Therapeutic potential of Curcuma longa against monkeypox: antioxidant, anti-inflammatory, and computational insights by Farouk Boudou, Amal Belakredar, Ahcen Keziz, Linda Aissani, Huda Alsaeedi, David Cronu, Mikhael Bechelany, Mikhael Bechelany, Ahmed Barhoum

“…Molecular docking and molecular dynamics (MD) simulations were performed to evaluate the interactions between curcuminoids and monkeypox virus proteins.ResultsThe aqueous extract of C. longa was prepared via decoction, yielding 7.80% ± 0.81% extract with curcumin as the predominant compound (36.33%). …”
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Designing a multi-epitope vaccine candidate against human rhinovirus C utilizing immunoinformatics approach by Tajul Islam Mamun, Tajul Islam Mamun, Md. Ahad Ali, Md. Nazmul Hosen, Jillur Rahman, Md. Anwarul Islam, Md. Golam Akib, Kamruz Zaman, Md. Masudur Rahman, Md. Masudur Rahman, Ferdaus Mohd Altaf Hossain, Ferdaus Mohd Altaf Hossain, Samir Ibenmoussa, Mohammed Bourhia, Turki M. Dawoud

“…V2 exhibited strong antigenicity, non-allergenicity, and solubility, with a solubility score greater than 0.550, and demonstrated excellent structural stability, with 91.9% of residues in the most favorable regions of the Ramachandran plot. Molecular dynamics and simulation studies revealed a stable Vaccine-TLR8 complex, with a binding energy of -296.15 and consistent RMSD values. …”
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3D-QSAR, design, molecular docking and dynamics simulation studies of novel 6-hydroxybenzothiazole-2-carboxamides as potentially potent and selective monoamine oxidase B inhibitors by Dong Xie, Dong Xie, Yongzheng Tian, Li Cao, Penghang Guo, Penghang Guo, Zhibiao Cai, Jie Zhou

“…Finally, the binding stability and dynamic behavior of these compounds with MAO-B receptors were analyzed by molecular dynamics simulation (MD).ResultsThe 3D-QSAR model showed good predictive ability, with a q2 value of 0.569, r2 value of 0.915, SEE of 0.109 and F value of 52.714 for the COMSIA model. …”
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Deciphering the role of flutamide, fluorouracil, and furomollugin based ionic liquids in potent anticancer agents: Quantum chemical, medicinal, molecular docking and MD simulation... by Danish Ali, Muhammad Arif Ali, Muhammad Sarfraz, Afifa Yousuf, Rasham Zulfiqar, Abdul Rauf, Hong-Liang Xu, Muhammad Arshad

“…Additionally, in silico docking investigations against the protein (PDB ID: 1B38) showed that all designed ligands [FT1]+, [FT2]+, [FU1]+, [FM1]+, and [FM2]+ display binding affinities values of −7.82, −6.30, −6.09, −5.86, and −7.72 kcal/mol superior to both the reference and reported drug fluorouracil. Molecular dynamics (MD) simulation reinforced the docking results by utilizing root mean square deviation (RMSD) values of [FT1]+ varies from 0.147387 to 0.539310 Å and [FM2]+ lies between 0.138098 Å and 0.583763 Å and root means square fluctuation (RMSF) values for [FT1]+ was 0.069428–0.298235Å and [FM2]+ 0.070097–0.364413Å provides insight into stability and the time-dependent atomic deviations. …”
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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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Targeting KRAS G12C and G12S mutations in lung cancer: In silico drug repurposing and antiproliferative assessment on A549 cells by Mansour S. Alturki, Nada Tawfeeq, Amal Alissa, Zahra Ahbail, Mohamed S. Gomaa, Abdulaziz H. Al Khzem, Thankhoe A. Rants'o, Mohammad J. Akbar, Waleed S. Alharbi, Bayan Y. Alshehri, Amjad N. Alotaibi, Fahad A. Almughem, Abdullah A. Alshehri

