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X-ray crystal structure, UV–Vis and NMR spectroscopic, and molecular docking studies of pyribencarb isomers

Eunyoung Park, Jiho Lee, Jeong-Han Kim, Joon-Kwan Moon • Applied Biological Chemistry (2023)

Abstract The crystal structures of the pyribencarb E and Z stereoisomers were determined using single-crystal X-ray crystallography. The isomers were confirmed a single data respectively by crystal analysis, LC-UVD mass spectrometry, and NM...

DOAJ Open Access (DOAJ) DOI: 10.1186/s13765-023-00770-w

Evaluating the Effects of Molecular Dynamic And Docking of Abemaciclib, Hymenialdisine, and Indirubin on CDK-2 Inhibition by Simulation Study

Majid Asadi-Samani, Navid Jamali, Javad Saffari-Chaleshtori, Korosh Ashrafi-Dehkordi • Journal of Ardabil University of Medical Sciences (2022)

Background & objectives: Cyclin-dependent kinase 2 (CDK-2) is a serine/threonine protein kinase with regulatory activity in the cell cycle. Inhibitors of this protein are the treatment of choice for a variety of cancers by stopping the cell...

DOAJ Open Access (DOAJ)

Computational methods meet in vitro techniques: A case study on fusaric acid and its possible detoxification through cytochrome P450 enzymes

Lorenzo Pedroni, Daniel Zocchi Doherty, Chiara Dall’Asta, Gianni Galaverna et al. • Ecotoxicology and Environmental Safety (2024)

Mycotoxins are known environmental pollutants that may contaminate food and feed chains. Some mycotoxins are regulated in many countries to limit the trading of contaminated and harmful commodities. However, the so-called emerging mycotoxin...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.ecoenv.2024.116167

Pairwise Performance Comparison of Docking Scoring Functions: Computational Approach Using InterCriteria Analysis

Maria Angelova, Petko Alov, Ivanka Tsakovska, Dessislava Jereva et al. • Molecules (2025)

Scoring functions are key elements in docking protocols as they approximate the binding affinity of a ligand (usually a small bioactive molecule) by calculating its interaction energy with a biomacromolecule (usually a protein). In this stu...

DOAJ Open Access (DOAJ) DOI: 10.3390/molecules30132777

Multi-Cohort Transcriptomics Combined with Mendelian Randomization Identifies PPARGC1A, NAAA and GIPC2 as NLRP3 Inflammasome-Related Key Genes in Ulcerative Colitis

Cheng J, Huang Y • Journal of Inflammation Research (2026)

Jian Cheng, Yangfeng Huang Department of Traditional Chinese Medicine, Sichuan Provincial People’s Hospital, School of Medicine,University of Electronic Science and Technology of China, Chengdu, Sichuan, People’s Republic of ChinaCorrespond...

DOAJ Open Access (DOAJ)

Molecular docking and mouse modeling suggest CMKLR1 and INSR as targets for improving PCOS phenotypes by minocycline

Mahdie Kian, Elham Hosseini, Tooba Abdizadeh, Taimour Langaee et al. • EXCLI Journal : Experimental and Clinical Sciences (2022)

Polycystic ovary syndrome (PCOS) is the most common cause of women’s infertility. Some inflammatory pathways play a pivotal role in the pathogenesis of PCOS. This study aimed to investigate the possible beneficial effects of minocycline on ...

DOAJ Open Access (DOAJ) DOI: 10.17179/excli2021-4534

Isoliquiritigenin Attenuates Staphylococcus aureus Adhesion and Invasion to Counteract Staphylococcus aureus Pathogenicity and Infection

Lili Tian, Lili Tian, Jian Sun, Hong Jiang et al. • Frontiers in Cellular and Infection Microbiology (2025)

IntroductionMethicillin-resistant Staphylococcus aureus (MRSA) is a major clinical challenge due to its virulence and multidrug resistance. Antivirulence strategies targeting key pathogenic mechanisms without affecting bacterial viability p...

DOAJ Open Access (DOAJ) DOI: 10.3389/fcimb.2025.1686699

Effects of urea, metal ions and surfactants on the binding of baicalein with bovine serum albumin

Atanu Singha Roy, Amit Kumar Dinda, Nitin Kumar Pandey, Swagata Dasgupta • Journal of Pharmaceutical Analysis (2016)

The interaction of baicalein with bovine serum albumin (BSA) was investigated with the help of spectroscopic and molecular docking studies. The binding affinity of baicalein towards BSA was estimated to be in order of 105 M−1 from fluoresce...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.jpha.2016.04.001

Efficacy of heel lifts versus calf muscle eccentric exercise for mid-portion Achilles tendinopathy (the HEALTHY trial): study protocol for a randomised trial

Chantel L. Rabusin, Hylton B. Menz, Jodie A. McClelland, Angela M. Evans et al. • Journal of Foot and Ankle Research (2019)

Abstract Background Mid-portion Achilles tendinopathy is a common musculoskeletal condition characterised by degeneration of the Achilles tendon, which causes pain and disability. Multiple non-surgical treatments have been advocated for thi...

DOAJ Open Access (DOAJ) DOI: 10.1186/s13047-019-0325-2

SARS-CoV-2 Omicron BA.2.75 Variant May Be Much More Infective than Preexisting Variants Based on In Silico Model

Aki Sugano, Yutaka Takaoka, Haruyuki Kataguchi, Mika Ohta et al. • Microorganisms (2022)

Previously, we developed a mathematical model via molecular simulation analysis to predict the infectivity of six SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 based on o...

