Computational Studies of Difference in Binding Modes of Peptide and Non-Peptide Inhibitors to MDM2/MDMX Based on Molecular Dynamics Simulations

Inhibition of p53-MDM2/MDMX interaction is considered to be a promising strategy for anticancer drug design to activate wild-type p53 in tumors. We carry out molecular dynamics (MD) simulations to study the binding mechanisms of peptide and non-peptide inhibitors to MDM2/MDMX. The rank of binding free energies calculated by molecular mechanics generalized Born surface area (MM-GBSA) method agrees with one of the experimental values. The results suggest that van der Waals energy drives two kinds of inhibitors to MDM2/MDMX. We also find that the peptide inhibitors can produce more interaction contacts with MDM2/MDMX than the non-peptide inhibitors. Binding mode predictions based on the inhibitor-residue interactions show that the π-π, CH-π and CH-CH interactions dominated by shape complimentarity, govern the binding of the inhibitors in the hydrophobic cleft of MDM2/MDMX. Our studies confirm the residue Tyr99 in MDMX can generate a steric clash with the inhibitors due to energy and structure. This finding may theoretically provide help to develop potent dual-specific or MDMX inhibitors.     

Molecular Mechanism of Food-Derived Polyphenols on PD-L1 Dimerization: A Molecular Dynamics Simulation Study

In cancer immunotherapy, an emerging approach is to block the interactions of programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) using small-molecule inhibitors. The food-derived polyphenols curcumin (CC), resveratrol (RSV) and epigallocatechin gallate (EGCG) have anticancer immunologic functions, which, recently, have been proposed to act via the downregulation of PD-L1 expression. However, it remains unclear whether they can directly target PD-L1 dimerization and, thus, interrupt the PD-1/PD-L1 pathway. To elucidate the molecular mechanism of such compounds on PD-L1 dimerization, molecular docking and nanosecond molecular dynamics simulations were performed. Binding free energy calculations show that the affinities of CC, RSV and EGCG to the PD-L1 dimer follow a trend of CC > RSV > EGCG. Hence, CC is the most effective inhibitor of the PD-1/PD-L1 pathway. Analysis on contact numbers, nonbonded interactions and residue energy decomposition indicate that such compounds mainly interact with the C-, F- and G-sheet fragments of the PD-L1 dimer, which are involved in interactions with PD-1. More importantly, nonpolar interactions between these compounds and the key residues Ile54, Tyr56, Met115, Ala121 and Tyr123 play a dominant role in binding. Free energy landscape and secondary structure analyses further demonstrate that such compounds can stably interact with the binding domain of the PD-L1 dimer. The results provide evidence that CC, RSV and EGCG can inhibit PD-1/PD-L1 interactions by directly targeting PD-L1 dimerization. This provides a novel approach to discovering food-derived small-molecule inhibitors of the PD-1/PD-L1 pathway with potential applications in cancer immunotherapy.     

气体在水中的分子动力学模拟

采用分子动力学（ＭＤ）模拟的方法在常温及工业应用背景条件下对ＣＨ４、ＮＨ３、ＣＯ２、Ｏ２这些气体在水中的结构及扩散情形进行了研究。ＭＤ模拟可以为这些涉及到气体在水中的工业应用情形的机理提供分子水平的解释,同时ＭＤ模拟还可为一些不易实验测定扩散性质的体系提供工程初步设计和过程开发所需的数据。     

The Free Energy of Xenon Binding to Myoglobin from Molecular Dynamics Simulation

The interaction of xenon atoms with the interior of the myoglobin molecule has been simulated by molecular dynamics calculations. The standard free energy of binding has been computed from a simulation in which a forcing potential was applied; computed and experimental values differ by only 2 kJ/mole. In agreement with experimental evidence, the simulations indicate that insertion of the first xenon atom causes a perturbation of the protein conformation that facilitates insertion of one or more additional xenona.     

A Combination of 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation Studies of Benzimidazole-Quinolinone Derivatives as iNOS Inhibitors

Inducible Nitric Oxide Synthase (iNOS) has been involved in a variety of diseases, and thus it is interesting to discover and optimize new iNOS inhibitors. In previous studies, a series of benzimidazole-quinolinone derivatives with high inhibitory activity against human iNOS were discovered. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics (MD) simulation approaches were applied to investigate the functionalities of active molecular interaction between these active ligands and iNOS. A QSAR model with R² of 0.9356, Q² of 0.8373 and Pearson-R value of 0.9406 was constructed, which presents a good predictive ability in both internal and external validation. Furthermore, a combined analysis incorporating the obtained model and the MD results indicates: (1) compounds with the proper-size hydrophobic substituents at position 3 in ring-C (R₃ substituent), hydrophilic substituents near the X₆ of ring-D and hydrophilic or H-bond acceptor groups at position 2 in ring-B show enhanced biological activities; (2) Met368, Trp366, Gly365, Tyr367, Phe363, Pro344, Gln257, Val346, Asn364, Met349, Thr370, Glu371 and Tyr485 are key amino acids in the active pocket, and activities of iNOS inhibitors are consistent with their capability to alter the position of these important residues, especially Glu371 and Thr370. The results provide a set of useful guidelines for the rational design of novel iNOS inhibitors.     

Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus

Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular dynamics simulations combined with the solvated interaction energies technique was applied to predict the docking models of the inhibitors in the binding pocket of the H1N1 influenza neuraminidase. In the simulations, the correlation of the predicted and experimental binding free energies of all 20 flavonoid derivatives inhibitors is satisfactory, as indicated by R(2) = 0.75.     

NPT系综分子动力学模拟水的密度和扩散系数

采用常温常压(NPT)系综分子动力学方法模拟了298.15K、0.1013MPa条件下水的密度和自扩散系数,模拟结果与实验值一致,相对误差分别为1.74%和3.83%。     

Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein

Plasmepsins II (EC number: 3.4.23.39) and IV (EC number: 3.4.23.B14) are aspartic proteases present in the food vacuole of the malaria parasite Plasmodium falciparum and are involved in host hemoglobin degradation. A series of pyrrolidine derivatives, originally synthesized as HIV‐1 protease inhibitors, were tested for activity against plasmepsin (Plm). Inhibitors in the nanomolar range were discovered for the Plm II and IV isoforms. Detailed studies were carried out to identify putative binding modes that help to explain the underlying structure–activity relationships. Reasonable binding modes were generated for pyrrolidine‐3,4‐diester derivatives and a substituted 3,4‐diaminopyrrolidine inhibitor by using a crystal structure of inhibitor‐bound Plm II (PDB ID: 1LEE). Modeling studies indicated that the flap of available Plm crystal structures is not sufficiently opened to accommodate the 3,4‐bis(aminomethylene)pyrrolidines. Molecular dynamics simulations were performed to analyze the flexibility of the protein in greater detail, leading to a binding mode hypothesis for the 3,4‐bis(aminomethylene)pyrrolidines and providing further insight and general implications for the design of Plm II inhibitors.     

氨的自扩散系数的分子动力学模拟研究

采用分子动力学模拟方法研究了氨在较宽温度和压力范围的分子自扩散系数。从常温到高温,自扩散系数的模拟值与实验值吻合得很好,这表明可以采用分子动力学模拟来代替实验,获得高温高压条件下实验难以测量的自扩散系数。     

甲烷的自扩散系数的分子动力学模拟研究

运用分子动力学模拟方法研究了甲烷在较宽温度和压力范围的分子自扩散系数。结果表明,甲烷自扩散系数的模拟值与文献实验值吻合得较好。因此,可以采用分子动力学模拟来代替实验,获得高温高压条件下实验难以测量的甲烷自扩散系数。     

高能推进剂NEPE组分PEG与铝颗粒模型的分子动力学模拟

在COMPASS力场下,对高能推进剂NEPE组分PEG／Al球型包覆模型进行了分子动力学模拟。以预测PEG／Al模型结构的静力学性能和界面结合能。模拟结果得出PEG／Al的力学性能（拉伸模量、泊松比、体积模量、剪切模量）及其界面结合能,这对NEPE推进剂体系的进一步研究奠定了理论基础,从而为在推进剂中固体颗粒与黏结剂的脱粘研究提供一定的理论依据。     

Structure-Based Design,Docking and Binding Free Energy Calculations of A366 Derivatives as Spindlin1 Inhibitors

The chromatin reader protein Spindlin1 plays an important role in epigenetic regulation, through which it has been linked to several types of malignant tumors. In the current work, we report on the development of novel analogs of the previously published lead inhibitor A366. In an effort to improve the activity and explore the structure–activity relationship (SAR), a series of 21 derivatives was synthesized, tested in vitro, and investigated by means of molecular modeling tools. Docking studies and molecular dynamics (MD) simulations were performed to analyze and rationalize the structural differences responsible for the Spindlin1 activity. The analysis of MD simulations shed light on the important interactions. Our study highlighted the main structural features that are required for Spindlin1 inhibitory activity, which include a positively charged pyrrolidine moiety embedded into the aromatic cage connected via a propyloxy linker to the 2-aminoindole core. Of the latter, the amidine group anchor the compounds into the pocket through salt bridge interactions with Asp184. Different protocols were tested to identify a fast in silico method that could help to discriminate between active and inactive compounds within the A366 series. Rescoring the docking poses with MM-GBSA calculations was successful in this regard. Because A366 is known to be a G9a inhibitor, the most active developed Spindlin1 inhibitors were also tested over G9a and GLP to verify the selectivity profile of the A366 analogs. This resulted in the discovery of diverse selective compounds, among which 1s and 1t showed Spindlin1 activity in the nanomolar range and selectivity over G9a and GLP. Finally, future design hypotheses were suggested based on our findings.     

