First molecules to reactivate RASG12V GTPase activity by Aneta Wlodarczyk, Cezary Treda, Marcin Pacholczyk, Adrianna Rutkowska, Marta Wegierska, Amelia Kierasinska-Kalka, Katarzyna Wasiak, Damian Ciunowicz, Dagmara Grot, Pawel Glowacki, Ewelina Stoczynska-Fidelus, Piotr Rieske

“…Methods The compounds were initially identified through virtual screening, and their optimal binding conformation in the RAS SW-II pocket was determined using the flexible docking technique. Efficacy was verified based on the IC50 determination, GTPase activity, as well as the AKT and ERK phospho WB assays. …”
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Proteome-Wide Identification and Comparison of Drug Pockets for Discovering New Drug Indications and Side Effects by Renxin Zhang, Zhiyuan Chen, Shuhan Li, Haohao Lv, Jinjun Li, Naixue Yang, Shaoxing Dai

“…We repositioned progesterone to ADGRD1 for pemphigus and breast cancer, as well as estradiol to ANO2 for shingles and medulloblastoma, which were validated via molecular docking. Off-target effects were analyzed to assess the safety of drugs such as axitinib, linking newly identified targets with known side effects. …”
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The future of plant lectinology: Advanced technologies and computational tools by Vinicius J.S. Osterne, Kyria S. Nascimento, Benildo S. Cavada, Els J.M. Van Damme

“…Additionally, computational methods—including molecular docking, molecular dynamics simulations, and machine learning pipelines—support predictions of lectin structures and binding properties, underpinning experimental efforts. …”
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Nystose attenuates bone loss and promotes BMSCs differentiation to osteoblasts through BMP and Wnt/β-catenin pathway in ovariectomized mice by Qi Zhang, Sijing Hu, Jianjun Wu, Peng Sun, Quanlong Zhang, Yang Wang, Qiming Zhao, Ting Han, Luping Qin, Qiaoyan Zhang

“…The luciferase activities and the molecular docking analysis further supported the mechanism of NST. …”
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Mitochondrial Mayhem: How cigarette smoke induces placental dysfunction through MMS19 degradation by Pei Zhou, Feng Jin, Shenshen Yao, Ben Sun, Ni Sun, Hongbo Guan, Xiaomei Liu

“…Studies using HTR-8/Sneo cells demonstrated that cigarette smoke extract (CSE) inhibits trophoblast proliferation, activates autophagy, and induces apoptosis by impairing the CIA pathway and ISC proteins. Molecular docking analysis revealed that nicotine and nicotyrine bind to and promote the autophagic-dependent degradation of MMS19, a key component of the CIA complex. …”
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Study on the regulation of tea polyphenols on the structure and gel properties of myofibrillar protein from Neosalanx taihuensis by Xiangxiang Ni, Mengting Li, Zhiwei Huang, Yinyin Wei, Chaoyi Duan, Ruixi Li, Yajie Fang, Xiu Wang, Mingfeng Xu, Rongrong Yu

“…The research results indicated that the WHC of the EGCG group had increased by 17.06 % compared to the oxidized group, and the decrease in amino content reached as much as 40.09 %. Finally, molecular docking simulations were performed to explore the ways in which TP and MP interact. …”
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Design, synthesis, and anti-inflammatory activity of 2H-1,4-benzoxazin-3(4H)-one derivatives modified with 1,2,3-triazole in LPS-induced BV-2 cells by Xixi Hou, Xixi Hou, Longfei Mao, Huibin Zhang, Lan Wang, Baoyu He, Jingjing Guo, Jianji Wang

“…The results indicated that the 2H-1,4-benzoxazin-3(4H)-one derivatives significantly activated the Nrf2-HO-1 pathway, reduced LPS-induced ROS production, and alleviated microglial inflammation. Molecular docking studies suggested that compounds e2, e16, and e20 could interact with Nrf2-related binding sites, preventing its degradation by Keap1. …”
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Deep-Sea-Derived Isobisvertinol Targets TLR4 to Exhibit Neuroprotective Activity via Anti-Inflammatory and Ferroptosis-Inhibitory Effects by Zi-Han Xu, Ming-Min Xie, Chun-Lan Xie, Xian-Wen Yang, Jun-Song Wang

“…Using LPS-induced microglial inflammation and RSL3-induced neuronal ferroptosis models, we found that <b>17</b> targets TLR4 to provide neuroprotection. Molecular docking studies revealed that <b>17</b> inhibits TLR4 activation by occupying the hydrophobic pocket at the TLR4-MD2 binding site. …”
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Organophosphate esters inhibit enzymatic proteolysis through non-covalent interactions by Zeming Wang, Wei Zhang, Xiaojie Hu, Yanzheng Gao

“…Further spectroscopic experiments and molecular docking simulations showed that OPEs could entered the pocket structure of GB1 and induced secondary structural changes and protein folding through non-covalent interactions dominated by hydrogen bonding and van der Waals forces. …”
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Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis by Hamza Arshad Dar, Yasir Waheed, Muzammil Hasan Najmi, Saba Ismail, Helal F. Hetta, Amjad Ali, Khalid Muhammad

“…Structural modeling of the vaccine was performed, and molecular docking analysis strongly suggested a positive association of a multiepitope vaccine with Toll-like Receptor 3. …”
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Dummy Template Molecularly Imprinted Polymers for Electrochemical Detection of Cardiac Troponin I: A Combined Computational and Experimental Approach by Mohammad Sadegh Sadeghi Googheri, Davide Campagnol, Paolo Ugo, Samira Hozhabr Araghi, Najmeh Karimian

