Amentoflavone from Selaginella bryopteris leaf extracts modulate MAPK signaling - Molecular modeling study for therapeutic target analysis by Praveen Mallari, Mashooq Ahmad Bhat

“…Interaction networks were built for the corresponding proteins, molecular docking, molecular dynamics, and molecular mechanics. …”
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Structure-guided identification of mitogen-activated protein kinase-1 inhibitors towards anticancer therapeutics. by Md Nayab Sulaimani, Shazia Ahmed, Farah Anjum, Taj Mohammad, Anas Shamsi, Ravins Dohare, Md Imtaiyaz Hassan

“…The screened compounds were prioritized based on their binding affinity, docking scores, and specificity towards the kinase domain of MAPK1 during the molecular docking process. …”
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The Mechanism of Scopolamine’s Effect on Migration Function of Lung Cancer Cells: A Network Pharmacology and Bioinformatics Perspective by Yang Xiao, Mengcong Ma, Qing Gu, Yunfeng Xiao

“…Furthermore, molecular docking experiments demonstrated that scopolamine binds and forms stable complexes with the protein products of all four aforementioned genes. …”
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In silico development of a multi-epitope-based vaccine against Burkholderia cepacia complex using reverse vaccinology by Donya Ghorbani, Donya Ghorbani, Masoumeh Beig, Masoumeh Beig, Narjes Noori Goodarzi, Mohammad Sholeh, Mohammad Sholeh, Behzad Shahbazi, Behzad Shahbazi, Yaser Moghaddam, Farzad Badmasti

“…In addition, molecular docking and MD indicated stable and feasible interactions between MEV and TLRs. …”
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Anti-Inflammatory Activity of Phyllanthus niruri L. Leaf Extract: In Vitro Study on RAW 264.7 Macrophage Cells and In Silico Analysis by Ngurah Intan Wiratmini, Made Pharmawati, Anak Agung Sagung Alit Sukmaningsih, Sentot Joko Raharjo, Wahyu Widowati

“…Treatment with the extract significantly reduced the levels of pro-inflammatory cytokines TNF-α and IL-1β in LPS-induced RAW 264.7 cells, with the most effective concentration being 50 µg/ml. Molecular docking studies further supported the anti-inflammatory potential of the extract by demonstrating its ability to inhibit COX-2 and TNF-alpha. …”
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Vitamin C exerts anti-cadmium induced fracture functions/targets: bioinformatic and biostructural findings by Rong Li, Songzuo Yu, Xiao Liang, Yu Li, Keng Po Lai

“…Interestingly, findings of molecular docking analysis indicated that VC exerted effective binding capacity in cadmium-induced fracture. …”
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A phytotherapeutic approach to hinder the resistance against clindamycin by MRSA: in vitro and in silico studies by Amal Mayyas, Ali Al-Samydai, Nehaya Al-Karablieh, Waleed A Zalloum, Deniz Al-Tawalbeh, Farah Al-Mamoori, Rula A. Amr, Hamdi Al Nsairat, Simone Carradori, Lidia Kamal Al-Halaseh, Talal Aburjai

“…A synergistic test with clindamycin was performed, and molecular docking studies evaluated the interaction between a key compound (trans-cinnamaldehyde) and MRSA protein.Results EOs from Cinnamomum verum, Rosmarinus officinalis, Salvia officinalis, and Thymus vulgaris demonstrated significant inhibitory and synergistic activities against MRSA, standard strain, and human clinical isolates. …”
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The effect of silver nitrate on the alkaline phosphatase activity, TNF and IL-10 gene expression; Experimental and computational studies by Nader jadid, Ali Asghar Moshtaghie, Hashem Nayeri, Masoud Foladgar, Maryam Ostadsharif

“…However, a statistically significant alteration was detected in both groups 45 days post-injection (P < 0.005). Molecular docking analysis further revealed that the optimal binding pose for ALP, based on the docking score, was −5.28 kcal/mol, with a re-ranking score of −7.43 kcal/mol. …”
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Overcoming beta-lactam resistance in Pseudomonas aeruginosa by targeting metallo-beta-lactamase VIM-1: a one-microsecond molecular dynamics simulation study by Mohammed Salleh M. Ardawi, Samar A. Badreddine, Muhammad Yasir, Muhammad Yasir, Aiah M. Khateb, Aiah M. Khateb, Safaa A. Turkistani, Ahmed Afandi, Samah O. Noor, Adhari Alselmi, Adhari Alselmi, Vivek Dhar Dwivedi, Vivek Dhar Dwivedi, Esam I. Azhar, Esam I. Azhar

“…The virtual screening process selected four top-performing compounds (CNP0390322, CNP03905695, CNP0079056, and CNP0338283) that exhibited promising docking scores. These compounds were then subjected to re-docking and one-microsecond molecular dynamics (MD) simulations to assess their binding stability and interactions within the MBL-VIM-1 active site. …”
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A Computational Approach towards the Development of Newer Anticancer Agents by Javed I. Sheikh, H. D. Juneja, V. N. Ingle

