Exploration of Potent Human α-Glucosidase Inhibitors Using In Silico Approaches: Molecular Docking, DFT, Molecular Dynamics Simulations, and MMPBSA by Jyoti Bashyal, Bimal Kumar Raut, Siddha Raj Upadhyaya, Kabita Sharma, Niranjan Parajuli

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Machine learning based QSAR and Molecular Dynamics simulations in the structural design and mechanism of action of imidazole derivatives with anti-melanoma activity by Rosalvo Ferreira de Oliveira Neto, Sérgio Ruschi Bergamachi Silva, Cintia Emi Yanaguibashi Leal, Edilson Beserra de Alencar Filho

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Screening of SIRT2 inhibitors from natural product databases using computer-aided drug design and molecular dynamics simulation by Tianyi Liu, Hongli Yin, Xue Dong, Qingyang Hu, Xuejiao Hu, Wenxin Yan, Huanhuan Wang, Zhong Li

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Thermal behavior of silica aerogel-paraffin nanocomposites in a nanochannel under varying magnetic fields: A molecular dynamics study by Yi Ru, Ali B.M. Ali, Shahram Babadoust, Rasha Abed Hussein, Mohammed Al-Bahrani, Barno Abdullaeva, Soheil Salahshour, S. Mohammad Sajadi, Sh Esmaeili

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To Probe Full and Partial Activation of Human Peroxisome Proliferator-Activated Receptors by Pan-Agonist Chiglitazar Using Molecular Dynamics Simulations by Holli-Joi Sullivan, Xiaoyan Wang, Shaina Nogle, Siyan Liao, Chun Wu

“…In this study, we docked chiglitazar into three experimentally resolved crystal structures of hPPAR subtypes, PPARα, PPARβ/δ, and PPARγ, followed by 3 μs molecular dynamics simulations for each system. Our MM-GBSA binding energy calculation revealed that chiglitazar most favorably bound to hPPARγ (-144.6 kcal/mol), followed by hPPARα (-138.0 kcal/mol) and hPPARβ (-135.9 kcal/mol), and the order is consistent with the experimental data. …”
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Predicting the polyspecificity of aminoacyl-tRNA synthetase for non-canonical amino acids using molecular dynamics simulation and MM/PBSA. by Dongheon Lee, Jong-Il Choi

“…We constructed a mutant aaRS structure specific for AzF through homology modelling and conducted docking studies with tyrosine and five ncAAs, followed by molecular dynamics simulations. The binding affinity was calculated using the molecular mechanics/Poisson-Boltzmann surface area, focusing on nonpolar solvation terms. …”
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Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis by Huan Yang, Umberto Raucci, Siddharth Iyer, Galib Hasan, Thomas Golin Almeida, Shawon Barua, Anni Savolainen, Juha Kangasluoma, Matti Rissanen, Hanna Vehkamäki, Theo Kurtén

“…Here, we explore the oxidation of α-pinene, a critical atmospheric biogenic VOC, using a novel reaction discovery approach based on molecular dynamics and state-of-the-art enhanced sampling techniques. …”
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Binding Mode Investigation of Polyphenols from Scrophularia Targeting Human Aldose Reductase Using Molecular Docking and Molecular Dynamics Simulations by Abinaya Manivannan, Prabhakaran Soundararajan, Yoo Gyeong Park, Sugunadevi Sakkiah, Byoung Ryong Jeong

“…Interestingly, the biological activity predictions also ranked acacetin with higher probability score for aldose reductase inhibition activity. Moreover, the molecular dynamics simulation of ALR2-acacetin complex was validated for the stability of ligand binding and the refined complex was used for generation of receptor-ligand pharmacophore model. …”
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Microstructure and transport properties of lithium hexafluorophosphate solutions in binary mixture of dimethyl carbonate with ethylene carbonate from molecular dynamics simulation by Dmytro Dudariev, Yevhenii Holubenko, Rebie Jallah, Oleg Kalugin

“…For the microscopic interpretation of this phenomenon for one of the most popular electrolytes, LiPF6 solutions in a binary mixture of dimethyl carbonate (DMC) / ethylene carbonate (EC) (1:1), molecular dynamics simulations of the corresponding systems with a salt content of 0.1, 0.5, 1.0, 1.5 and 2.0 M were performed. …”
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Leveraging computational approaches in identifying novel HER-2 + breast cancer potential therapeutics: integrating virtual screening and molecular dynamics simulation by Olawale Quadri Bolaji, Temitope Isaac Adelusi, Taiwo Ooreoluwa Ojo, Ibrahim Damilare Boyenle, Abdul-Quddus Kehinde Oyedele, Taiwo Temitope Ogunjobi, Adegboye Oyewole Oyaronbi, Sukurat Oluwatoyin Ayoola, Abdeen Tunde Ogunlana