“…This study aimed to design a DT-MIP for cTnI detection using cytochrome <i>c</i> (Cyt <i>c</i>) as the template, combining computational and experimental approaches. Molecular docking identified binding sites on Cyt <i>c</i> and cTnI for poly(o-phenylenediamine) (5PoPD) pentamers. …”
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An In silico Approach towards Finding the Cancer-Causing Mutations in Human MET Gene by Fayeza Sadia Laskar, Md. Nazmul Islam Bappy, Md. Sowrov Hossain, Zenifer Alam, Dilruba Afrin, Sudeb Saha, Kazi Md. Ali Zinnah

“…These findings along with the docking results are indicating the potency of the identified SNPs to alter the structure and function of the protein, which may lead to the development of cancers. …”
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Utilizing the subtractive proteomics approach to design ensemble vaccine against Candida lusitaniae for immune response stimulation; a bioinformatics study. by Habiba Naz, Rimsha Timotheous, Muhammad Farhan Sarwar, Tariq Nadeem, Mudassar Fareed Awan, Sajed Ali, Sophia Awais, Irfan Ahmed

“…The structural modelling of all the selected vaccine candidates was then performed to proceed them further for docking with the human toll-like receptor 2 (TLR2). …”
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Synthesis, in silico and antimicrobial activity study of substituted aromatic imines and their corresponding amines by Hanna Abbo, Darin Edward Holman, Mohamed-Deen Hendricks, Christiana Abimbola Salubi, Marshall Keyster, Salam Titinchi

“…The present study involved the synthesis of Schiff base compounds and their corresponding sec-amines, characterization, antibacterial testing, and molecular docking studies. These compounds featured diverse structural components, including alkyl chains, phenyl and methoxy groups. …”
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Temporal and Spatial eDNA Analysis of Fish Assemblages in Postindustrial, Urban Coastal Habitats by Alice Cunnington, Erika Neave, Peter Shum, Rupert Collins, Stefano Mariani

“…Over a 12‐month period, we conducted nine water sampling trips at two locations: the Albert Docks in central Liverpool, and the Marine Lake in West Kirby. …”
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In Silico Inhibitability of Copper Carbenes and Silylenes against Rhizoctonia solani and Magnaporthe oryzae by Nguyen Thi Thanh Hai, Thanh Q. Bui, Tran Thi Ai My, Huynh Thi Phuong Loan, Tran Thai Hoa, Phan Tu Quy, Nguyen Thi Thu Thuy, Dang Thanh Nhan, Nguyen Thi Ai Nhung

“…Their inhibitability towards the targeted proteins was evaluated using molecular docking simulation. Quantum analysis predicts the stability of the investigated complexes and thus their practical existability and practicable synthesisability. …”
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Network pharmacology combined with experimental verification for exploring the potential mechanism of phellodendrine against depression by Lili Hu, Na Wu, Jue Wang, Donghui Cai

“…The intersection targets between PHE and MDD were obtained to identify as targets for PHE against MDD, followed by protein–protein interaction network, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. Molecular docking was applied to further confirm the anti-MDD effects of PHE. …”
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Explication of Pharmacological Proficiency of Phytoconstituents from Adansonia digitata Bark: An In Vitro and In Silico Approaches by Sangavi P., Gowtham Kumar S., Nachammai KT., Chandrabose Selvaraj, Langeswaran K.

“…The study concluded that the Adansonia digitata bark extract and its phytocompound have potential therapeutic efficacy against the target proteins. The best docking scores were about −7.053 kcal/mol and −7.573 kcal/mol for Pseudomonas aeruginosa and C2 kinase (antioxidant), respectively. …”
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Virtual Screening, Toxicity Evaluation and Pharmacokinetics of Erythrina Alkaloids as Acetylcholinesterase Inhibitor Candidates from Natural Products by Permana A, Akili AWR, Hardianto A, Latip JB, Sulaeman AP, Herlina T

“…The objective of this study is to identify Erythrina alkaloids with strong inhibitory capacity against AChE and favorable pharmacokinetic profiles.Materials and Methods: A multi-step computational approach was employed, beginning with the virtual screening of 143 Erythrina alkaloid structures using molecular docking against the human AChE crystal structure. …”
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In-silico screening and analysis of missense SNPs in human CYP3A4/5 affecting drug-enzyme interactions of FDA-approved COVID-19 antiviral drugs by Amro A. Abdelazim, Mohamad Maged, Ahmed I. Abdelmaksoud, Sameh E. Hassanein

“…An ensemble of bioinformatics tools, [SIFT, PolyPhen-2, cadd, revel, metaLr, mutation assessor, Panther, SNP&GO, PhD-SNP, SNAP, Meta-SNP, FATHMM, I-Mutant, MuPro, INPS, CONSURF, GPS 5.0, MusiteDeep and NetPhos], identified a total of 94 variants (47 SNPs in CYP3A4, 47 SNPs in CYP3A5) to potentially impact the structural integrity as well as the activity of the CYP3A4/5 enzymes. Molecular docking was done to recognize the structural stability and binding properties of the CYP3A4/5 protein isoforms with 3 FDA-approved antiviral drugs. …”
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