“…In silico molecular docking analyses of the novel 1-(2', 4'-dihydroxy-5'-chlorophenyl)-3-aryl-propane-1, 3-diones were performed in the active sites of enzyme cytochrome P450 reductase to obtain new anticancer agents computationally. 1-(2', 4'-dihydroxy-5'-chlorophenyl)-3-(4"-methoxy-phenyl)-propane-1, 3-dione (3f) was found to have maximum affinity for the active sites of enzyme.…”
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Mahogany seeds extract showed potential immunomodulator by in-silico and in vivo testing by Yati Sumiyati, Alessandro Gunady, Perwira Tua, Warni Warni, Heppy Novia, Emilda

“…Docking simulation was done towards 16 bioactive contents using Protein Data Bank, PubChem, Marvinsketch, Chimera, Swissdock and pkCSM. …”
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Spectroscopic, DFT, anti-bacterial, and in-silico investigations of novel semicarbazone and thiosemicarbazone synthesised from asymmetrical chalcones by Nikita Sharma, Har Lal Singh

“…Based on the docking score and binding affinity calculation, these derivatives were found to have a greater affinity than standard antibiotics against selected the pathogens. …”
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Exploring the Mechanisms of Zhenbao Pills in the Treatment of Stroke through Network Pharmacology Combined with Mendelian Randomization by Yanhong Liu, Yunqi Hua, Xiaoe Jia

“…Furthermore, molecular docking and Gene Expression Omnibus (GEO) datasets were used for preliminary confirmation. …”
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Harnessing marine bacteria for next-gen antibiotics: potent inhibition of S. aureus and Riemerella anatipestifer through in vitro, omics, and chemoinformatics approach with enhance... by Syed Shams ul Hassan, Huizi Jin

“…To investigate the anti-bacterial mechanism, all compounds were docked with two enzymes and TLR4 protein for predicting the vaccine construct, and the best docking score was achieved against RMFP with the highest score of -12.9 for compound 4. …”
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Le port romain du quartier de Saint-Lupien à Rezé/Ratiatum (Loire-Atlantique) : origine et évolution by Jimmy Mouchard, David Guitton, Martial Monteil, Xavier Favreau, Nicolas Ménez, Matthieu Yacger

“…These structures, which served as docks along the riverbank of the main river bed, present a mixed framework, consisting of wood and stone, specifically a very elaborate and robust oak frame, including half-timbered facades and significant dry-stone filling. …”
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Current Perspectives in Detection of Bioactive Compounds From Costus spicatus Through GC–MS and LC-MS/MS: Antioxidant Properties and In Silico Analysis for Industrial Applications... by Dharmar Manimaran, Ararsa Tessema, M. Govindarajulu Yadav, S. Parthasarathi, Vasan Palanisamy

“…In this study, we performed molecular docking and found that four compounds exhibited promising binding affinities with predicted binding sites on alpha-synuclein. …”
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Multistaged In Silico Discovery of the Best SARS-CoV-2 Main Protease Inhibitors amongst 3009 Clinical and FDA-Approved Compounds by Ibrahim H. Eissa, Abdulrahman M. Saleh, Sara T. Al-Rashood, Abdul-Aziz M. M. El-Attar, Ahmed M. Metwaly

“…Levobupivacaine (2840) showed the most accurate docking and pharmacophore scores and was picked for further MD simulations experiments (RMSD, RMSF, Rg, SASA, and H-H bonding) over 100 ns. …”
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Inhibitory Effect of (2S)-Pinocembrin From Goniothalamus macrophyllus on the Prostaglandin E2 Production in Macrophage Cell Lines by Hilwan Yuda Teruna, Kamal Rullah, Rudi Hendra, Rahayu Utami, Deri Islami, Siti Munirah Mohd Faudzi, Mohd Fadhlizil Fasihi Mohd Aluwi, Kok Wai Lam

“…The docking simulations revealed that (2S)-PCB reduced PGE2 levels by suppressing mitogen-activated protein kinase (MAPK) activation through inhibiting p38 and extracellular signal-regulated kinases (ERK). …”
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Exploration of the Potential Mechanisms of Wumei Pill for the Treatment of Ulcerative Colitis by Network Pharmacology by Jinke Huang, Yijun Zheng, Jinxin Ma, Jing Ma, Mengxiong Lu, Xiangxue Ma, Fengyun Wang, Xudong Tang

“…PPI network identified 13 core target genes. The molecular docking results indicated the formation of stable bonds between the active ingredients and core target genes. …”
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Integrating network pharmacology and experimental validation to explore the pharmacological mechanism of Astragaloside IV in alleviating urotensin II-mediated renal tubular epithel... by Wenyuan Liu, Qianwei Liu, Ziyuan Zhang, Yaling Hu, Jingai Fang

“…DAVID software was then used to perform GO and KEGG enrichment analysis on these target genes, and STRING and cytoscape were used to construct a protein interaction network. Molecular docking analysis was performed on key genes. The CCK8 assay was applied to detect the cell viability. …”
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