Identification of Potential SARS-CoV-2 Main Protease and Spike Protein Inhibitors from the Genus Aloe: An In Silico Study for Drug Development

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) disease is a global rapidly spreading virus showing very high rates of complications and mortality. Till now, there is no effective specific treatment for the disease. Aloe is a rich source of isolated phytoconstituents that have an enormous range of biological activities. Since there are no available experimental techniques to examine these compounds for antiviral activity against SARS-CoV-2, we employed an in silico approach involving molecular docking, dynamics simulation, and binding free energy calculation using SARS-CoV-2 essential proteins as main protease and spike protein to identify lead compounds from Aloe that may help in novel drug discovery. Results retrieved from docking and molecular dynamics simulation suggested a number of promising inhibitors from Aloe. Root mean square deviation (RMSD) and root mean square fluctuation (RMSF) calculations indicated that compounds 132, 134, and 159 were the best scoring compounds against main protease, while compounds 115, 120, and 131 were the best scoring ones against spike glycoprotein. Compounds 120 and 131 were able to achieve significant stability and binding free energies during molecular dynamics simulation. In addition, the highest scoring compounds were investigated for their pharmacokinetic properties and drug-likeness. The Aloe compounds are promising active phytoconstituents for drug development for SARS-CoV-2.     

The evolution of numerical methods for predicting the distribution of surfactant in the bubble-scale dynamics of foams

Many numerical methods now exist to simulate the structure and dynamics of surface-tension-dominated aqueous foams at the level of the individual films and the liquid structures where they meet. We review these methods, focusing in particular on bubble-scale simulations of foam rheology. We highlight methods that allow the distribution of surfactant during flow to be taken into account.     

Combined Experimental and Theoretical Insights into the Corrosion Inhibition Activity on Carbon Steel Iron of Phosphonic Acids

The inhibition effect of N,N′-phosphonomethylglycine (PMG) and vinyl phosphonic acid (VPA) on the 3% NaCl acidic solution corrosion of carbon steel iron was studied at different immersion times by potentiodynamic polarization, electrochemical impedance spectroscopy, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, and computational methods. It is found from the polarization studies that PMG and VPA behave as mixed-type inhibitors in NaCl. Values of charge transfer resistance (R_ct) and double layer capacitance (C_dl) in the absence and presence of inhibitors are determined. The PMG and VPA inhibitors were capable of inhibiting the corrosion process up to ≈91% and ≈85%, respectively. In the presence of PMG, the synergic effect of chlorine ions was observed. Density functional theory (DFT) was engaged to establish the adsorption site of PMG, VPA, and their deprotonated states. For studied compounds, the resulted values of E_LUMO, E_HOMO, energy gap (∆E), dipole moment (μ), electronic hardness (η), global softness (σ), electrophilic index (ω), and the electronic potential map are in concordance with the experimental data results regarding their corrosion inhibition behavior and adsorption on the metal surface.     

基于虚拟现实的分子对接教学软件*

由于其强大的沉浸性和交互性等特征,虚拟现实技术在教育教学方面有着独特的优势。基于分子建模工具和虚拟现实技术构建了一种关于分子对接的教学软件,该软件将语音讲解、动画演示、分子可视化、交互操作等内容有机整合在虚拟现实环境中,从理论知识讲解和VR实验操作2个方面展开,深入浅出地讲解了分子对接的知识点,达到辅助教学的目的。     

Inhibitor Development against p7 Channel in Hepatitis C Virus

Hepatitis C Virus (HCV) is the key cause of chronic and severe liver diseases. The recent direct-acting antiviral agents have shown the clinical success on HCV-related diseases, but the rapid HCV mutations of the virus highlight the sustaining necessity to develop new drugs. p7, the viroporin protein from HCV, has been sought after as a potential anti-HCV drug target. Several classes of compounds, such as amantadine and rimantadine have been testified for p7 inhibition. However, the efficacies of these compounds are not high. Here, we screened some novel p7 inhibitors with amantadine scaffold for the inhibitor development. The dissociation constant (Kd) of 42 ARD-series compounds were determined by nuclear magnetic resonance (NMR) titrations. The efficacies of the two best inhibitors, ARD87 and ARD112, were further confirmed using viral production assay. The binding mode analysis and binding stability for the strongest inhibitor were deciphered by molecular dynamics (MD) simulation. These ARD-series compounds together with 49 previously published compounds were further analyzed by molecular docking. Key pharmacophores were identified among the structure-similar compounds. Our studies suggest that different functional groups are highly correlated with the efficacy for inhibiting p7 of HCV, in which hydrophobic interactions are the dominant forces for the inhibition potency. Our findings provide guiding principles for designing higher affinity inhibitors of p7 as potential anti-HCV drug candidates.     

