalidated (by leave-one-out) r2 and q2 were 0.99 and 0.61, respectively. The hydrophobic nature of the binding pocket of the protein model was also examined using the GRID21 program. The possibility of improving the potency of the current series of EV 71 VP1 inhibitors was discussed based on all the studies presented.     

人类胞外信号调节激酶1的同源模建及其抑制剂的对接与结构改造

通过同源模建和分子动力学模拟构建了人类胞外信号调节激酶1(hERK1)的三维结构,并利用profile-3D和procheck方法评估了模型的合理性.对所得的结构使用分子对接程序Affinity和CDOCKER进行了两种抑制剂的对接.结果显示这两种抑制剂与酶的结合方式相似,它们均与残基K36,Q87之间存在氢键作用,二者取代基的不同导致了抑制能力的差别.基于对接结果分析,对已知抑制剂进行结构改造,得到了一个理论上结合能力更强的抑制剂.它在保持与K36和Q87之间氢键的同时,又与残基D93,K96,S135形成了四条氢键,显著提高了与酶的相互作用.对接相互作用能显著下降,MM-PBSA结合自由能降为负值,这些均体现了抑制能力的提高.本工作对于针对该酶的抑制剂设计和相关疾病的新药开发具有理论指导价值.     

Homology modeling,force field design,and free energy simulation studies to optimize the activities of histone deacetylase inhibitors

As an effort to develop therapeutics for cancer treatments, a number of effective histone deacetylase inhibitors with structural diversity have been discovered. To gain insight into optimizing the activity of an identified lead compound, a computational protocol sequentially involving homology modeling, docking experiments, molecular dynamics simulation, and free energy perturbation calculations was applied for rationalizing the relative activities of known histone deacetylase inhibitors. With the newly developed force field parameters for the coordination environment of the catalytic zinc ion in hand, the computational strategy proved to be successful in predicting the rank orders for 12 derivatives of three hydroxamate-based inhibitor scaffolds with indole amide, pyrrole, and sulfonamide moieties. The results showed that the free energy of an inhibitor in aqueous solution should be an important factor in determining the binding free energy. Hence, in order to enhance the inhibitory activity by adding or substituting a chemical group, the increased stabilization in solution due to the structural changes must be overcome by a stronger enzyme-inhibitor interaction. It was also found that to optimize inhibitor potency, the hydrophobic head of an inhibitor should be elongated or enlarged so that it can interact with Pro29 and His28 that are components of the flexible loop at the top of the active site.     

非对称二甲基精氨酸二甲胺水解酶-2的理论研究

利用同源模建的方法,构建了DDAH-2的三位结构.并与L-瓜氨酸、L-高半胱氨酸分别进行对接研究.其中,Asp77,Gly269,Glu27和Arg96是与L-瓜氨酸相互作用较强的残基,Asp77,His171,Asp125和Ala270是与-L高半胱氨酸相互作用较强的残基.尤其Asp77是在两种复合物中同时起重要作用的氨基酸,并且它与抑制剂之间都形成了氢键.     

CCK1受体的同源模拟和分子对接研究

采用同源建模法对CCK1受体的三维结构进行了模拟,并采用分子动力学方法对模型进行修正和优化,再采用与训练集激动剂和拮抗剂分子对接的方法分别得到激动状态和拮抗状态CCK1受体的三维结构模型。得到的模型使用DOCK对接软件对训练集中的分子进行对接,所得结果与其实际活性拟合度较好,说明我们建立的激动和拮抗状态下的CCK1受体的三维结构模型比较合理,可以作为化合物虚拟筛选的模型对新化合物进行虚拟筛选。