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Investigation the CMP process of 6 H-SiC in H2O2 solution with ReaxFF molecular dynamics simulation by Yanzhang Gu, Kaiping Feng, Lanxing Xu, Liang Zhao, Tianchen Zhao, Binghai Lyu

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Active Ingredients and Potential Mechanism of Additive Sishen Decoction in Treating Rheumatoid Arthritis with Network Pharmacology and Molecular Dynamics Simulation and Experimental Verification by Ren J, Liu Z, Qi X, Meng X, Guo L, Yu Y, Dong T, Li Q

“…The binding mode between the key ingredients and key targets was elucidated using molecular docking and molecular dynamics simulation.Results: In all, 75 ASSD active ingredients and 1258 RA targets were analyzed, of which kaempferol, luteolin, and quercetin were considered key components that mainly act through inflammation-related pathways, such as the PI3K-AKT, TNF, and IL-17 signaling pathways, to ameliorate RA. …”
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Engineering and design of a COF-coated probe for the detection and removal of flumequine and enrofloxacin antibiotics in foodstuffs: a molecular dynamics simulation approach by Alireza Nakhaei, Heidar Raissi, Maryam Alaei, Farzaneh Farzad

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Mechanism of Radix Bupleuri and Hedysarum Multijugum Maxim drug pairs on liver fibrosis based on network pharmacology, bioinformatics and molecular dynamics simulation. by Lefei Yu, Pan Yu, Yongchang Cao, Weiya Cao

“…This study aims to explore the mechanism of RB-HMM drug pairs in treating liver fibrosis by using network pharmacology, bioinformatics, molecular docking, molecular dynamics simulation technology and in vitro experiments. …”
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Molecular dynamics simulations reveal efficient heavy metal ion removal by two-dimensional Cu-THQ metal-organic framework membrane by Jinjun Chen, Zonglin Gu, Jose Manuel Perez-Aguilar, Yanbo Luo, Kuifeng Tian, Yuqi Luo

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How cells align to structured collagen fibrils: a hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions by Koen A. E. Keijzer, Erika Tsingos, Erika Tsingos, Roeland M. H. Merks, Roeland M. H. Merks

“…We present a hybrid computational model coupling three mathematical approaches: first, the cellular Potts model (CPM) describes an individual contractile cell; second, molecular dynamics (MD) represent the ECM as a network of cross-linked, deformable fibers; third, a set of ordinary differential equations (ODEs) describes the dynamics of the cell’s FAs, in terms of a balance between assembly and a mechanoresponsive disassembly. …”
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Enhanced Ion Solvation and Conductivity in Lithium-Ion Electrolytes via Tailored EMC-TMS Solvent Mixtures: A Molecular Dynamics Study by Jitti Kasemchainan, Siriporn Teeraburanapong, Manaswee Suttipong

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Molecular docking and molecular dynamics simulation studies of inhibitor candidates against Anopheles gambiae 3-hydroxykynurenine transaminase and implications on vector control by Eunice O. Adedeji, Olubanke O. Ogunlana, Gbolahan O. Oduselu, Rainer Koenig, Ezekiel Adebiyi, Opeyemi S. Soremekun, Segun Fatumo

“…The top three identified hits were subjected to 300 ns molecular dynamics simulation using AMBER 18 and ADMET analysis using SWISSADME predictor and ADMETSAR. …”
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Unveiling the mechanism of action of a novel natural dual inhibitor of SARS-CoV-2 Mpro and PLpro with molecular dynamics simulations by Xiaoxia Gu, Xiaotian Zhang, Xueke Zhang, Xinyu Wang, Weiguang Sun, Yonghui Zhang, Zhengxi Hu

“…Sydowiol B interacts with the nano-channel at the Mpro dimer interface and the PLpro active site. Molecular dynamics simulations suggest that sydowiol B inhibits Mpro by limiting active site expansion rather than inducing collapse. …”
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Structural tailoring of etoricoxib: A spectrochemical, medicinal and pharmacological study by Bakul Akter, Silvia Aishee, Abdullah Hridoy, Md. Mehedi Hasan Pulok, Mohammad Ariful Islam, Antu Biswas, Aurna Patwary, Majedul Hoque, MD. Sazidul Islam, Md. Nipatul Hasan Nirob, Faisal Islam Chowdhury, Monir Uzzaman

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