Valerenic acid attenuates pathological myocardial hypertrophy by promoting the utilization of multiple substrates in the mitochondrial energy metabolism by Tiantian Liu, Xu Chen, Qianbin Sun, Junjun Li, Qiyan Wang, Peng Wei, Wei Wang, Chun Li, Yong Wang

“…Methods: The efficacy of VA on PMH was confirmed by in vivo and in vitro experiments and the underlying mechanism was investigated by molecular dynamics (MD) simulations and specific siRNA interference. …”
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Nitidine chloride inhibits the progression of hepatocellular carcinoma by suppressing IGF2BP3 and modulates metabolic pathways in an m6A-dependent manner by Dan-dan Xiong, Zhen-dong Chen, Jian-di Li, Yu-long Deng, Rong-quan He, Zhi-guang Huang, San-qi An, Yi-wu Dang, Gang Chen

“…The target effect of NC on IGF2BP3 was verified through RT-qPCR, WB, molecular docking, molecular dynamics (MD) simulation, surface plasmon resonance (SPR), and CCK8 off-target assays. …”
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Enhanced multistress tolerance of Saccharomyces cerevisiae with the sugar transporter-like protein Stl1F427L mutation in the presence of glycerol by Zixiong Liu, Lingling Shangguan, Linglong Xu, Huiyan Zhang, Wenxin Wang, Qiao Yang, Xiaoling Zhang, Lan Yao, Shihui Yang, Xiong Chen, Jun Dai

“…Herein, we showed that the Stl1F427L mutant strain (STL) exhibits significantly improved multistress tolerance in the presence of glycerol. Molecular dynamics simulations indicated that Stl1F427L may enhance glycerol molecular binding, resulting in a significant increase in the intracellular glycerol content of the mutant strain STL. …”
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Discovery of Novel Nav1.7-Selective Inhibitors with the 1H-Indole-3-Propionamide Scaffold for Effective Pain Relief by Gaoang Wang, Hang Wu, Yingying Wang, Xiangying Liu, Shuijiao Peng, Wenxing Wang, Meijing Wu, Yifei Liu, Ercheng Wang, Zhe Wang, Lei Xu, Xiaojian Wang, Wei Yang, Haiyi Chen, Xi Zhou, Tingjun Hou

“…Notably, the structure of WN2 is quite different from previously reported aryl sulfonamide inhibitors. Molecular dynamics simulations and experimental findings reveal that the R configuration of WN2 (WN2-R) is the preferred form (IC50 = 24.7 ± 9.4 nM) within the VSDIV pocket of Nav1.7. …”
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Discovery of phloridzin as a new antagonist for Di(2-ethylhexyl) phthalate-induced male reproductive toxicity based on the adverse outcome pathway network and drug-target gene set... by Huan Gao, Xue Zhang, Ziqi Liu, Xiaoge Yang, Yajie Li, Mengxing Cui, Han Wang, Xiaoyu Chen, Weiying Zhang, Zhihan Liu, Yongjiang Yu, Liping Chen, Daochuan Li, Yongmei Xiao, Wen Chen, Qing Wang

“…Molecular docking and molecular dynamics simulations suggest that STAT3 and RUNX1 may be important targets for phloridzin to antagonize MEHP-induced MRT. …”
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A universal gelation strategy of bivalent anions to construct nanofibrous lysozyme hydrogels for immunomemory anti‐recurrence of diabetic wound infection by activating the cGAS‐STI... by Aihui Wang, Liqun Li, Liqian Zheng, Bang‐Ping Jiang, Yihao Liu, Rimei Huang, Huimin Qiu, Shichen Ji, Hong Liang, Xing‐Can Shen

“…In particular, divalent anions are found to universally drive LZF for the aggregation and transformation into three‐dimensional nanofibrous network hydrogels via electrostatic interaction, and the key role of divalent anions in the gelation is further proved by molecular dynamics simulation. In addition, near‐infrared light‐mediated photothermal characteristics are endowed with LZF to enhance its inhibitory activity of multidrug‐resistant bacteria by the skeleton modification with genipin to produce genipin‐conjuagted LZF (GLZF). …”
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On the Nature of Interplay among Major Flexibility Channels in Molecular Rotors by M. S. A. Abdel-Mottaleb

“…Furthermore, effects of molecular dynamic simulations on molecular properties in the femtosecond to picosecond time domain are studied to validate the results. …”
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Structural Properties of Liquid SiC during Rapid Solidification by WanJun Yan, TingHong Gao, XiaoTian Guo, YunXiang Qin, Quan Xie

“…The rapid solidification of liquid silicon carbide (SiC) is studied by molecular dynamic simulation using the Tersoff potential. …”
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Prediction of angiogenesis suppression by myricetin from Aeginetia indica via inhibiting VEGFR2 signaling pathway using computer-aided analysis by Marjanur Rahman Bhuiyan, Khondoker Shahin Ahmed, Md Sharif Reza, Hemayet Hossain, Syed Mumtahin Mannan Siam, Shahriar Nayan, Sarah Jafrin, Sadikur Rahman Shuvo, A.F.M.Shahid Ud Daula

“…However, among the polyphenols, myricetin exhibited an almost similar hydrogen bonding pattern with the active site of VEGFR2. The all-atom molecular dynamic simulation revealed that myricetin showed a very stable interaction with the active site of VEGFR2 throughout the simulation. …”
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Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 by López-Orozco Wendolyne, Mendoza-Huizar Humberto Luis, Álvarez-Romero Giaan Arturo, Torres-Valencia Jesús Martín, Sanchez-Zavala Maricruz