In silico virtual screening of potent inhibitor to hamper the interaction between HIV-1 integrase and LEDGF/p75 interaction using E-pharmacophore modeling,molecular docking,and dynamics simulations

The rapid increase of HIV-1 infection throughout the globe has a high demand for a superior drug with lesser side effects. LEDGF/p75, the human Lens Epithelium-Derived Growth Factor is identified as a promising cellular cofactor with integrase in facilitating the viral replication in an early stage by acting as a tethering factor in the pre-integration to the chromatin. Therefore, the present study was designed to identify a potent inhibitor by applying an E-pharmacophore based virtual screening, molecular docking, and dynamics simulation approaches. Finally, ZINC22077550 and ZINC32124441 were best identified potent molecules with the efficient binding affinity, strong hydrogen bonding, and acceptable pharmacological properties to hamper the interaction between integrase and LEDGF/p75. Further, the DFT and MDS studies were also analyzed, and shown a favorable energetic state and dynamic stability then reference compound. In conclusion, we suggest that these findings could be novel therapeutics in the future and may increase the lifespan of individuals suffering from viral infection.     

爆轰波对碰驱动平面锡飞层的动力学及动载行为特征研究

强冲击下的物质变形、破坏及诱发的轻重介质混合问题,是内爆压缩科学和工程应用领域的研究重点.本文针对爆轰波对碰条件下的复杂加载动力学过程及其动载破坏形态特征,开展数值模拟研究与极曲线理论分析.设计了爆轰波对碰驱动平面锡飞层的计算模型,获得了爆轰加载动力学过程及波系相互作用物理图像,分析了锡飞层对碰区自由表面速度历史的典型特征.给出了锡飞层中折射激波对碰发生马赫反射的临界条件,解读了三波结构的传播行为,阐明了对碰区内存在"一维正冲击"区域,一维区外存在单次斜冲击向两次斜冲击过渡的复杂加载动力学过程,提出了对碰区冲击动力学模型,揭示了影响对碰区动载行为特征的机理.数值模拟结果与极曲线理论分析结果相互印证,符合较好.本文的研究成果,将为深入理解和解读对碰区特殊的物质破坏及混合现象提供重要的理论支撑.     

基于临界电子密度的多载波微放电全局阈值分析

多载波微放电即发生在宽带、大功率真空无源微波部件中的二次电子倍增放电现象, 是影响空间和加速器应用中无源微波部件长期可靠性的主要隐患. 多载波微放电全局阈值功率的预测对于工作在真空环境中的微波部件至关重要, 但迄今尚无有效方法进行上述阈值的准确分析. 本文将微放电发生过程中二次电子分布区域等效为等离子体, 通过在理论上建立微波部件的电磁特性和电子密度间的对应关系, 提出了一种基于测试系统可检测水平的多载波微放电全局阈值功率分析方法. 为了能够通过蒙特卡罗优化方法得到全局阈值, 进一步基于电子加速的类半正弦等效, 提出了微放电演化过程中电子数涨落的快速计算方法. 基于以上两种方法得到的针对实际微波部件的全局阈值分析结果与实验结果相符合. 不同于传统基于多载波信号功率分析的经验方法, 本文基于临界电子密度判断依据和电子数涨落快速计算, 为多载波微放电全局阈值的准确预测提供了一种高效的分析方法.     

飞机外露物隐身改进设计研究

外露物在一定程度上影响飞机隐身性能,而外露物的共形设计会增加成本。针对低成本准隐身飞机,本文探讨了一种外露物的隐身改进设计,主要采取优化外形,涂敷吸波材料、提升加工工艺等措施实现低成本飞机RCS值的缩减。经过隐身仿真、隐身测试等手段,获取了外露物在不同频点、不同极化下的RCS值,并通过仿真、测试数据对比验证采取隐身改进措施的有效性,并为其它外露物隐身设计提供了设计依据和手段。     

Exciton-polaritons in lattices: A non-linear photonic simulator

Microcavity polaritons are mixed light–matter quasiparticles with extraordinary nonlinear properties, which can be easily accessed in photoluminescence experiments. Thanks to the possibility of designing the potential landscape of polaritons, this system provides a versatile photonic platform to emulate 1D and 2D Hamiltonians. Polaritons allow transposing to the photonic world some of the properties of electrons in solid-state systems, and to engineer Hamiltonians for photons with novel transport properties. Here we review some experimental implementations of polariton Hamiltonians using lattice geometries.