基于配体与受体结构的酪氨酸酶抑制剂定量构效关系分析

酪氨酸酶是细胞内催化合成黑素的关键酶。 理解酪氨酸酶抑制剂结构与活性之间的关系对于设计新药和化妆品具有重要意义。 然而,酪氨酸酶抑制剂的定量构效关系仍不清楚。 本文利用配体和结构描述符构建了隐式和显式模型,阐明了酪氨酸酶抑制剂定量构效关系。 隐式模型的相关系数R高达0.961,显式模型的相关系数为0.775。 两个模型很好地预测了3个茶多酚的酪氨酸酶抑制活性,表儿茶素没食子酸酯(ECG)>表没食子儿茶素没食子酸酯(EGCG)>没食子酸(G)。 相关性分析发现,抑制剂与酪氨酸酶结合引起的构象熵损失与抑制剂的活性密切相关。 具有较少构象熵损失的ECG在4种茶多酚中具有较高酪氨酸酶抑制活性。 结合自由能计算也证实ECG与酪氨酸酶的结合能力最强。 此外,通过分解结合自由能发现,酪氨酸酶活性中心的氨基酸残基(His57、His201、Asn202、His205、Glu192和Val215)与抑制剂形成了较强的范德华和静电相互作用,进而稳定了复合物结构。     

配体活性构象搜寻方法及其应用研究——Ⅰ.搜寻方法及凝血酶抑制剂活性构象的搜寻

在综合系统构象搜寻和配体-生物大分子对接(Dock)方法的基础上,发展了根据受体活性部位三维结构搜寻配体活性构象的搜寻方法BCSPL.用此方法搜寻了凝血酶抑制剂PPACK的活性构象,结果与晶体结构非常吻合,又用此方法搜寻了膦酰肽类和二肽、三肽类凝血酶抑制剂与人体α凝血酶结合时的活性构象,并在此基础上用分子力学计算了抑制剂与凝血酶的结合能,结果表明结合能与活性有很好的相关性,计算结果能合理地解释抑制剂与凝血酶的相互作用方式及结构与活性的关系.     

基于分子对接和自由能计算的高活性苯并噻唑类ROCK抑制剂的设计、合成和生物学评价

以3个已报道的苯并噻唑类Rho关联含卷曲螺旋蛋白激酶(ROCK)抑制剂(化合物1~3)为研究对象,经分子动力学模拟获得其在ROCK2蛋白结合口袋中的稳定结合构象,通过分子对接结果从氨基酸角度初步揭示了此类抑制剂的结构-活性关系(SAR);然后,对这3个抑制剂进行MM/GBSA结合自由能(ΔG_(bind))研究,结合自由能计算可知ΔG_(bind)与化合物活性之间具有良好的相关性,且范德华作用能(ΔG_(VDW))对ΔG_(bind)的贡献最大.通过自由能分解获得了对于高活性抑制剂具有重要影响的关键残基.最后,根据分子对接和自由能研究结果设计并合成了3类新型苯并噻唑类似物(D1~D10).生物学评价结果表明,这10个化合物分别具有11~288 nmol/L(ROCK1)和2~105 nmol/L(ROCK2)的抑制活性.其中,化合物D3~D5在人肝微粒体代谢研究中展现出比已报道化合物更高的代谢稳定性.本研究不仅为高活性ROCK抑制剂的设计提供了理论指导,也为ROCK的应用研究提供了一系列结构新颖的高活性抑制剂.     

新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算

通过分子对接建立了一系列含二氟甲基磷酸基团(DFMP)或二氟甲基硫酸基团(DFMS)的抑制剂与酪氨酸蛋白磷酸酯酶1B(PTP1B)的相互作用模式, 并通过1 ns的分子动力学模拟和molecular mechanics/generalized Born surface area (MM/GBSA)方法计算了其结合自由能. 计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致; 通过基于主方程的自由能计算方法, 获得了抑制剂与靶酶残基间相互作用的信息, 这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性, 进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

