Inhibition Mechanism of Hydroxyproline-like Small Inhibitors to Disorder HIF-VHL Interaction by Molecular Dynamic Simulations and Binding Free Energy Calculations

Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.

Free Energy of Binding of Coiled-Coil Complexes with Different Electrostatic Environments:The Influence of Force Field Polarisation and Capping

Coiled-coils are well known protein–protein interaction motifs,with the leucine zipper region of activator protein-1(AP-1)consisting of the c-Jun and c-Fos proteins being a typical example.Molecular dynamics(MD)simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins.The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge)were investigated.Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding,peptide capping has the largest influence on the predicted free energy of binding.Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.

Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase

The results of computer simulations of the binding of etravirine (TMC125) and rilpivirine (TMC278) to HIV reverse transcriptase are reported. It is confirmed that consistent binding free energy estimates are obtained with or without the application of torsional restraints when the free energies of imposing the restraints are taken into account. The restraints have a smaller influence on the thermodynamics and apparent kinetics of binding of TMC125 compared to the more flexible TMC278 inhibitor. The concept of the reorganization free energy of binding is useful to understand and categorize these effects. Contrary to expectations, the use of conformational restraints did not consistently enhance convergence of binding free energy estimates due to suppression of binding/unbinding pathways and due to the influence of rotational degrees of freedom not directly controlled by the restraints. Physical insights concerning the thermodynamic driving forces for binding and the role of “jiggling” and “wiggling” motion of the ligands are discussed. Based on these insights we conclude that an ideal inhibitor, if chemically realizable, would possess the electrostatic charge distribution of TMC125, so as to form strong interactions with the receptor, and the larger and more flexible substituents of TMC278, so as to minimize reorganization free energy penalties and the effects of resistance mutations, suitably modified, as in TMC125, so as to disfavor the formation of non-binding competent extended conformations when free in solution.

Mechanism of inhibitor ADS-J1 and ADS-J2 binding to HIV-1 gp41

In order to analyze and explain the mechanism of the two small inhibitors （ADS-JI and ADS-J2） binding to HIV-1 gp41, a computational study is carried out to help identifying possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and characterize structures of binding complexes. The binding interactions of gp41-molecule and free energies of binding are obtained through molecular dynamics simulation and molecular mechanic/Poisson- Boitzmann surface area （ MM/PBSA ） calculation. Specific molecular interactions in the gp41-inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point tbr further refinement of small molecular gp41 inhibitors.

Computational Analysis for Residue-Specific CDK2-Inhibitor Bindings

Cyclin-dependent kinase 2 (CDK2) is a key macromolecule in cell cycle regulation. In cancer cells, CDK2 is often overexpressed and its inhibition is an effective therapy of many cancers including breast carcinomas, leukemia, and lymphomas. Quantitative characterization of the interactions between CDK2 and its inhibitors at atomic level may provide a deep understanding of protein-inhibitor interactions and clues for more effective drug discovery. In this study, we have used the computational alanine scanning approach in combination with an efficient interaction entropy method to study the microscopic mechanism of binding between CDK2 and its 13 inhibitors. The total binding free energy from the method shows a correlation of 0.76?0.83 with the experimental values. The free energy component reveals two binding mode in the 13 complexes, namely van der Waals dominant, and electrostatic dominant. Decomposition of the total energy to per-residue contribution allows us to identify five hydrophobic residues as hot spots during the binding. Residues that are responsible for determining the strength of the binding were also analyzed.

Binding studies of trans-resveratrol with superoxide dismutase (SOD1): Docking assessment and Thermoanalysis

The binding pursuits of trans-resveratrol(t-RSV),an amazing health supplement are investigated with an antioxidant enzyme,superoxide dismutase(SOD1).The aim of the study is to dock t-RSV on the adrenaline binding site on SOD1 in order to explore its potential to act as a safety net against amyotrophic lateral sclerosis(ALS),a fatal neurodegenerative disorder that affects motor neurons.In silico GLIDE docking methodology and in vitro microcalorimetry technique is utilized for the investigation of binding parameters of t-RSV with SOD1.The study provides useful and distinct information about the amino acids involved in the interactions at molecular level along with the nature of forces involved in binding of t-RSV with SOD1.The docking analysis using the scoring functions of Schrodinger’s Glide package depicts that GLU100,PRO28,LYS23,TRP32 residues of the peptide backbone on SOD1 interact with phenolic groups of t-RSV.The information on thermodynamic parameters,i.e.binding constant(Kb),free energy(△G)and enthalpy(△H)generated through calorimetric titrations suggests that the reaction between t-RSV and SOD1 is spontaneous and exothermic.Both the studies are found to be in close agreement with each other based as far as the magnitude of binding constant(Kb=9.9×10^4)is concerned.

