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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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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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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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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Helicobacter pylori SlyD stabilizes TPT1 via hnRNPK and enhances OCT1-mediated CDX2 transcriptional activation to drive gastric intestinal metaplasia by Shuwen Zheng, Yingying Wang, Chuxuan Ni, Rui Guo, Xunan Qiu, Jijun Chen, Lu Wang, Xiaohu Sun, Moye Chen, Yunen Liu, Yuan Yuan, Yuehua Gong

“…Additionally, molecular docking was utilized to predict TPT1 inhibitors. Immunohistochemistry staining was conducted to validate hnRNPK, TPT1, OCT1, and CDX2 expression in gastric tissue samples from both human and Mongolian gerbils. …”
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Artificial intelligence-enabled discovery of a RIPK3 inhibitor with neuroprotective effects in an acute glaucoma mouse model by Xing Tu, Zixing Zou, Jiahui Li, Simiao Zeng, Zhengchao Luo, Gen Li, Yuanxu Gao, Kang Zhang, Jing Ni

“…Subsequently, these target candidates were validated using molecular simulations (molecular docking, absorption, distribution, metabolism, excretion, and toxicity [ADMET] prediction, and molecular dynamics simulations) and biological experiments (Western blotting and fluorescence staining) in vitro and in vivo. …”
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Hybridization-based discovery of novel quinazoline-2-indolinone derivatives as potent and selective PI3Kα inhibitors by Changqun Liu, Yuening Cao, Yi Zuo, Chaozheng Zhang, Senmiao Ren, Xin Zhang, Chuanqi Wang, Yingjie Zeng, Jie Ling, Yilan Liu, Zixian Chen, Xiujun Cao, Zhengzhi Wu, Chuantao Zhang, Jun Lu

“…Methods: 26 quinazoline-2-indolinone derivatives were obtained by molecular hybridization, and their structure–activity relationship was analyzed by MTT, in vitro kinase activity and molecular docking. The biological evaluation of compound 8 was performed by transwell, flow cytometry, laser scanning confocal microscopy, Western blot, CTESA and immunohistochemistry. …”
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Immune regulatory genes impact the hot/cold tumor microenvironment, affecting cancer treatment and patient outcomes by Mengmeng Sang, Jia Ge, Juan Ge, Juan Ge, Gu Tang, Qiwen Wang, Jiarun Wu, Liming Mao, Liming Mao, Xiaoling Ding, Xiaorong Zhou

“…Furthermore, drug sensitivity and molecular docking analyses were performed to identify potential drug candidates capable of transforming cold tumors into hot tumors. …”
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Amantadine modulates novel macrophage phenotypes to enhance neural repair following spinal cord injury by Shijie Yang, Beibei Yu, Qing Zhang, Yongfeng Zhang, Longhui Fu, Bisheng Zhou, Haining Wu, Jianzhong Li, Shouping Gong

“…Given the importance of these pathways in the injury response, we utilized molecular docking to hypothesize that amantadine might modulate this process. …”
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Potential Interaction of Pinocembrin with Drug Transporters and Hepatic Drug-Metabolizing Enzymes by Sirima Sangkapat, Rattiporn Boonnop, Jeerawat Pimta, Napason Chabang, Bodee Nutho, Promsuk Jutabha, Sunhapas Soodvilai

“…Based on the kinetic study and molecular docking, pinocembrin inhibited OAT1 and OAT3 via a competitive inhibition. …”
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Exploring the mechanism of rosmarinic acid in the treatment of lung adenocarcinoma based on bioinformatics methods and experimental validation by Chaowang Zhou, Ruqian Zhong, Lei Zhang, Renyi Yang, Yuxin Luo, Huijun Lei, Liang Li, Jianzhong Cao, Zhiying Yuan, Xiaoning Tan, Mengzhou Xie, Haoyu Qu, Zuomei He

“…Secondly, GO and KEGG enrichment analysis of RDEGs were performed, and protein–protein interaction networks (PPIs) were constructed to identify and visualize hub RDEGs. Then, molecular docking between hub RDEGs and RosA was performed, and further evaluation was carried out by using bioinformatics for the predictive value of the hub RDEGs. …”
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Cinnamic acid alleviates endothelial dysfunction and oxidative stress by targeting PPARδ in obesity and diabetes by Yizhen Bai, Dechao Tan, Qiaowen Deng, Lingchao Miao, Yuehan Wang, Yan Zhou, Yifan Yang, Shengpeng Wang, Chi Teng Vong, Wai San Cheang

“…Importantly, PPARδ antagonist GSK0660 abolished the vasoprotective effects of CA. Molecular docking analysis suggested a high likelihood of mutual binding between CA and PPARδ. …”
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