Identification of a putative novel polycyclic aromatic hydrocarbon-biodegrading gene cluster in a marine Roseobacteraceae bacterium Sagittula sp. MA-2 by Mayuko Abe, Miharu Sakai, Robert A. Kanaly, Jiro F. Mori

“…Catabolic functions of the enzymes encoded in strain MA-2 were predicted through the profiling of phenanthrene biotransformation products by liquid chromatography-electrospray ionization high-resolution mass spectrometry and substrate docking simulations using predicted three-dimensional structures of selected proteins, and phenanthrene biodegradation pathways were proposed. …”
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Angesinenolide B, A Phthalide Dimeric Peroxide, Exerts Anti-Inflammatory Properties by Suppressing MAPK/STATs Signaling Pathways and ROS Production by Zhang L, Liu Y, Wang H, Guo S, Lv J

“…Moreover, the affinities between ASB and the target proteins were verified by molecular docking analysis. In vivo, ROS generation was explored using fluorescent probe DCFH-DA, and the TNF-α and IL-6 mRNA expressions were also evaluated in CuSO4-induced zebrafish inflammation model.Results: ASB treatment was found to suppress the levels of NO, TNF-α, IL-6 and ROS, restrain the expressions of iNOS and COX-2 proteins and mRNA, as well as down-regulate MAPK and STATs signaling pathways in LPS-stimulated RAW264.7 cells. …”
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Two-dimensional cell membrane chromatography guided screening of myocardial protective compounds from Yindan Xinnaotong soft capsule by Si-Min Shao, Xuan Ji, Xing Wang, Run-Zhou Liu, Yu-Ru Cai, Xiaobing Lin, Ze-Jie Zeng, Ling Chen, Liu Yang, Hua Yang, Wen Gao

“…Furthermore, all 24 screened compounds exhibit strong binding affinities with FOXO3 evaluated by molecular docking. Conclusion A highly stable and efficient 2D imidazole-modified H9c2/CMC-RPLC-MS system was developed, allowing for the screening of potentially active compounds from YD. …”
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Baicalein induces apoptosis by inhibiting the glutamine-mTOR metabolic pathway in lung cancer by Jingyang Li, Di Zhang, Shaohui Wang, Peng Yu, Jiayi Sun, Yi Zhang, Xianli Meng, Juan Li, Li Xiang

“…The binding of baicalein to glutamine transporters and glutaminase was examined using molecular docking. The overexpression of glutamine transporters was validated using qRT–PCR and western blot analyses. …”
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In vitro gastrointestinal digestion simulation screening of novel ACEI peptides from broccoli: mechanism in high glucose-induced VSMCs dysfunction by Shuzhi Zhang, Jingjing Guo, Shikun Suo, Li Ju, Zhaoqiang Jiang, Pingshuan Dong, Yanli Wang, Yali Dang, Laijing Du

“…In this study, peptides were initially digested from broccoli in vitro, and absorption was simulated by Caco2 cells transport and then analyzed by Peptideomics and molecular docking. Subsequently, the mechanisms were verified using a high glucose-induced vascular smooth muscle cells (VSMCs) dysfunction model. …”
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Amebicidal and Antiadhesion Activities of Knema retusa Extract Against Acanthamoeba triangularis T4 Genotype on Contact Lenses and Modeling Simulation of Its Main Compound, E2N, Ag... by Watcharapong Mitsuwan, Imran Sama-ae, Suthinee Sangkanu, Dhrubo Ahmed Khan, Partha Biswas, Md. Nazmul Hasan, Julalak Chuprom, Tajudeen O. Jimoh, Christophe Wiart, Masyitah Binti Zulkipli, Nor Hayati Abdullah, Maria de Lourdes Pereira, Sonia M. Rodrigues Oliveira, Shanmuga Sundar Saravanabhavan, Polrat Wilairatana, Tooba Mahboob, Veeranoot Nissapatorn