DOAJ Open Access (DOAJ) DOI: 10.3390/microorganisms10102090

Effective analysis of neurotoxicity and mechanisms of dioctyl terephthalate using network toxicology

Hao Tang, Ting Qin, Zhiwen Yan, Changqing Li et al. • Frontiers in Neuroscience (2026)

ObjectiveDioctyl terephthalate (DOTP), a widely used plasticizer in food packaging and environmental materials, has raised concerns regarding its potential impact on human health. This study aims to investigate the neurotoxicity-related mec...

DOAJ Open Access (DOAJ) DOI: 10.3389/fnins.2026.1783807

Emodin inhibits Newcastle disease virus replication via regulating the phosphorylation levels of eEF2K/eEF2 and targeting viral N protein to reduce viral protein production

Wenjie Wu, Rongjing Xia, Si Ma, Zenglei Hu et al. • Poultry Science (2026)

Newcastle disease (ND) caused by Newcastle disease virus (NDV) infection is a highly contagious avian disease that causes substantial threat to the global poultry industry. Emodin (EMO), a member of the free anthraquinone compounds derived ...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.psj.2026.107180

UPLC-MS/MS Metabolomics Reveals Babao Dan’s Mechanisms in MASH Treatment with Integrating Network Pharmacology and Molecular Docking

Shijiao Zhang, Yanding Su, Ao Han, He Qi et al. • Pharmaceuticals (2025)

Background: Metabolic dysfunction-associated steatohepatitis (MASH) is a progressive disease that easily develops into cirrhosis and hepatocellular carcinoma, but its pathogenesis is not clear, and most therapeutic drugs have obvious limita...

DOAJ Open Access (DOAJ) DOI: 10.3390/ph18081111

VirtualToxLab™ - In silico prediction of the toxic (endocrine-disrupting) potential of drugs, chemicals and natural products. Two years and 2,000 compounds of experience: a progress report

Angelo Vedani, Martin Smiesko, Morena Spreafico, Ourania Peristera et al. • ALTEX: Alternatives to Animal Experimentation (2009)

The VirtualToxLab™ is an in silico tool for predicting the toxic (endocrine-disrupting) potential of drugs, chemicals and natural products. It is based on a fully automated protocol and calculates the binding affinity of any molecule of int...

DOAJ Open Access (DOAJ) DOI: 10.14573/altex.2009.3.167

Neurotoxicity of PM<sub>2.5</sub>-Bound Multi-Pollutant Mixtures in Parkinson’s Disease: Exploring the <i>INPP5D</i>/SHIP1-PI3K-AKT Axis via an Integrative Multi-Omics Study

Lufei Chen, Chaoxian Dai, Zhenfang Wu, Yuhan Lin et al. • Journal of Xenobiotics (2026)

Accumulating epidemiological evidence links ambient PM2.5 exposure to elevated Parkinson’s disease (PD) risk, yet the neurotoxicity triggered by PM2.5 multi-pollutant mixtures under real co-exposure scenarios remains insufficiently elucidat...

DOAJ Open Access (DOAJ) DOI: 10.3390/jox16060184

Antimicrobial topical polymeric films loaded with Acetyl-11-keto-β-boswellic acid (AKBA), boswellic acid and silver nanoparticles: Optimization, characterization, and biological activity

Muhammad Jawad, Saurabh Bhatia, Ahmed Al-Harrasi, Sana Ullah et al. • Heliyon (2024)

The study examined the antimicrobial and antioxidant potential of pure Acetyl-11-keto-β-boswellic acid (AKBA), boswellic acid (70%) and AKBA loaded nanoparticles as topical polymeric films. The optimized concentration (0.05 % w/v) of pure A...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.heliyon.2024.e31671

Coffee Silverskin Phytocompounds as a Novel Anti-Aging Functional Food: A Pharmacoinformatic Approach Combined with In Vitro Study

Clarin Hayes, Fahrul Nurkolis, Dewa Ayu Agus Sri Laksemi, Sanghyun Chung et al. • Molecules (2023)

Coffee became a beverage that was in demand in the world and consequently produced millions of tons of coffee byproducts namely coffee silverskin (CS). Unutilized CS will be waste and cause environmental pollution such as greenhouse gas emi...

DOAJ Open Access (DOAJ) DOI: 10.3390/molecules28207037

Semi-rational design and modification of phosphoketolase to improve the yield of tyrosol in Saccharomyces cerevisiae

Na Song, Huili Xia, Yaoru Xie, Shuaikang Guo et al. • Synthetic and Systems Biotechnology (2025)

Tyrosol is an important component of pharmaceuticals, nutraceuticals, and cosmetics, and their biosynthetic pathways are currently a hot research topic. d-Erythrose 4-phosphate is a key precursor for the biosynthesis of tyrosol in Saccharom...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.synbio.2024.11.007

Molecular Informatics, Chemometrics, and Sensory Omics for Constructing an Umami Peptide Cluster Library Across the Entire Lager Beer Brewing Process

Yashuai Wu, Ruiyang Yin, Wenjing Tian, Wanqiu Zhao et al. • Foods (2026)

Umami taste in lager beer not only determined body fullness and the backbone of aftertaste, but also affected the controllability and interpretability of flavor expression across the entire brewing process. Based on stage-wise sampling, pep...

DOAJ Open Access (DOAJ) DOI: 10.3390/foods15040641

In silico analysis of ciprofloxacin analogs as inhibitors of DNA gyrase of Staphylococcus aureus

Md. Rakhibul Hasan, Surid Mohammad Chowdhury, Md. Abdul Aziz, Asif Shahriar et al. • Informatics in Medicine Unlocked (2021)

In this in silico study, thirty-five ciprofloxacin analogs were docked to the active site of DNA gyrase, the prime target of ciprofloxacin type antibiotics. Prior to docking all the structures were optimized using MM2 force field parameters...

DOAJ Open Access (DOAJ) DOI: 10.1016/j.imu.2021.100748