Discovery of a heparan sulfate binding domain in monkeypox virus H3 as an anti-poxviral drug target combining AI and MD simulations by Bin Zheng, Meimei Duan, Yifen Huang, Shangchen Wang, Jun Qiu, Zhuojian Lu, Lichao Liu, Guojin Tang, Lin Cheng, Peng Zheng

“…Using AI-based structural prediction tools and molecular dynamics (MD) simulations, we identified a novel, positively charged α-helical domain in H3 that is essential for HS binding. …”
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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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Exploration of urease-aided calcium carbonate mineralization by enzyme analyses of Neobacillus mesonae strain NS-6 by Zhiwei Ma, Mengyao Chen, Juncheng Lu, Shichuang Liu, Yanling Ma

“…Four metrics, including root mean square deviation values for mutations of those key residues in urease-urea complexes severally and wild-type, were calculated by molecular dynamics simulations when they were mutated into alanine, respectively. …”
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Membrane-targeted push-pull azobenzenes for the optical modulation of membrane potential by Valentina Sesti, Arianna Magni, Matteo Moschetta, Chiara Florindi, Marlene E. Pfeffer, Mattia Lorenzo DiFrancesco, Michele Guizzardi, Giulia Folpini, Luca Sala, Alessandra Gilda Ritacca, Beatrice Campanelli, Paola Moretti, Giuseppe Maria Paternò, Luca Maragliano, Matteo Tommasini, Francesco Lodola, Elisabetta Colombo, Fabio Benfenati, Chiara Bertarelli, Guglielmo Lanzani

“…Time-resolved spectroscopy techniques provide insights into the excited state evolution and a complete understanding of its isomerization reaction. Molecular Dynamics simulations reveal the spontaneous and stable partitioning of the compound into the cellular membrane, without significant alterations to the bilayer thickness. …”
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Harnessing the Power of Machine Learning Guided Discovery of NLRP3 Inhibitors Towards the Effective Treatment of Rheumatoid Arthritis by Sidra Ilyas, Abdul Manan, Chanyoon Park, Hee-Geun Jo, Donghun Lee

“…In this study, a multidisciplinary approach combining machine learning, quantitative structure–activity relationship (QSAR) modeling, structure–activity landscape index (SALI), docking, molecular dynamics (MD), and molecular mechanics Poisson–Boltzmann surface area MM/PBSA assays was employed to identify novel NLRP3 inhibitors. …”
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Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease by Angel D'Oliviera, Xuhang Dai, Saba Mottaghinia, Sophie Olson, Evan P Geissler, Lucie Etienne, Yingkai Zhang, Jeffrey S Mugridge

“…Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. …”
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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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Danlian-Tongmai formula improves diabetic vascular calcification by regulating CCN3/NOTCH signal axis to inhibit inflammatory reaction by Wenting Wang, Yiwen Li, Mengmeng Zhu, Qian Xu, Jing Cui, Yanfei Liu, Yanfei Liu, Yue Liu

“…Molecular docking and molecular dynamics simulation demonstrated strong binding interactions between DLTM metabolites and key molecules within the CCN3/NOTCH pathway, including NOTCH1, DLL1, DLL4, hes1, and hey1. …”
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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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Effect of hard segment content on the phase separation and properties of hydroxyl-terminated polybutadiene thermoplastic polyurethane by Boxin Liu, Zhihao Niu, Zhanglei Wang, Yimin Wang, Hua Zou, Xiuying Zhao, Shikai Hu

“…Additionally, all-atom molecular dynamics simulations were conducted to determine the number of hydrogen bonds. …”
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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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Etoposide targets 2A protease to inhibit enterovirus 71 replication by Qinqin Liang, Sai Shi, Qingjie Zhang, Yaxin Wang, Sheng Ye, Binghong Xu

“…Furthermore, both molecular dynamics simulations and site-directed mutagenesis assays revealed that Etoposide inhibited the activity of the EV71 2A protease by mainly binding to two residues, Y89 and P107. …”
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In silico analysis of the effect of HCV genotype-specific polymorphisms in Core, NS3, NS5A, and NS5B proteins on T-cell epitope processing and presentation by Samina Baig, Samina Baig, Assel Berikkara, Ramsha Khalid, Syed A. Subhan, Tanveer Abbas, Syed Hani Abidi

“…PEP-FOLD was used to model selected epitopes, followed by peptide-HLA docking using HPEPDOCK. Finally, molecular dynamics simulations were conducted for 200 ns using Desmond software to analyze differences in HLA-epitope (from different HCV genotypes) interaction kinetics and dynamics.ResultsA total of 3,410, 8,054, 6,532, and 14,015 CTL epitopes were observed in the HCV Core, NS3, NS5A, and NS5B sequences, respectively. …”
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Oxypeucedanin hydrate alleviates rheumatoid arthritis by inhibiting the TLR4-MD2/NF-κB/MAPK signaling axis by Liu Mengdan, Huo Xueyan, Li Congcong, Hu Yunjie, Lei Haoran, Wang Dong, Zhu Lin, Gu Yucheng, Guo Dale, Huang Lijun, Deng Yun

“…</sc> Molecular docking analysis suggests that OXH binds to the pocket of the TLR4/MD2 complex and interacts with specific amino acids, such as GLY-343, LYS-388, and PHE-345. Molecular dynamics simulations further confirm this conclusion. …”
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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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