葡萄糖苷酶抑制剂作用机理的分子动力学模拟和自由能计算

含有锍离子的葡萄糖苷酶抑制剂如kotalanol (SK)和它除去磺酸基团后的衍生物(DSK), 是潜在的毒副作用较小的治疗II 型糖尿病的候选药物. α-葡萄糖苷酶抑制活性实验显示, DSK活性比SK略高, 而将二者环上的S原子替换成NH后(分别称为DSN和SN), DSN的活性要比SN高1500倍左右. 本文用分子动力学模拟, 结合自由能计算和自由能分解的方法对上述四个抑制剂的作用机理进行了研究. 研究结果表明活性的巨大差异是由NH基团取代效应和磺酸基团立体效应共同作用的结果, 由于N―C键长比S―C键长短, NH基团取代导致烷基链的翻转, 同时, 磺酸基团限制了链的翻转, 因此改变了抑制剂的结合模式. 计算结果与实验基本一致.本文的研究结果有助于进一步理解含锍离子的葡萄糖苷酶抑制剂的结合机理, 并为设计更有潜力的葡萄糖苷酶抑制剂提供了有价值的信息.     

新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算（英文）

通过分子对接建立了一系列含二氟甲基磷酸基团（DFMP）或二氟甲基硫酸基团（DFMS）的抑制剂与酪氨酸蛋白磷酸酯酶1B（PTP1B）的相互作用模式,并通过1ns的分子动力学模拟和molecular mechanics/generalized Born surface area（MM/GBSA）方法计算了其结合自由能.计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致;通过基于主方程的自由能计算方法,获得了抑制剂与靶酶残基间相互作用的信息,这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性,进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

3MBA类FtsZ蛋白抑制剂的分子动力学模拟及抗菌作用机制

采用分子动力学模拟、蛋白质二级结构测定(DSSP)、口袋体积测量(POVME)以及MM-PBSA(molecular mechanics Poisson-Boltzmann surface area)方法, 系统研究了金黄色葡萄球菌丝状温度敏感性蛋白Z (SaFtsZ)-二磷酸鸟苷(GDP)二元复合物和SaFtsZ-GDP-3MBA (3-甲氧基苯甲酰胺)类衍生物三元复合物体系的稳定性、蛋白质二级结构、蛋白质构象、关键残基质心距、活性口袋体积以及相对结合自由能的变化规律. 研究表明: 当不含抑制剂存在时SaFtsZ-GDP二元复合物体系稳定性较差, 其T7Loop区域残基(203-209)波动较大, 且蛋白二级结构发生明显变化, 活性口袋体积急剧减小, 底物通道显著变窄且不稳定. 而含有抑制剂PC190723、Compound1 的类衍生物三元复合物体系的表现截然不同, 这主要是由于它们均能和活性口袋T7Loop区周围残基形成关键性的氢键以及疏水作用, 与FtsZ 蛋白紧密结合. 在SaFtsZ-GDP-3MBA三元复合物体系中, 3MBA仅能与活性口袋中部分残基形成疏水作用, 与FtsZ 蛋白亲和力较弱, 使其不能稳定地存在于活性口袋中, 进一步导致它的抗菌活性明显低于PC190723、Compound1. 这些发现深入揭示了3MBA类衍生物对FtsZ 蛋白的作用机制和影响规律, 为该类FtsZ 蛋白抑制剂的结构优化和产品开发应用提供了重要的理论依据.     

分子动力学研究2-乙酸苯并噻吩在HIV-1蛋白酶与抑制剂结合中的作用

为了研究别构小分子2-乙酸苯并噻吩(2FX)在HIV-1蛋白酶与抑制剂结合中的作用, 利用分子动力学方法分别对未结合和结合2FX的HIV-1蛋白酶抑制剂体系进行了100 ns的模拟, 模拟计算中对每种体系均采用两种新的分子力场ff99SBildn和ff12SB. 研究了2FX对体系构象的影响和两体系在不同力场下的动力学行为, 分析了两体系的均方根偏差和残基的B因子, 比较了计算结构和晶体结构, 最后采用MM-PB/GBSA两种方法计算了两体系的结合自由能. 研究表明, 两种力场计算的结果虽有差异, 但都说明2FX的结合导致蛋白酶构象的变化, 使得体系更加稳定, 尤其是flap的柔性减弱, 使得蛋白酶和抑制剂的结合更牢固; 另外, 还发现ff12SB力场动力学过程更稳定. 研究结果有助于为设计新的别构抑制剂提供理论依据.     

