Design and fabrication of {111}-textured nanotwinned silver coating for enhancing surface wear resistance of depleted uranium by Kunming Yang, Xiaobo Wang, Shengfa Zhu, Yawen Zhao, Qingdong Xu, Yiyun Wei, Chao Lu, Zhiyuan Wen, Tongxiang Fan, Mingyu Gong, Anyi Yin, Wenhua Luo

“…Meanwhile, molecular statics (MS) and molecular dynamics (MD) simulations were carried out to understand the behaviors of Ag adatoms and the tribological performance of subsequent different textured Ag. …”
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High Catalytic Selectivity of Electron/Proton Dual‐Conductive Sulfonated Polyaniline Micropore Encased IrO2 Electrocatalyst by Screening Effect for Oxygen Evolution of Seawater Ele... by Yuhan Shen, Shengqiu Zhao, Fanglin Wu, Hao Zhang, Liyan Zhu, Mingjuan Wu, Tian Tian, Haolin Tang

“…The SPTTPAB/IrO2 presents a ‐SO3H concentration of 5.62 × 10−4 mol g−1 and micropore below 2 nm numbering 1.026 × 1016 g−1. Molecular dynamics simulations demonstrate that the conjugated organic framework blocked 98.62% of Cl− in seawater from reaching the catalyst. …”
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Domperidone inhibits dengue virus infection by targeting the viral envelope protein and nonstructural protein 1 by Nuttapong Kaewjiw, Thanawat Thaingtamtanha, Damini Mehra, Wanida Chawnawa, Tanapan Prommool, Chunya Puttikhunt, Adisak Songjaeng, Kessiri Kongmanas, Panisadee Avirutnan, Prasit Luangaram, Chatchawan Srisawat, Sittiruk Roytrakul, Stephan A. Bäurle, Sansanee Noisakran

“…Domperidone was identified by pharmacophore-based virtual screening as a small molecule that can bind to both the viral envelope (E) and the nonstructural protein 1 (NS1) of DENV. Molecular dynamics (MD) simulations and surface plasmon resonance (SPR) analysis were subsequently performed to determine specific interactions of domperidone with the DENV E and NS1 proteins and their binding affinity. …”
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Systemic antihyperalgesic effect of a novel conotoxin from Californiconus californicus in an inflammatory pain model by Joaquín López-Carrillo, Johanna Bernáldez-Sarabia, Tushar J. Pawar, Samanta Jiménez, Salvador Dueñas, Andrea Figueroa-Montiel, José L. Olivares-Romero, Vinicio Granados-Soto, Alexei F. Licea-Navarro, Alexei F. Licea-Navarro, Nadia L. Caram-Salas, Nadia L. Caram-Salas

“…Structural differences between O1_cal6.4b and O1_cal6.4d were examined using in silico modeling and molecular dynamics simulations.ResultsSystemic administration of O1_cal6.4b significantly reduced thermal hyperalgesia in a dose-dependent manner without impairing motor coordination. …”
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Amebicidal and Antiadhesion Activities of Knema retusa Extract Against Acanthamoeba triangularis T4 Genotype on Contact Lenses and Modeling Simulation of Its Main Compound, E2N, Ag... by Watcharapong Mitsuwan, Imran Sama-ae, Suthinee Sangkanu, Dhrubo Ahmed Khan, Partha Biswas, Md. Nazmul Hasan, Julalak Chuprom, Tajudeen O. Jimoh, Christophe Wiart, Masyitah Binti Zulkipli, Nor Hayati Abdullah, Maria de Lourdes Pereira, Sonia M. Rodrigues Oliveira, Shanmuga Sundar Saravanabhavan, Polrat Wilairatana, Tooba Mahboob, Veeranoot Nissapatorn

“…E2N generated multiple connections via hydrogen, hydrophobic, ionic, and water bridge bonding and maintained these connections until the simulation finished, facilitating the creation of stable bindings with the β-tubulin protein as measured by molecular dynamics simulation. These findings suggest that Kre exhibits amebicidal and antiadhesion activities which could be used for the prevention of A. triangularis adhesion to contact lenses.…”
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Unveiling the inhibitory effect of hydrogen-decorated voids and dislocation loops on the glide of edge dislocation in tungsten by Qing-Yuan Ren, Yu-Hao Li, Yu-Chen Du, Tian-Ren Yang, Dmitry Terentyev, Wei-Zhong Han, Hong-Bo Zhou, Guang-Hong Lu