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase:molecular dynamics simulations and binding free energy calculations

Acetohydroxyacid synthase(AHAS) is the target enzyme of several classes of herbicides,such as sulfonylureas and imidazolinones.Now many mutant AHASs with herbicide resistance have emerged along with extensive use of herbicides,therefore it is imperative to understand the detailed interaction mechanism and resistance mechanism so as to develop new potent inhibitors for wild-type or resistant AHAS.With the aid of available crystal structures of the Arabidopsis thaliana(At) AHAS-inhibitor complex,molecular dynamics(MD) simulations were used to investigate the interaction and resistance mechanism directly and dynamically at the atomic level.Nanosecond-level MD simulations were performed on six systems consisting of wild-type or W574L mutant AtAHAS in the complex with three sulfonylurea inhibitors,separately,and binding free energy was calculated for each system using the MM-GBSA method.Comprehensive analyses from structural and energetic aspects confirmed the importance of residue W574,and also indicated that W574L mutation might alert the structural charactersistic of the substrate access channel and decrease the binding affinity of inhibitors,which cooperatively weaken the effective channel-blocked effect and finally result in weaker inhibitory effect of inhibitor and corresponding herbicide resistance of W574L mutant.To our knowledge,it is the first report about MD simulations study on the AHAS-related system,which will pave the way to study the interactions between herbicides and wild-type or mutant AHAS dynamically,and decipher the resistance mechanism at the atomic level for better designing new potent anti-resistance herbicides.

Discovery of highly potent phosphodiesterase-1 inhibitors by a combined-structure free energy perturbation approach

Accurate receptor/ligand binding free energy calculations can greatly accelerate drug discov-ery by identifying highly potent ligands.By simulating the change from one compound structure to another,the relative binding free energy(RBFE)change can be calculated based on the theoretically rigorous free energy perturbation(FEP)method.However,existing FEP-RBFE approaches may face convergence challenges due to difficulties in simulating non-physical intermediate states,which can lead to increased computational costs to obtain the converged results.To fundamentally overcome these issues and accelerate drug discovery,a new combined-structure RBFE(CS-FEP)calculation strategy was proposed,which solved the existing issues by constructing a new alchemical pathway,smoothed the alchemical transformation,increased the phase-space overlap between adjacent states,and thus signif-icantly increased the convergence and accelerated the relative binding free energy calculations.This method was extensively tested in a practical drug discovery effort by targeting phosphodiesterase-1(PDE1).Starting from a PDE1 inhibitor(compound 9,IC_(50)=16.8 mmol/L),the CS-FEP guided hit-to-lead optimizations resulted in a promising lead(11b and its mesylate salt formulation 11b-Mesylate,IC_(50)=7.0 nmol/L),with w2400-fold improved inhibitory activity.Further experimental studies re-vealed that the lead showed reasonable metabolic stability and significant anti-fibrotic effects in vivo.

Discovery of Potential SARS-CoV-2M Protease Inhibitors by Virtual Screening,Molecular Dynamics,and Binding Free Energy Analyses

The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)gained tremendous attention due to its high infectivity and pathogenicity.The 3-chymotrypsin-like hydrolase protease(Mpro)of SARS-CoV-2 has been proven to be an important target for anti-SARS-CoV-2 activity.To better identify the drugs with potential in treating coronavirus disease 2019(COVID-19)caused by SARS-CoV-2 and according to the crystal structure of Mpro,we conducted a virtual screening of FDA-approved drugs and chemical agents that have entered clinical trials.As a result,9 drug candidates with therapeutic potential for the treatment of COVID-19 and with good docking scores were identified to target SARS-CoV-2.Consequently,molecular dynamics(MD)simulation was performed to explore the dynamic interactions between the predicted drugs and Mpro.The binding mode during MD simulation showed that hydrogen bonding and hydrophobic interactions played an important role in the binding processes.Based on the binding free energy calculated by using MM/PBSA,Lopiravir,an inhibitor of human immunodeficiency virus(HIV)protease,is under investigation for the treatment of COVID-19 in combination with ritionavir,and it might inhibit Mpro effectively.Moreover,Ombitasvir,an inhibitor for non-structural protein 5 A of hepatitis C virus(HCV),has good inhibitory potency for Mpro.It is notable that the GS-6620 has a binding free energy,with respect to binding Mpro,comparable to that of ombitasvir.Our study suggests that ombitasvir and lopinavir are good drug candidates for the treatment of COVID-19,and that GS-6620 has good anti-SARS-CoV-2 activity.