苯硼酸衍生物的晶体工程：用能量较高的syn,syn-构象设计共晶

研苯硼酸衍生物有3种不同构象（syn,syn-;syn,anti-和anti,anti-构象）,这3种构象能量非常不同.苯硼酸衍生物通常是采用能量最低的syn,anti-构象存在.然而在配合物中,苯硼酸衍生物展现了硼酸功能团的构象多样性.在本文中,我们采用syn,syn-构象的硼酸衍生物作为结构单元,与含氮给体化合物反应,合成了一系列共晶配合物.采用的含氮给体化合物包括含1,2-重氮片段的化合物（阿普唑仑,1H-四唑,乙酰唑胺和苯并三唑）、邻菲罗啉和2,2′-联吡啶.结果表明,只有1,2-重氮片段不一定能与syn,syn-构象的硼酸及衍生物生成共晶.     

氯硝柳胺及其衍生物与钥孔戚血蓝蛋白的相互作用

以氯硝柳胺为原料合成了聚乙二醇200基氯硝柳胺. 采用荧光光谱、同步荧光光谱、紫外吸收光谱和圆二色谱研究了氯硝柳胺及其衍生物与钥孔戚血蓝蛋白(KLH)的相互作用. 结果表明, 两种药物分子对KLH的荧光猝灭机制属于静态猝灭; 由Lineweaver-Burk方程计算出不同温度下结合常数K, 但是聚乙二醇200基氯硝柳胺与KLH的作用相对较弱; 由Van′t Hoff方程计算出ΔH和ΔS平均值, 结合力主要为静电作用力; 热力学函数计算结果表明, 氯硝柳胺及其衍生物与KLH的作用过程是一个熵增加、Gibbs自由能降低的自发分子间作用过程; 根据Förster非辐射能量转移机制求得给体与受体间的结合距离r均小于7 nm; 同步荧光光谱表明, 氯硝柳胺及其衍生物能够被血蓝蛋白存储和转运, 但结合时对蛋白构象有一定影响; 圆二色谱测得加入两种药物后, KLH的α-螺旋含量均降低, 二级结构发生改变. 通过比较氯硝柳胺及其衍生物与KLH的相互作用, 初步探讨了分子结构与其结合能力之间的联系.     

Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations

A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor–enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents.     

Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors

(V600E)B-RAF kinase is the most frequent onco-genic protein kinase mutation in melanoma and is a promising target to treat malignant melanoma. In this work, a molecular modeling study combining QM-polarized ligand docking, molecular dynamics, free energy calculation, and three-dimensional quantitative structure-activity relationships (3D-QSAR) was performed on a series of pyridoimidazolone compounds as the inhibitors of (V600E)B-RAF kinase to understand the binding mode between the inhibitors and (V600E)B-RAF kinase and the structural requirement for the inhibiting activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by QM-polarized ligand docking strategy. The obtained models have a good predictive ability in both internal and external validation. Furthermore, molecular dynamics simulation and free energy calculations were employed to determine the detailed binding process and to compare the binding mode of the inhibitors with different activities. The binding free energies calculated by MM/PBSA gave a good correlation with the experimental biological activity. The decomposition of free energies by MM/GBSA indicates the van der Waals interaction is the major driving force for the interaction between the inhibitors and (V600E)B-RAF kinase. The hydrogen bond interactions between the inhibitors with Glu501 and Asp594 of the (V600E)B-RAF kinase help to stabilize the DFG-out conformation. The results from this study can provide some insights into the development of novel potent (V600E)B-RAF kinase inhibitors.     

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure–activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q² values of 0.723 and 0.993 for cross-validated and non-cross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site.     