“…Hydrogen (H) can further exacerbate the hardening effect, but the underlying physical mechanisms remain unclear. Using molecular dynamics simulations, we investigate the impact of H aggregation within voids and ½ <111> dislocation loops on obstructing the glide of ½ <111> edge dislocations. …”
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Cooperative mechanisms of LexA and HtpG in the regulation of virulence gene expression in Pseudomonas plecoglossicida by Rongchao He, Yanfei Zuo, Qiu Li, Qingpi Yan, Lixing Huang

“…We employed an array of methods including molecular dynamics simulations, molecular docking, ChIP-seq, RNA-seq, mass spectrometry, gene mutagenesis, LacZ reporter assays, electrophoretic mobility shift assays, co-immunoprecipitation, and in vitro LexA degradation experiments. …”
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Lopinavir and Ritonavir have High Affinity Toward the SARS-CoV-2 S-protein Receptor-binding Domain Sequenced in Brazil by Aline Diogo Marinho, Helyson Lucas Bezerra Braz, João Alison de Moraes Silveira, Danilo Galvão Rocha, Roberta Jeane Bezerra Jorge, Geanne Matos de Andrade

“…Ritonavir showed a binding affinity of −8.9 kcal/mol, interacting with residues ARG148, ASN130, VAL23, SER81, ASN33, PHE29, TYR33, SER31, ASN132, ALA26, ALA30, ALA34, and TYR133.Molecular dynamics simulations confirmed the stability of the complexes formed between lopinavir and ritonavir and the RBD active site. …”
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Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis by Chen Wang, Cheng Ma, Yuanyou Xu, Shenghai Chang, Hangjun Wu, Chunlan Yan, Jinghua Chen, Yongping Wu, Shaoya An, Jiaqi Xu, Qin Han, Yujie Jiang, Zhinong Jiang, Xiakun Chu, Haichun Gao, Xing Zhang, Yunjie Chang

“…In addition, we observed dynamic interactions of the substrate translocating lipoyl domains (LDs) with both E1 and E2, and the interaction interfaces were further analyzed by molecular dynamics simulations. By revealing intrinsic dynamics of PDHc peripheral compositions, our findings indicate a distinctive activity regulation mechanism, through which the number of E1, E3 and functional LDs may be coordinated to meet constantly changing demands of metabolism.…”
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In silico development of a multi-epitope-based vaccine against Burkholderia cepacia complex using reverse vaccinology by Donya Ghorbani, Donya Ghorbani, Masoumeh Beig, Masoumeh Beig, Narjes Noori Goodarzi, Mohammad Sholeh, Mohammad Sholeh, Behzad Shahbazi, Behzad Shahbazi, Yaser Moghaddam, Farzad Badmasti

“…Molecular docking analysis was performed to assess the interaction of the selected proteins. Finally, molecular dynamics (MD) simulations were conducted using GROMACS 2019 to evaluate the feasibility and dynamics of the interactions between the chimeric MEV and Toll-like receptor complexes, TLR2 and TLR4.ResultsOf 16,723 proteins identified in B. multivorans and B. cenocepacia strains, nine proteins (six OMPs and three extracellular) were selected as ideal candidates based on established criteria. …”
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In vivo and in silico study of europinidin against streptozotocin-isoproterenol-induced myocardial damage via alteration of hs-CRP/CPK-MB/Caspase-3/Bcl-2 pathways by Khalid Saad Alharbi, Muhammad Afzal, Fahad A. Al-Abbasi, Ehssan Moglad, Salwa D. Al-Qahtani, Naif A. R. Almalki, Faisal Imam, Nadeem Sayyed, Imran Kazmi

“…Europinidin binds in silico to proteins 1NME, 1I0E, 3I2Y and 4AQ3 with energies of -7.038, -6.682, -8.6 and − 8.761 kcal/mol, respectively. While molecular dynamics simulation studies supported the interactions of europinidin with important therapeutic target proteins. …”
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Membrane-bound model of the ternary complex between factor VIIa/tissue factor and factor X by Melanie P. Muller, Alex Mortenson, Josepha C. Sedzro, Po-Chao Wen, James H. Morrissey, Emad Tajkhorshid