“…Furthermore, 1 log cells/mL (90%) of the contact lens adhesive trophozoites were reduced and removed after treatment with Kre. Molecular docking indicated that E2N, the main compound in Kre, exhibited strong binding to the ligand binding sites at β-tubulin, with a binding energy of −7.01 kcal/mol and an inhibitory constant of 2.43–7.32 μM. …”
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Aqueous extracts of Moringa oleifera and Cinnamomum cassia as promising sources of antibiofilm compounds against mucoid and small colony variants of Pseudomonas aeruginosa and Stap... by Eduarda Silva, Pedro Ferreira-Santos, José A. Teixeira, Maria Olivia Pereira, Cristina M.R. Rocha, Ana Margarida Sousa

“…Recognizing that the antibiofilm properties of moringin, a common compound in both moringa seed and cinnamon bark extracts, remain underexplored, we conducted potential target identification via PharmMapper and molecular docking analyses to provide a foundation for future research. …”
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Combining In Vitro, In Vivo, and In Silico Approaches to Explore the Effect of <i>Ceratonia siliqua</i> and <i>Ocimum basilicum</i> Rich Phenolic Formula on Lipid Metabolism and Pl... by Mohammadine Moumou, Amani Tayebi, Abderrahmane Hadini, Omar M. Noman, Abdulsalam Alhalmi, Hamza Ahmoda, Souliman Amrani, Hicham Harnafi

“…Accordingly, the CBF decreased the plasma atherogenic index and the LDL-C to HDL-C ratio and reduced the level of fats accumulated in the liver. The molecular docking study revealed that chicoric, rosmarinic, and caftaric acids, and naringenin bound particularly strongly to many proteins involved in the regulation of lipid and cholesterol metabolism. …”
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Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virus by Brézellec, Pierre

“…We first show that the C-terminal part of Spike S (the protein that binds the virion to the cell membrane by interacting with the host receptor, triggering infection) has similarities with the human prominin-1/CD133; after reviewing what is known about prominin-1/CD133, we suggest that the C-terminal part of Spike S could both improve the docking of Spike S to ACE2 (the main cell entry receptor for SARS-CoV-2) and be involved in the delivery of virions to regions where ACE2 is located in cells. …”
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Pyrrolizine-5-carboxamides: Exploring the impact of various substituents on anti-inflammatory and anticancer activities by Gouda Ahmed M., Abdelazeem Ahmed H., Abdalla Ashraf N., Ahmed Muhammad

“…New compounds showed promising drug-likeness scores while the docking study revealed high binding affinity to COX-2. …”
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Scutellarein Inhibits Osteosarcoma Growth by Targeting the TLR4/TRAF6/NF-&kappa;B Pathway by Shi Y, Tang Y, Sun Z, Sui P, Shao Y, Wang Z, Zhang J, Gao M

“…TLR4/TRAF6/NF-κB signaling transduction was investigated by RNA sequencing analysis, quantitative real-time polymerase chain reaction, Western blotting, NF-κB luciferase reporter assay, immunofluorescent staining, and immunoprecipitation. Molecular docking and cellular thermal shift assay were employed to confirm the binding interaction between SCU and TLR4. …”
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Imaging abnormalities of the acromioclavicular joint and subacromial space are common in asymptomatic shoulders: a systematic review by Thomas Ibounig, Lasse Rämö, Romi Haas, Mark Jones, Teppo L. N. Järvinen, Simo Taimela, Sean Docking, Sharon Sanders, Rachelle Buchbinder

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Nicotine-induced CHRNA5 activation modulates CES1 expression, impacting head and neck squamous cell carcinoma recurrence and metastasis via MEK/ERK pathway by Chen Feng, Wei Mao, Chenyang Yuan, Pin Dong, Yuying Liu

“…The interaction between CHRNA5 and CES1 is examined using molecular docking, co-immunoprecipitation, and immunofluorescence. …”
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Combating COVID-19 and its co-infection by Aspergillus tamarii SP73-EGY using in vitro and in silico Studies by Eman Abdelsalam, Amal Mosad Ibrahim, Ahmed A. El-Rashedy, Mohamed S. Abdel-Aziz, Omnia Kutkat, Faten K. Abd EL-Hady