PDE4B专一性抑制剂选择性的起源

采用分子动力学模拟和结合自由能计算研究了PDE4B抑制剂选择性的起源.首先,探索了模拟时间、溶质介电常数、配体的电荷方案和结合自由能的计算方法对结合自由能预测值准确度的影响,确定最佳模拟条件为:模拟时间40~50 ns,溶质介电常数ε=2,采用MM/GBSA方法以及RESP配体电荷计算方案.接着,通过能量分解分析了抑制剂A33与PDE4B/PDE4D的相互作用,发现PDE4B酶上的Ile410、Gln443、Phe446和Phe506对抑制剂的选择性识别贡献较大.最后,通过位点突变方法探索了PDE4B的CR3螺旋上的Leu502残基对A33选择性所起的作用.当前的工作为设计高活性、高选择性的PDE4B抑制剂提供了有价值的结构与活性关系信息.

EGFR和4-苯胺喹唑啉类抑制剂之间相互作用模式的研究

采用分子动力学和MM PBSA相结合的方法预测了表皮生长因子受体和 4 苯胺喹唑啉类抑制剂的相互作用模式 .在分子动力学采样的基础上 ,采用MM PBSA的方法分别预测了四种可能结合模式下表皮生长因子受体和 4 苯胺喹唑啉类抑制剂间的结合自由能 .在MM PBSA计算中 ,受体和抑制剂之间的非键相互作用能采用分子力学(MM)的方法得到 ;溶剂效应中极性部分对自由能的贡献通过解Possion Boltzmanne (PB)方程的方法得到 ;溶液效应中非极性部分对自由能的贡献则通过分子表面积计算 (SA)的方法得到 .计算表明 ,在四种结合模式下 ,表皮生长因子受体和 4 苯胺喹唑啉类抑制剂之间的结合自由能有较大的差别 .在最佳的相互作用模式中 ,抑制剂的苯胺部分位于活性口袋的底部 ,能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用 .抑制剂喹唑啉环上的N(1)原子能够和Met 76 9上的NH形成稳定的氢键 ,而抑制剂上的N(3)原子则和周围的一个水分子形成氢键 .同时 ,抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水相互作用 .

CDK2-抑制剂结合自由能计算

细胞周期蛋白依赖性激酶II (cyclin dependentkinase 2 ,CDK2 )是一种重要的治疗癌症的靶标 .本文中采用分子动力学取样 ,运用MM PBSA/GBSA两种方法计算了CDK2 NU610 2复合物的绝对结合自由能 .通过能量分解的方法考察了CDK2大分子主要残基与配体NU610 2之间的相互作用和识别 .

NTO与黏结剂的界面作用

采用DCAT 21型动态接触角/表面张力仪测量了NTO、GAP、HTPB、聚氨酯的接触角,通过接触角计算出NTO、GAP、HTPB、聚氨酯的表面自由能,并计算了NTO与GAP、HTPB、聚氨酯之间的黏合功W和铺展系数S。NTO-GAP、NTO-HTPB和NTO-聚氨酯界面之间的黏合功分别为114.59、76.13和101.81N/m,铺展系数为63.57、33.14和53.27 N/m。结果表明,NTO与GAP、HTPB、聚氨酯界面之间的相互作用大小顺序为NTO-GAP>NTO-聚氨酯>NTO-HTPB。红外光谱研究结果也显示,NTO-聚氨酯的界面相互作用比NTO-HTPB的界面相互作用强。

染料敏化太阳能电池中具有不同电子给体的吩噻嗪类有机光敏染料的理论研究

采用密度泛函理论和含时密度泛函理论方法计算了2个吩噻嗪类染料及其吸附到TiO2上后分子的基态和激发态光物理性质与热力学参数.结果表明,电子给体的改变虽未明显改变染料的光谱性质(垂直跃迁能和振子强度),但可以改变分子的前线轨道能级,进而影响染料分子的激子结合能Eb及激发态电子注入到半导体TiO2中的驱动力ΔGint的大小,并最终影响电池的能量转换效率.

