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

“…The solubility, structural characteristics, transmission electron microscopy, asymmetric-flow field-flow fractionation, steady shear rheological property and multiple light scattering of MP deamidated by PG (MP-PG) and MP pretreated with ultrasound followed by PG deamidation (MP-U-PG) were determined. Molecular docking and molecular dynamics (MD) simulations were used to estimate the interaction between PG and MP. …”
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Repurposing the Antidiabetic Drugs Glyburide, Gliquidone, and Glipizide in Combination with Benznidazole for <i>Trypanosoma cruzi</i> Infection by Citlali Vázquez, Rusely Encalada, Isabel Jiménez-Galicia, Rogelio Gómez-Escobedo, Gildardo Rivera, Benjamín Nogueda-Torres, Emma Saavedra

“…<b>Background/Objective</b>: Glyburide, glipizide, and gliquidone, hypoglycemic drugs for diabetes treatment, were previously predicted to bind to dihydrofolate reductase-thymidylate synthase from <i>T. cruzi</i> by in silico docking analysis; they also showed antiproliferative effects against <i>T. cruzi</i> epimastigotes, the stage of the insect vector. …”
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Theoretical Study of Sphingomyelinases from <i>Entamoeba histolytica</i> and <i>Trichomonas vaginalis</i> Sheds Light on the Evolution of Enzymes Needed for Survival and Colonizati... by Fátima Berenice Ramírez-Montiel, Sairy Yarely Andrade-Guillen, Ana Laura Medina-Nieto, Ángeles Rangel-Serrano, José A. Martínez-Álvarez, Javier de la Mora, Naurú Idalia Vargas-Maya, Claudia Leticia Mendoza-Macías, Felipe Padilla-Vaca, Bernardo Franco

“…AlphaFold3 models predicted the occupancy of cobalt ions in the active site of the aSMase6 enzyme. Cavity blind docking showed that the substrate is pushed outward of the active site when cobalt is bound instead of magnesium ions. …”
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In Silico Analysis Revealed Five Novel High-Risk Single-Nucleotide Polymorphisms (rs200384291, rs201163886, rs193141883, rs201139487, and rs201723157) in ELANE Gene Causing Autosom... by Khyber Shinwari, Mikhail A. Bolkov, Muhammad Yasir Akbar, Liu Guojun, Svetlana S. Deryabina, Irina A. Tuzankina, Valery. A. Chereshnev

“…We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking. This research sheds light on how ELANE failure upon mutation results in disease progression, including congenital neutropenia, and validation of these novel predicted nsSNPs is required through the wet lab.…”
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Typical and atypical metabolic characteristics of three iridaceae isoflavone components: in vitro and in silico studies by Jifeng Gu, Jifeng Gu, Huishan Zhang, Mei Wang, Yuyang Zhou, Yuyang Zhou, Zhipeng Deng, Rong Shi

“…However, the metabolic characteristics of isoflavone aglycones remain unclear.MethodsIn this study, human liver microsomes (HLMs) and Cytochrome P450 (CYP) recombinant enzymes were used to study the metabolic stability, identify the metabolic pathways and enzyme kinetics of these three components, and elucidate their possible binding sites through molecular docking.ResultsWhen tectorigenin, irigenin, and irisflorentin were co-incubated with HLMs and CYP recombinant enzymes, hydroxylation metabolite for tectorigenin, demethylated metabolite for irigenin, and 6,7-dihydroxy-5,3′,4′,5′-tetramethoxy isoflavone originating from irisflorentin were identified. …”
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Mechanisms underlying the effects of cyanogenesis on development and reproduction of Tetranychus urticae: Insights from enzyme activity and gene expression aspects by Mufeng Wu, Xiao Liang, Ying Liu, Chunling Wu, Xingkui An, Zihua Zhao, Guifeng Hao, Ijiti Oluwole Gregory, Zhihong Li, Qing Chen

“…Linamarin-β-GLU (lima bean-derived) presented prompt HCN release, and molecular docking indicated higher binding energy and more robust binding sites compared with other two groups, i.e., lotaustralin-β-GLU (lima bean-derived) and amygdalin-β-GLU (almond-derived). …”
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Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach by Rohit Pritam Das, V. Badireenath Konkimalla, Surya Narayan Rath, Jagadish Hansa, Manaswini Jagdeb