“…The extract showed significant efficacy against E. coli and P. aeruginosa , with an inhibition range of 3.5–10 mm at a concentration of 200 mg/ml. A molecular docking study showed that hexadecanoic, Kojic, octanoic acids, and 4(4-Methylbenzylidene)cyclohexane-1,3-dione have stronger binding affinity to the SARS-CoV-2 Mpro than Remdesivir. …”
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Mapping knowledge landscapes and emerging trends in artificial intelligence for antimicrobial resistance: bibliometric and visualization analysis by Zhongli Wang, Zhongli Wang, Gaopei Zhu, Shixue Li, Shixue Li

“…Keyword analysis identified six enduring research clusters from 2014 to 2024: sepsis, artificial neural networks, antimicrobial resistance, antimicrobial peptides, drug repurposing, and molecular docking, demonstrating the sustained integration of AI in antimicrobial therapy development. …”
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Comprehensive metabolite profiling and evaluation of anti-nociceptive and anti-inflammatory potencies of Nypa fruticans (Wurmb.) leaves: Experimental and in-silico approaches by Farhana Islam, Md. Aktaruzzaman, Md. Tarikul Islam, Fariya Islam Rodru, Saquiba Yesmine

“…Among, the 23 identified phytocompounds, the most promising ones were determined to be potential anti-nociceptive and anti-inflammatory agents through molecular docking studies and ADME/T analysis. Molecular dynamics simulations (MDS) confirmed the stability of the protein-ligand complexes. …”
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Fraxinellone-mediated targeting of cathepsin B leakage from lysosomes induces ferroptosis in fibroblasts to inhibit hypertrophic scar formation by Wei Xu, Hao Lv, Yaxin Xue, Xiaofeng Shi, Shaotian Fu, Xiaojun Li, Chuandong Wang, Danyang Zhao, Dong Han

“…The mechanisms underlying FRA-induced HSF ferroptosis were examined through fluorescence staining, qRT‒PCR, WB and molecular docking study. The therapeutic efficacy of FRA was further validated in vivo using a rabbit ear scar model. …”
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Baicalin Mitigates Cardiac Hypertrophy and Fibrosis by Inhibiting the p85a Subunit of PI3K by Lu He, Min Zhu, Rui Yin, Liangli Dai, Juan Chen, Jie Zhou

“…Potential pharmacological targets of baicalin and genes related to heart failure were identified via different databases, which suggested that PI3K–Akt may be involved in the effects of baicalin. Molecular docking was carried out to reveal the effect of baicalin on p85a. …”
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Mechanisms of L-citrulline on phosphodiesterase 5 in erectile dysfunction intervention by Abdulhakeem Olarewaju Sulyman, Olawale Moshood Aliyu, Emmanuel Oladipo Ajani, Yusuf Folohunsho Abdulkareem, Isaac Ade Afe, Fathia Oluwakemi Abdulyakeen, Halimat Yusuf Lukman, Saheed Sabiu, Karishma Singh, Kuben Naidoo

“…Citrulline was extracted from Citrullus lanatus using an adsorbent-based method, and its inhibitory effect on PDE5 was assessed through enzymatic and kinetic analyses. Molecular docking and dynamics simulations were used to evaluate citrulline's binding interaction and stability with PDE5, validated by the RMSD value obtained following superimposition of citrulline with the native ligand of PDE5 and post-dynamic analyses. …”
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(<i>E</i>)-1-(3-(3-Hydroxy-4-Methoxyphenyl)-1-(3,4,5-Trimethoxyphenyl)allyl)-1<i>H</i>-1,2,4-Triazole and Related Compounds: Their Synthesis and Biological Evaluation as Novel Anti... by Gloria Ana, Azizah M. Malebari, Sara Noorani, Darren Fayne, Niamh M. O’Boyle, Daniela M. Zisterer, Elisangela Flavia Pimentel, Denise Coutinho Endringer, Mary J. Meegan

“…Immunofluorescence studies confirmed that compound <b>22b</b> targeted tubulin in MCF-7 cells, while computational docking studies predicted binding conformations for <b>22b</b> in the colchicine binding site of tubulin. …”
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