Computer simulations of ligand–protein binding with ensembles of protein conformations: A Monte Carlo study of HIV‐1 protease binding energy landscapes

We present the results of molecular docking simulations with HIV‐1 protease for the sb203386 and skf107457 inhibitors by Monte Carlo simulated annealing. A simplified piecewise linear energy function, the standard AMBER force field, and the AMBER force field with solvation and a soft‐core smoothing component are employed in simulations with a single‐protein conformation to determine the relationship between docking simulations with a simple energy function and more realistic force fields. The temperature‐dependent binding free energy profiles of the inhibitors interacting with a single protein conformation provide a detailed picture of relative thermodynamic stability and a distribution of ligand binding modes in agreement with experimental crystallographic data. Using the simplified piecewise linear energy function, we also performed Monte Carlo docking simulations with an ensemble of protein conformations employing preferential biased sampling of low‐energy protein conformations, and the results are analyzed in connection with the free energy profiles. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 73–84, 1999     

A computational analysis of the binding model of MDM2 with inhibitors

Abstract  

It is a new and promising strategy for anticancer drug design to block the MDM2-p53 interaction using a non-peptide small-molecule inhibitor. We carry out molecular dynamics simulations to study the binding of a set of six non-peptide small-molecule inhibitors with the MDM2. The relative binding free energies calculated using molecular mechanics Poisson–Boltzmann surface area method produce a good correlation with experimentally determined results. The study shows that the van der Waals energies are the largest component of the binding free energy for each complex, which indicates that the affinities of these inhibitors for MDM2 are dominated by shape complementarity. The A-ligands and the B-ligands are the same except for the conformation of 2,2-dimethylbutane group. The quantum mechanics and the binding free energies calculation also show the B-ligands are the more possible conformation of ligands. Detailed binding free energies between inhibitors and individual protein residues are calculated to provide insights into the inhibitor-protein binding model through interpretation of the structural and energetic results from the simulations. The study shows that G1, G2 and G3 group mimic the Phe19, Trp23 and Leu26 residues in p53 and their interactions with MDM2, but the binding model of G4 group differs from the original design strategy to mimic Leu22 residue in p53.     

Microscopic modes and free energies of 3-phosphoinositide-dependent kinase-1 (PDK1) binding with celecoxib and other inhibitors

Celecoxib, also known as Celebrex (approved by FDA in 1998) and remembered as the fastest-selling drug in history, was used as a cyclooxygenase-2 (COX-2) selective inhibitor having both anti-inflammatory and anticancer activities. Most recent studies have revealed that the apoptotic activity of celecoxib (and its derivatives) is actually independent of the COX-2 inhibitory activity and that celecoxib also inhibits the kinase activity of 3-phosphoinositide-dependent protein kinase-1 (PDK1), suggesting that the well-known anticancer activity of celecoxib is not due to the inhibition of COX-2, but possibly is due to the inhibition of PDK1. It is highly desirable to develop new celecoxib derivatives as PDK1-specifc inhibitors to avoid the side effects of COX-2 inhibitors. To understand how PDK1 binds with celecoxib and its derivatives, we have performed extensive molecular docking and combined molecular dynamics (MD) simulations and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations on eight representative PDK1 inhibitors, leading to the finding of a new, more favorable binding mode which is remarkably different from the previously proposed binding mode. Based on the determined most stable binding structures, the calculated binding free energies are all in good agreement with the corresponding experimental data, and the biological activity data available for celecoxib and its derivatives can be better interpreted. The obtained new insights, concerning both the binding mode and computational protocol, will be valuable not only for future rational design of novel, more potent PDK1-specific inhibitors as promising anticancer therapeutics, but also for rational design of drugs targeting other proteins.     