超临界水中气体扩散系数的分子动力学模拟

采用分子动力学（MD）方法计算T＝703.2-763.2K,p=30-45MPa范围内,氧气和氮气在超临界水中的无限稀释扩散系数。计算结果表明,在超临界条件下的扩散系数较常温常压下要大1－2个数量级。扩散系数随温度的升高而增大,随压力的增高而降低,且氧的扩散系数稍大于氮的扩散系数。     

蒙脱石狭缝中二氧化碳的分子动力学模拟

本文采用分子动力学方法研究稠密二氧化碳在蒙脱石狭缝孔中的结构性质。二氧化碳在孔内固体表面形成高密度层,孔宽不同时该密度层与固体表面的距离固定。二氧化碳分子轴线与固体表面法向量的夹角在一定范围之内。随着孔宽的减少,受限二氧化碳的C-C径向分布函数第一峰的高度增加,在宽孔中只有处在接触层位置的流体才表现出长程有序的结构。     

Study on the Characteristics of Gas Molecular Mean Free Path in Nanopores by Molecular Dynamics Simulations

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale.     

二氧化碳汽—液界面特性的分子动力学模拟

采用EPM2二氧化碳分子势能模型,以二氧化碳分子内各原子作为统计对象进行统计计算,探讨温度、薄层切片数及截断半径对其汽—液界面特性参数的影响规律。结果表明,随着截断半径的增大,液相主体密度逐渐增大,汽相主体密度逐渐减小,界面层厚度有所减小;薄层切片数对界面层厚度、液相主体和汽相主体的密度影响不大;随着温度的升高,汽相主体密度增加,液相主体密度降低,汽—液界面厚度增大,界面张力逐渐减小。     

异丙醇汽液界面特性的平衡分子动力学模拟

采用OPLS刚性联合原子模型,以异丙醇分子的作用位点为统计对象,对异丙醇的汽液界面特性进行了平衡分子动力学模拟研究。模拟结果表明,随着温度的升高,液相主体密度减小,汽相主体密度增大,汽液界面厚度增大;截断半径和薄片数对汽相主体密度体、液相主体密度及汽液界面厚度的影响不大;随着模拟分子数的增大,汽液界面厚度有所增大。     

水汽液界面特性的平衡分子动力学模拟

采用SPC模型作为水分子动力学模拟的势能模型,以水分子内各原子作为统计对象进行统计计算,模拟得到其汽液界面特性参数的分布规律。结果表明,随着温度的升高,汽相主体密度增加,汽液界面厚度增大,液相主体密度降低,界面张力逐渐减小,液相主体区域势能的势阱深度也逐渐降低。随着模拟分子数的增加,液相主体密度增加,汽液界面厚度稍有增大。随着截断半径的增加,液相主体密度增加,汽液界面厚度变化不大。     

Synthesis of Dihydrobenzofuro[3,2-b]chromenes as Potential 3CLpro Inhibitors of SARS-CoV-2: A Molecular Docking and Molecular Dynamics Study

The recent emergence of pandemic of coronavirus (COVID-19) caused by SARS-CoV-2 has raised significant global health concerns. More importantly, there is no specific therapeutics currently available to combat against this deadly infection. The enzyme 3-chymotrypsin-like cysteine protease (3CLpro) is known to be essential for viral life cycle as it controls the coronavirus replication. 3CLpro could be a potential drug target as established before in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In the current study, we wanted to explore the potential of fused flavonoids as 3CLpro inhibitors. Fused flavonoids (5a,10a-dihydro-11H-benzofuro[3,2-b]chromene) are unexplored for their potential bioactivities due to their low natural occurrences. Their synthetic congeners are also rare due to unavailability of general synthetic methodology. Here we designed a simple strategy to synthesize 5a,10a-dihydro-11H-benzofuro[3,2-b]chromene skeleton and it's four novel derivatives. Our structural bioinformatics study clearly shows excellent potential of the synthesized compounds in comparison to experimentally validated inhibitor N3. Moreover, in-silico ADMET study displays excellent druggability and extremely low level of toxicity of the synthesized molecules. Further, for better understanding, the molecular dynamic approach was implemented to study the change in dynamicity after the compounds bind to the protein. A detailed investigation through clustering analysis and distance calculation gave us sound comprehensive data about their molecular interaction. In summary, we anticipate that the currently synthesized molecules could not only be a potential set of inhibitors against 3CLpro but also the insights acquired from the current study would be instrumental in further developing novel natural flavonoid based anti-COVID therapeutic spectrums.