“…Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. …”
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Antioxidant Bio-Compounds from Chestnut Waste: A Value-Adding and Food Sustainability Strategy by Roberta Barletta, Alfonso Trezza, Andrea Bernini, Lia Millucci, Michela Geminiani, Annalisa Santucci

“…Furthermore, the cytotoxicity assay demonstrated the safety of all three extracts in the tested human cell lines. In silico docking simulations further validated the biological relevance of these compounds by predicting strong hydrophobic and polar interactions with oxidative stress-related protein targets. …”
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Increased TSPO alleviates neuropathic pain by preventing pyroptosis via the AMPK-PGC-1α pathway by Baolong Li, Kaiming Yu, Xiongyao Zhou, Jialu Sun, Le Qi, Weiye Li, Tuo Yang, Weizhen Li, Ningning Wang, Xiaosong Gu, Shusen Cui, Rangjuan Cao

“…Through drug screening, molecular docking, and behavioral assays, we identified zopiclone as a promising TSPO-targeting drug for pain treatment. …”
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Exploring purine analogues as inhibitors against Katanin, a microtubule severing enzyme using molecular modeling approach by Vibhuti Saxena, Pruthanka Patil, Purva Khodke, Bajarang Vasant Kumbhar

“…A total of 276,280 purine-type compounds from the PubChem database were subjected to structure-based high-throughput virtual screening, followed by ADME prediction, PASS analysis, and molecular docking studies. These efforts led to the identification of two potent compounds: PubChem CID 122589735 and 123629569, which demonstrated strong binding interactions with katanin. …”
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Exploring the anti-metastatic potential of sunitinib and novel analogs in colorectal cancer: insights into HIF-1α mediated metastasis by Fatemeh B. Rassouli, Maryam M. Matin, Maryam M. Matin, Farzin Hadizadeh, Farzin Hadizadeh, Masoud Nejabat, Hossein Allahverdizadeh, Hamidreza Jamali, Shahin Gharedaghi, Halimeh Hassanzadeh

“…For in vitro studies, analogs of sunitinib were synthesized, and cells were assessed for viability, migration, invasion, MMPs activity and gene expression in hypoxic condition.Results and DiscussionComputational analyses highlighted the importance of HIF-1α as a crucial mediator of metastasis in CRC. Molecular docking and dynamics simulations demonstrated favorable and stable interaction of sunitinib and three novel analogs with HIF-1α PAS-B domain. …”
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Structural and free energy landscape analysis for the discovery of antiviral compounds targeting the cap-binding domain of influenza polymerase PB2 by Amr S. Abouzied, Saad Alqarni, Kareem M. Younes, Sanad M. Alanazi, Dana M. Alrsheed, Rawabi K. Alhathal, Bader Huwaimel, Akram M. Elkashlan

“…We employed a comprehensive computational approach involving virtual screening, molecular docking, and 500 ns molecular dynamics (MD) simulations. …”
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Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein by Oscar Herrera-Calderon, Abdulrahman M. Saleh, Andres F. Yepes-Perez, Nada H. Aljarba, Saad Alkahtani, Gaber El-Saber Batiha, Renan Dilton Hañari-Quispe, Haydee Chavez, Josefa Bertha Pari-Olarte, Eddie Loyola-Gonzales, José Santiago Almeida-Galindo, José Francisco Kong-Chirinos, Taoufiq Benali

“…The aim in this computational study was to determine the main phytochemical constituents from U. tomentosa stem bark against the SARS-CoV-2 Omicron spike protein based on molecular modeling. A molecular docking was carried out on the isolated phytochemicals in a previous work against the SARS-CoV-2 Omicron spike protein-binding domain (PDB ID: 7T9K). …”
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The multi-target mechanism of action of Selaginella doederleinii Hieron in the treatment of nasopharyngeal carcinoma: a network pharmacology and multi-omics analysis by Huaguo Liang, Caifu Fang, Meng Qiu