顶空-固相微萃取-气相色谱-质谱联用法分析白鲢鱼肉蛋白质与特征腥味物结合作用

采用顶空-固相微萃取-气相色谱-质谱联用技术对4种典型呈腥味挥发物(庚醛、辛醛、壬醛和1-辛烯-3-醇)与白鲢鱼肉肌原纤维蛋白质、肌球蛋白和肌动蛋白的结合能力进行分析。结果表明,肌球蛋白作为肌原纤维蛋白主要的组分,是白鲢鱼肉中典型腥味物质的主要结合受体。基于热力学模型(Scatchard方程及其Klotz图)的研究发现,肌球蛋白与4种腥味物质的结合自由能(ΔG)均小于0,表明所有结合反应均是自发的。与直链醛(庚醛、辛醛、壬醛)相比,1-辛烯-3-醇和肌球蛋白有更多的结合位点数(n)和较高的结合常数(K),且肌球蛋白对直链醛的结合能力随着链长的增加而有所降低。该研究结果可为今后在淡水鱼糜生产过程中改良现有漂洗方法以实现有效脱腥提供理论依据。

谷氨酰胺结合蛋白的分子动力学模拟和自由能计算

谷氨酰胺结合蛋白(Glutamine-bindingprotein,GlnBp)是大肠杆菌透性酶系统中一个细胞外液底物专一性结合蛋白,对于细胞外液中谷氨酰胺(Gln)的运输和传递至关重要.本文运用分子动力学(Moleculardynamics,MD)模拟采样,考察了GlnBp关键残基与底物Gln之间的相互作用和GlnBp两条铰链的功能差别;并采用MM-PBSA方法计算了GlnBp与底物Gln的结合自由能.结果表明:Ph13,Phe50,Thr118和Ile69与底物Gln的范德华相互作用和Arg75,Thr70,Asp157,Gly68,Lys115,Ala67,His156与底物Gln的静电相互作用是结合Gln的主要推动力;复合物的铰链区85～89柔性大,对构象开合提供了结构基础;而铰链区181～185柔性小,其作用更多是在功能上把底物Gln限制在口袋中;自由能预测值与实验值吻合.本研究很好地解释了GlnBp结构与功能的关系,为进一步了解GlnBp的开合及转运Gln的机制提供了重要的结构信息.

p53-MDM2相互作用的分子力学和动力学研究

p53-MDM2相互作用的抑制已经成为治疗癌症的新方法.本文将分子动力学模拟和MM-PBSA(molecular mechanics/passion-Boltzman surface area)方法结合起来研究MDM2-p53相互作用机制。结果证明范德华相互作用驱动了MDM2与p53的结合.基于残基-残基相互作用的计算不仅证明p53的三个残基Phe19′,Trp23′和Leu26′与MDM2有较强的相互作用,而且还发现另外两个残基Leu22′和Pro27′也与MDM2有较强的相互作用,这为抗癌药物的设计提供了新靶标.同时也证明CH-CH,CH-π和π-π相互作用驱动了p53在MDM2疏水性裂缝中的结合.

皂苷类似物与肾素的分子对接和结合能分析

肾素是治疗高血压疾病的重要靶标之一,对肾素抑制剂大豆皂苷I及其类似物大豆皂苷II、甘草皂苷、单葡萄糖醛酸甘草皂苷元与肾素进行分子对接,采用分子动力学模拟和MMPBSA相结合的方法计算对接复合物的结合自由能,并且对各部分贡献能以及分子间相互作用进行分析。结果表明范德华力和静电相互作用是复合物形成的主要驱动力,S2和S3是肾素和皂苷相互作用重要的活性口袋,Ala229、Asp38、Asp226、Gly228和Tyr83是肾素中与这类抑制剂形成疏水作用的重要氨基酸残基,Ser230、Tyr231、Ser84则可与抑制剂形成氢键。对接结果与皂苷抑制能力吻合性较好,可为新的肾素抑制剂的发现奠定基础。

苯磺酰胺从碳酸酐酶Ⅱ中脱离过程的分子动力学模拟

综合运用分子动力学模拟和自由能计算方法研究了苯磺酰胺分子从碳酸酐酶Ⅱ(CAⅡ)的活性位点脱离过程中底物与酶之间的动态相互作用.脱离过程的平均力势(PMF)显示,底物脱离时存在一个特殊的结合状态.其中,静电相互作用占据了主导地位.轨迹分析显示,除了金属离子的配位作用之外,底物脱离路径上的关键残基Leu198、Thr199和Thr200通过与底物磺胺基的氢键作用阻碍了底物从酶中的脱离.当前的研究对于深入认识磺胺类药物与CAⅡ的详细结合过程和相关的药物改良与设计具有重要的指导意义.

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(Sa Fts Z)-二磷酸鸟苷(GDP)二元复合物和Sa Fts Z-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Sa Fts Z-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Fts Z蛋白紧密结合.在Sa Fts Z-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Fts Z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Fts Z蛋白的作用机制和影响规律,为该类Fts Z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.