“…Additionally, the molecular docking study revealed that, alliin is able to dock to the protease Mpro of SARS-CoV-2 through interactions with the catalytic CYS145-HSD164 dyad via van der Waals interactions, with MET49 with interactions alkyl-type ions and with PHE140 by hydrogen bonds. Also, the molecular dynamic study indicates that alliin remains in the pocket site. …”
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London dispersion forces and steric effects within nanocomposites tune interaction energies and chain conformation by Baode Zhang, Snežana D. Zarić, Sonja S. Zrilić, Iosif Gofman, Barbara Heck, Günter Reiter

“…Calculation of the interaction energy and chain conformations of each PI upon CNT was performed by accurate density functional theory (DFT) calculations and molecular dynamic simulation (MDS). OPI chain adopt helically wrapping conformation around CNT with relatively strong interaction energy. …”
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Exploring Substituted Tetrazoloquinazoline: Biological Activities, Molecular Docking Analysis, and Anti-Breast Cancer MCF7/HER2 Effects by Neni Frimayanti, Ihsan Ikhtiarudin, Rahma Dona, Rahul Oktarizal, Aprilia Cindy Nurfatimah

“…This research aims to synthesize substituted tetrazoloquinazoline and evaluate its potential as an anticancer agent using molecular docking studies with the Molecular Operating Environment (MOE) software. Furthermore, molecular dynamic was also performed to analyze the binding stability of this protein-ligand complex. …”
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Senyawa Fucodiphlorethol Dan Phloroglucinol Alga Coklat Sebagai Inhibitor Lipase Secara In Silico by Yohanes Bare, Dewi Ratih Tirto Sari, Marsiana Coo Mogi, Maria Marcelina Dua Nurak

“…Therefore, we predicted that both of fucodiphlorethol and phloroglucinol inhibit lipase allosterically by altering the protein structure conformations. molecular docking analysis suggested that fucodiphlorethol and phloroglucinol have potential antiobesity effect by inhibiting lipase. Molecular dynamic are needed for further investigation.…”
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Investigation on the Binding and Conformational Change of All-trans-Retinoic Acid with Peptidyl Prolyl cis/trans Isomerase Pin1 Using Spectroscopic and Computational Techniques by GuoFei Zhu, ShaoLi Lyu, Yang Liu, Chao Ma, Wang Wang

“…Circular dichroism, fluorescence spectra, and computational simulations revealed that ATRA interacted with residues Lys63 and Arg69 of Pin1 to affect its conformational changes. Molecular dynamic simulation, principal component analysis, and free energy landscape monitored the dynamical conformational characteristics of ATRA binding to Pin1. …”
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Computer-aided approaches reveal trihydroxychroman and pyrazolone derivatives as potential inhibitors of SARS-CoV-2 virus main protease by Atatreh Noor, Hasan Shaima, Ali Bassam R., Ghattas Mohammad A.

“…Consequently, > 580,000 ligands were processed via several filtration and docking steps, then the top 21 compounds were analysed extensively via MM-GBSA scoring and molecular dynamic simulations. Interestingly, the top compounds showed favorable binding energies and binding patterns to the protease enzyme, forming interactions with several key residues. …”
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Self-Healing Effect of Various Capsule-Core Materials on Asphalt Materials by Suhua Chen, Qi Liu, Yanqiu Bi, Bin Yu, Jiupeng Zhang

“…To further investigate the self-healing mechanism of microcapsules and exclude the interference of capsule-wall materials, a bi-plate test and a molecular model of asphalt and capsule-core materials were established using dynamic shear rheometer (DSR) and molecular dynamic (MD) simulation. Firstly, the models of asphalt-rejuvenator-asphalt and asphalt-epoxy resin-asphalt were established to simulate the interface of asphalt and capsule-core materials. …”
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Rational design, synthesis, in vitro, and in-silico studies of pyrazole‑phthalazine hybrids as new α‑glucosidase inhibitors by Mehrdad Roshan, Roghieh Mirzazadeh, Azadeh Tajmir-Riahi, Mohammad Sadegh Asgari

“…All of the pharmacophoric features used in the hybrid design were found to be involved in the interaction with the enzyme’s active site, as expected. Moreover, molecular dynamic simulation and the absorption, distribution, metabolism, and excretion (ADME) have been performed.…”
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In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses. by Abu Tayab Moin, Nurul Amin Rani, Rajesh B Patil, Tanjin Barketullah Robin, Md Asad Ullah, Zahidur Rahim, Md Foyzur Rahman, Talha Zubair, Mohabbat Hossain, A K M Moniruzzaman Mollah, Nurul Absar, Mahboob Hossain, Mohammed Abul Manchur, Nazneen Naher Islam

“…Vaccine construct 1 was selected for molecular dynamic simulation studies. The simulation studies revealed that the TLR8-vaccine complex was more stable than the TLR3-vaccine complex. …”
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A new potential of sodium anthraquinone-2-sulfonate as a corrosion inhibitor for carbon steel in 0.5 M H2SO4 by Nikolay Akatyev, Roza Kenzhegalieva, Meruyet Khapiyeva, Gauhar Uzakbay, Aruzhan Talapova, Ruben Vardanyan

“…Density functional theory DFT/B3LYP/6-311+G(d,p) and molecular dynamic simulation (MD) were applied for theoretical studies to evaluate the inhibiting effect and understand the mechanism of interaction of inhibitor molecules with Fe (110) surface. …”
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The Impact of Pore Structure on Kerogen Geomechanics by Saad Alafnan

“…Eight units were initially placed in a low-density cell. Then, a molecular dynamic protocol was followed to form a final structure with a density of 1.1 g/cc; the range of density values was consistent with what has been reported in the literature. …”
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