用分子模拟方法研究HIV-1整合酶与咖啡酰基类抑制剂的相互作用

用分子对接和分子动力学(MD)模拟方法研究了一类咖啡酰基和没食子酰基类HIV-1整合酶抑制剂与整合酶之间的相互作用模式, 结果表明该类抑制剂分子上的两个侧链基团(咖啡酰基或没食子酰基)与整合酶的DDE基序之间的相互作用对抑制整合酶活性起到关键作用. 当侧链基团为没食子酰基时, 可以提高该类抑制剂与整合酶的结合能力. 采用线性相互作用能方法(LIE)计算了该类抑制剂与整合酶之间的结合自由能, 预测值与实验值相吻合, 均方根偏差RMSD为1.39 kJ•mol^-1, 以上结果可为基于结构的HIV-1整合酶抑制剂设计提供有用的信息.     

Developing high affinity oligosaccharide inhibitors: conformational pre-organization paired with functional group modification

Intramolecular tethering combined with functional group modification has been investigated as an approach to design high affinity oligosaccharide ligands. The preceding paper reported successful tethering to constrain a trisaccharide in the conformation of its bound state with an antibody and thereby achieved a 15-fold increase in association constant. Here we report the synthesis of two beta-alanyl tethered derivatives that employ monochlorination and monodeoxygenation strategies to create inhibitors that should enhance the binding affinity of the target molecules by an additional 10-25-fold, provided that free energy changes are additive when tethering is paired with functional group changes. The binding parameters of the new ligands were measured by isothermal titration calorimetry and the results rationalized with molecular dynamics calculations and a simple docking analysis. The data indicate that while the alanine tether is a reasonable method to constrain trisaccharide , free energy gains obtained by pairing it with functional group modification are not additive and in one case counter-productive.     

Structure activity relationships of quinoxalin-2-one derivatives as platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors, derived from molecular modeling

We previously reported a quinoxalin-2-one compound (Compound 1) that had inhibitory activity equivalent to existing platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors. Lead optimization of Compound 1 to increase its activity and selectivity, using structural information regarding PDGFbeta R-ligand interactions, is urgently needed. Here we present models of the PDGFbeta R kinase domain complexed with quinoxalin-2-one derivatives. The models were constructed using comparative modeling, molecular dynamics (MD) and ligand docking. In particular, conformations derived from MD, and ligand binding site information presented by alpha-spheres in the pre-docking processing, allowed us to identify optimal protein structures for docking of target ligands. By carrying out molecular modeling and MD of PDGFbeta R in its inactive state, we obtained two structural models having good Compound 1 binding potentials. In order to distinguish the optimal candidate, we evaluated the structural activity relationships (SAR) between the ligand-binding free energies and inhibitory activity values (IC50 values) for available quinoxalin-2-one derivatives. Consequently, a final model with a high SAR was identified. This model included a molecular interaction between the hydrophobic pocket behind the ATP binding site and the substitution region of the quinoxalin-2-one derivatives. These findings should prove useful in lead optimization of quinoxalin-2-one derivatives as PDGFb R inhibitors.     

Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors

The paper describes the construction, validation and application of a structure-based 3D QSAR model of novel acetylcholinesterase (AChE) inhibitors. Initial use was made of four X-ray structures of AChE complexed with small, non-specific inhibitors to create a model of the binding of recently developed aminopyridazine derivatives. Combined automated and manual docking methods were applied to dock the co-crystallized inhibitors into the binding pocket. Validation of the modelling process was achieved by comparing the predicted enzyme-bound conformation with the known conformation in the X-ray structure. The successful prediction of the binding conformation of the known inhibitors gave confidence that we could use our model to evaluate the binding conformation of the aminopyridazine compounds. The alignment of 42 aminopyridazine compounds derived by the docking procedure was taken as the basis for a 3D QSAR analysis applying the GRID/GOLPE method. A model of high quality was obtained using the GRID water probe, as confirmed by the cross-validation method (q² _LOO=0.937, q² _{L50% O}=0.910). The validated model, together with the information obtained from the calculated AChE-inhibitor complexes, were considered for the design of novel compounds. Seven designed inhibitors which were synthesized and tested were shown to be highly active. After performing our modelling study the X-ray structure of AChE complexed with donepezil, an inhibitor structurally related to the developed aminopyirdazines, has been made available. The good agreement found between the predicted binding conformation of the aminopyridazines and the one observed for donepezil in the crystal structure further supports our developed model.