“…Using a novel computational methodology combining rigid-body protein-protein docking and extensive nonequilibrium molecular dynamics simulations in the explicit presence of a membrane, we developed, to our knowledge, the first atomic-level model of the EC, taking full account of the role of the membrane. …”
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Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2 by Huanyu Z. Li, Ashley C. W. Pike, Yung-Ning Chang, Dheeraj Prakaash, Zuzana Gelova, Josefina Stanka, Christophe Moreau, Hannah C. Scott, Frank Wunder, Gernot Wolf, Andreea Scacioc, Gavin McKinley, Helena Batoulis, Shubhashish Mukhopadhyay, Andrea Garofoli, Adán Pinto-Fernández, Benedikt M. Kessler, Nicola A. Burgess-Brown, Saša Štefanić, Tabea Wiedmer, Katharina L. Dürr, Vera Puetter, Alexander Ehrmann, Syma Khalid, Alvaro Ingles-Prieto, Giulio Superti-Furga, David B. Sauer

“…Here, we use a combination of cryo-electron microscopy, immunofluorescence, in vitro binding and in vivo S1P export assays, and molecular dynamics simulations to probe SPNS2’s substrate binding and transport. …”
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Artificial intelligence-enabled discovery of a RIPK3 inhibitor with neuroprotective effects in an acute glaucoma mouse model by Xing Tu, Zixing Zou, Jiahui Li, Simiao Zeng, Zhengchao Luo, Gen Li, Yuanxu Gao, Kang Zhang, Jing Ni

“…Subsequently, these target candidates were validated using molecular simulations (molecular docking, absorption, distribution, metabolism, excretion, and toxicity [ADMET] prediction, and molecular dynamics simulations) and biological experiments (Western blotting and fluorescence staining) in vitro and in vivo. …”
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Assessing the efficacy of iso-mukaadial acetate and betulinic acid against selected Plasmodium falciparum glycolytic pathway proteins: in silico and in vitro studies by Lindiwe Khumbuzile Zuma, Ofentse Jacob Pooe, Nonduduzo Hlengiwe Mabaso, John Alake, Vincent A. Obakachi, Sinethemba Yakobi, Nothando Gasa, Rajshekhar Karpoormath, Mthokozisi Simelane

“…Molecular docking and molecular dynamics simulation studies were used to measure and confirm the interactive strength of complexes. …”
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Ferula communis leaf extract: antioxidant capacity, UHPLC–MS/MS analysis, and in vivo and in silico toxicity investigations by Imad Ed-Dahmani, Mohamed El Fadili, Ghizlane Nouioura, Fahd Kandsi, Yassine El Atki, Hatem A. Abuelizz, Raffaele Conte, Fatima Zahra Lafdil, Abdeslam Taleb, Abdelfattah Abdellaoui, Mustapha Taleb

“…In addition, a detailed molecular dynamics simulation was carried out to examine the thermodynamic stability of the produced intermolecular interactions. …”
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Computational and in vitro evaluation of sumac-derived ©Rutan compounds towards Sars-CoV-2 Mpro inhibition by Muzaffar Kayumov, Parthiban Marimuthu, Parthiban Marimuthu, Jamoliddin Razzokov, Jamoliddin Razzokov, Jamoliddin Razzokov, Nurkhodja Mukhamedov, Nurkhodja Mukhamedov, Akmal Asrorov, Nodir S. Berdiev, Jamolitdin F. Ziyavitdinov, Ansor Yashinov, Ansor Yashinov, Yuliya Oshchepkova, Shavkat Salikhov, Sharafitdin Mirzaakhmedov

“…The representative docked complexes were subjected to long-range 500 ns molecular dynamics simulations. The binding free energy (BFE in kcal/mol) of components were calculated as follows: R8 (−104.636) &gt; R6 (−93.754) &gt; R7’ (−92.113) &gt; R5 (−81.115) &gt; R7 (−67.243). …”
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Breaking the biofilm barrier: Juglone derivatives as dual-action inhibitors and anti-quorum sensing agents by Muhammad Abdullah Bhatti, Atif Ali Khan Khalil, Sayed Muhammad Ata Ullah Shah Bukhari, Faisal Hanif, Mi-Jeong Ahn, Sumra Wajid Abbasi, Nazir Ahmed Lone, Wen-Jun Li, Wasim Sajjad

“…The docking studies and Molecular dynamics (MD) simulation results revealed that all molecules are actively binding in the target site that correlates well with the in-vitro inhibitory properties of compounds against S. aureus. …”
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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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