“…The computational studies involved virtual screening, induced fit, and covalent docking, and molecular dynamics simulations, and identified five promising candidates, the antibiotics; capreomycin, cefadroxil, and Cefdinir, the antifungal; natamycin, and the anti-inflammatory, cortisone. …”
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Systematic free energy insights into the enhanced dispersibility of myofibrillar protein in low-salt solutions through ultrasound-assisted enzymatic deamidation by Yating Liu, Zongyun Yang, Zhen Li, Juan Shen, Xia Wang, Ru Li, Ye Tao, Xinglian Xu, Peng Wang

“…Molecular docking and molecular dynamics (MD) simulations were used to estimate the interaction between PG and MP. …”
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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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Rapid spread of the SARS-CoV-2 Omicron XDR lineage derived from recombination between XBB and BA.2.86 subvariants circulating in Brazil in late 2023 by Ighor Arantes, Kimihito Ito, Marcelo Gomes, Felipe Cotrim de Carvalho, Walquiria Aparecida Ferreira de Almeida, Ricardo Khouri, Fabio Miyajima, Gabriel Luz Wallau, Felipe Gomes Naveca, Elisa Cavalcante Pereira, Marilda Mendonça Siqueira, Paola Cristina Resende, Gonzalo Bello

“…By utilizing phylogenetic and epidemiological methods, this research provides important insights into the molecular dynamics of XDR, which could inform public health responses and vaccine composition updates. …”
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Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels by Arnaud PJ Giese, Wei-Hsiang Weng, Katie S Kindt, Hui Ho Vanessa Chang, Jonathan S Montgomery, Evan M Ratzan, Alisha J Beirl, Roberto Aponte Rivera, Jeffrey M Lotthammer, Sanket Walujkar, Mark P Foster, Omid A Zobeiri, Jeffrey R Holt, Saima Riazuddin, Kathleen E Cullen, Marcos Sotomayor, Zubair M Ahmed

“…Our AlphaFold 2 models suggest that vertebrate CIB proteins can simultaneously interact with at least two cytoplasmic domains of TMC1 and TMC2 as validated using nuclear magnetic resonance spectroscopy of TMC1 fragments interacting with CIB2 and CIB3. Molecular dynamics simulations of TMC1/2 complexes with CIB2/3 predict that TMCs are structurally stabilized by CIB proteins to form cation channels. …”
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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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5,7-Dihydroxyflavone acts on eNOS to achieve hypotensive effects in spontaneously hypertensive rats by Zi-Han Shen, Tongjie Ye, Baozhen Chen, Congchao Wan, Xiaolin Lu, Ting-Hsu Chen, Shuang Lin, Jia-Xin Ye, Liping Xie, Yaw-Syan Fu

“…In-silico studies were applied by network pharmacology, molecular docking, and molecular dynamic simulation. Based on the information of network pharmacology, 5,7-dihydroxyflavone could act on several different blood pressure regulating pathways, molecular docking results confirmed it might direct binding on the active pocket of eNOS, and the average molecular distance between 5,7-dihydroxyflavone -eNOS is less than 0.4 Å by molecular dynamic simulation. …”
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Nitrogen Adsorption Studies on Non-Porous Silica: The Annealing Effect over Surface Non-Bridging Oxygen Atoms by Carmelo Herdes, Patrícia A. Russo, M. Manuela L. Ribeiro Carrott, Peter J.M. Carrott

“…This contribution compares experimental nitrogen adsorption isotherms with molecular simulation results on effective non-porous silica models. A Molecular Dynamic (MD) annealing temperature scheme was adopted for the formulation of three samples of the solid surface. …”
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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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The effects of disordered edge and vanishing friction in microscale structural superlubric graphite contact by Hengqian Hu, Jin Wang, Kaiwen Tian, Quanshui Zheng, Ming Ma

“…The mechanism is revealed by all-atom molecular dynamic simulations, which reproduce the measured friction qualitatively. …”
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