Suppression of mycotoxins production and efficient chelation of heavy metals using natural melanin originated from Aspergillus flavus and Aspergillus carbonarius by Nashwa El-Gazzar, Esraa Abdo, Gamal Rabie, Manal Tawfeek El-Sayed

“…HPLC was used to measure the mycotoxins produced in culture media supplemented with melanin. Molecular docking study investigated molecular interactions between melanin and mycotoxins through in silico approaches. …”
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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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Bio-computational modeling, POM analysis and molecular dynamic simulation for novel synthetic quinolone and benzo[d][1,3]oxazine candidates as antimicrobial inhibitors by Doaa A. Elsayed, Mohamed E. Abdu, Mohammed A. Marzouk, Elsayed M. Mahmoud, Walaa H. El-Shwiniy, Andrew M. Spring, Wesam S. Shehab

“…Furthermore, molecular docking investigations corroborated the biological studies using the Molecular Operating Environment and Petro Osiris Molinspiration (POM) experiments, which confirmed the activity of compounds 8, 15, and 17. …”
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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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Computational design of potent dimeric phenylthiazole NS5A inhibitors for hepatitis C virus by Wissal Liman, Mehdi Oubahmane, Nouhaila Ait Lahcen, Ismail Hdoufane, Driss Cherqaoui, Rachid Daoud, Achraf El Allali

“…These findings were used to design novel NS5A inhibitors. Moreover, molecular docking was used to predict the binding affinity of the newly designed inhibitors within the NS5A protein, followed by molecular dynamics simulations to investigate the dynamic interactions over time. …”
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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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Repurposing antiviral drugs targeting the PARP-1 and HER2 pathways with multifaceted impacts through integrated network analysis and molecular mechanics by Uma Maheshwari Mugundan, Praveen Sekar, Rajanandh Muhasaparur Ganesan

“…Protein sequence alignment further revealed conserved and semi-conserved amino acid regions, including residues such as Arginine (ARG), Aspartic acid (ASP), and Phenylalanine (PHE), offering valuable insights into the structural characteristics of the target proteins. Molecular docking studies were performed to evaluate drug-receptor interactions, leading to the selection of promising candidates: Fostemsavir, Efavirenz, Doravirine, and Didanosine for HER2, and Efavirenz, Lopinavir, Fostemsavir, and Elvitegravir for PARP-1. …”
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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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Examining Prenylated Xanthones as Potential Inhibitors Against Ketohexokinase C Isoform for the Treatment of Fructose-Driven Metabolic Disorders: An Integrated Computational Approa... by Tilal Elsaman, Magdi Awadalla Mohamed

“…<b>Methods:</b> A library of 1383 analogs was compiled from chemical databases and the literature. Molecular docking, binding free energy calculations, pharmacokinetic assessments, molecular dynamics simulations, and quantum mechani–cal analyses were used to screen and evaluate the compounds. α-Mangostin’s binding affinity (37.34 kcal/mol) served as the benchmark. …”
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Toll-like receptor 4 pathway evolutionary trajectory and functional emergence by Shailya Verma, Ramanathan Sowdhamini, Ramanathan Sowdhamini, Ramanathan Sowdhamini

“…Our previous work on pan-genome-wide survey, indicates Callorhincus milli to be the ancestral organism with both TRAM and TRIF proteins.MethodsTo gain a deeper insight into the protein function and to compare them with Homo sapiens adaptor proteins, we modeled the docking of the TRAM–TRIF complex of representative organisms across various taxa. …”
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Discovery of amino acid substitutions in penicillin-binding proteins associated with adaptation to D-Ala-D-Lac in vancomycin-resistant Enterococcus faecalis by Nese Caglayan, Banu Sancak, Zeynep Kanlidere, Tanil Kocagoz, Tanil Kocagoz

“…We then applied homology modeling to assess structural impacts of these changes on PBPs and conducted docking studies to investigate ligand-binding interactions. …”
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Deodorization of Egg White Powder by Ozone Treatment and Underlying Mechanism by XIN Xiaojuan, LIU Ying, MA Lulu, HUO Jiaying, GAO Ying, DONG Shijian, LIU Liya, WANG Fengzhong, LI Shugang

“…In addition, fluorescence quenching and molecular docking showed that the major binding force between egg white protein and off-flavor substances was hydrophobic interaction, and their main binding sites were in a hydrophobic cavity composed of amino acids such as Leu66, Lys69, Glu87E, Ala87F, Cys87H, Glu129, Tyr130, Cys133, and Gly320. …”
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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

“…Yet, it has no high-resolution complex structure with PPARs and its detailed interactions and activation mechanism remain unclear. 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. …”
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Golgin Subfamily A Member 5 Is Essential for Production of Extracellular Matrix Proteins during TGF-β1-Induced Periodontal Ligament-Fibroblastic Differentiation by Hyun-Jin Kim, Seong-Min Kim, Min-Jeong Choi, Young-Joo Jang

“…GOLGA5 plays a role in vesicle tethering and docking between the endoplasmic reticulum and the Golgi apparatus. siRNA-mediated depletion of endogenous GOLGA5 upregulated in TGF-β1-induced PDL-fibroblastic progenitors resulted in downregulation of representative PDL-fibroblastic markers and upregulation of osteoblast markers. …”
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Immunoinformatics design of a novel multiepitope vaccine candidate against non-typhoidal salmonellosis caused by Salmonella Kentucky using outer membrane proteins A, C, and F. by Elayoni E Igomu, Paul H Mamman, Jibril Adamu, Maryam Muhammad, Abubarkar O Woziri, Manasa Y Sugun, John A Benshak, Kingsley C Anyika, Rhoda Sam-Gyang, David O Ehizibolo

“…The resulting MEV construct demonstrated high structural quality and favorable physicochemical properties. Molecular docking studies with Toll-like receptors 1, 2, 4, and 5, followed by molecular dynamic simulations, suggested that the vaccine-receptor complexes are energetically feasible, stable, and robust. …”
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Management of intraocular pressure and inflammation using febuxostat film: in vitro - in vivo correlation by Mouli Das, Sk Habibullah, Tanisha Das, Rakesh Swain, Subrata Mallick

“…Disappearance of ocular inflammation was also observed in the test animals after 2.5 h of film application, whereas acute inflammation was continued in the group without treatment for more than 4 h. Docking study revealed good binding interaction of drug and NLRP3, A2A, and TLR4 receptor. …”
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