“…Single-cell RNA sequencing analysis revealed the expression distribution of key genes across different immune cell types and explored their roles in the differentiation process of malignant cells through pseudotime trajectory analysis. Molecular docking and dynamics simulation results indicated that the Berberine-MAPK14 and Matairesinol-PLK1 complexes have high binding affinity and stability. …”
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Rutaecarpine alleviates hepatic ischemia‒reperfusion injury in liver transplantation by inhibiting inflammatory response and oxidative stress by Yan Liu, Yan Liu, Feng Qi, Lun-Jian Xiang, Zhu-Jun Yi, Sheng-Wei Li

“…Mechanistically, bioinformatics analysis and in vivo and in vitro experiments revealed that PDE4B may be a key target by which Rut exerts its protective effect, and molecular docking and cellular thermal shift assay confirmed this result. …”
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Total glucosides of paeony ameliorates chemotherapy-induced neuropathic pain by suppressing microglia pyroptosis through the inhibition of KAT2A-mediated p38 pathway activation and... by Rong Chen, Jiantao Hu, Yang Zhang, Yang Liu, Jingsong Zhu, Zheng Pan, Hua Yang, Qin Wang, Ying Chen, Songjiang Tang, Baojun Min

“…Quantitative real-time PCR and molecular docking were employed to identify TGP targets, while phospho-kinase arrays, western blotting, and co-immunoprecipitation were used to elucidate the mechanism. …”
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Anticonvulsant Effects of Synthetic <i>N</i>-(3-Methoxybenzyl)oleamide and <i>N</i>-(3-Methoxybenzyl)linoleamide Macamides: An In Silico and In Vivo Study by Karin Jannet Vera-López, Jorge Alberto Aguilar-Pineda, Rodrigo Martín Moscoso-Palacios, Gonzalo Davila-Del-Carpio, José Luis Manrique-Murillo, Badhin Gómez, Minerva González-Melchor, Rita Nieto-Montesinos

“…MD simulations, molecular docking, and MM/PBSA calculations were used for these purposes. …”
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Baicalein inhibits PRRSV through direct binding, targeting EGFR, and enhancing immune response by Jing Wu, Qi Lu, Jing Hou, Yueqin Qiu, Min Tian, Li Wang, Kaiguo Gao, Xuefen Yang, Zongyong Jiang

“…The results of molecular docking and dynamics (MD) simulations confirmed that baicalein has a high binding affinity for EGFR, with a measured value of − 7.935 kcal/mol. …”
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Diet with high content of advanced glycation end products induces oxidative stress damage and systemic inflammation in experimental mice: protective effect of peanut skin procyanid... by Li Zhao, Xingxing Zhang, Langzhi He, Yubing Li, Yue Yu, Qun Lu, Rui Liu

“…In addition, the levels of superoxide dismutase (SOD), glutathione (GSH), catalase (CAT) in liver and kidney of mice were increased (P &lt; 0.05), and the level of malondialdehyde (MDA) was decreased (P &lt; 0.05), which enhanced the antioxidant capacity of mice in vivo, and improved the oxidative damage of liver and kidney. Molecular docking technique was used to confirm that the parent compound of procyanidins and its main metabolites, such as 3-hydroxyphenylacetic acid, could interact with RAGE, which might inhibit the activation of nuclear transcription factor (NF-κB), and ultimately reduce oxidative stress and inflammation in mice.…”
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Parishin B blocking TRIB3-AKT1 interaction inhibits breast cancer lung metastasis by Xiongtao Cheng, Xiongtao Cheng, Jianguo Sun, Shouhong Chen, Nan Wang, Weijing Tang, Zijian Xia, Yuhong Shu, Shouhong Gao, Zhipeng Wang, Xinxia Wang, Rongzi Shao, Jianxiong Cao, Jianxiong Cao

“…Thus, this study aim to find drugs that can bind to TRIB3 to inhibit BC progression, and further elucidate its mechanism.MethodsThe possible inhibitors of TRIB3 were screened by high-throughput molecular docking, CETSA, and CO-IP assay. Then, the effect of TRIB3 inhibitor anti BC was assessed by CCK-8 assay, flow cytometry, plate colony formation assay, and transwell assay; and the RNA-seq was empolyed to study the potential mechanism of Parishin B (PB) anti-BC. …”
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