Quantitative descriptive analysis, non-targeted metabolomics and molecular docking reveal the dynamic aging and taste formation mechanism in raw Pu-erh tea during the storage by Bingsong Ma, Cunqiang Ma, Binxing Zhou, Xuan Chen, Yuhua Wang, Yifan Li, Junfeng Yin, Xinghui Li

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AlphaFold-based AI docking reveals AMPK/SIRT1-TFEB pathway modulation by traditional Chinese medicine in metabolic-associated fatty liver disease by Lulu Zhang, Yi Zheng, Mingyan Shao, Aiping Chen, Meiyi Liu, Wenlong Sun, Tianxing Li, Yini Fang, Yang Dong, Shipeng Zhao, Hui Luo, Juan Feng, Qi Wang, Lingru Li, Yanfei Zheng

“…Liquid chromatography-mass spectrometry combined with molecular docking expounded its five compounds in QGJZF binding to AMPK protein. …”
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A Computational Study on Selected Alkaloids as SARS-CoV-2 Inhibitors: PASS Prediction, Molecular Docking, ADMET Analysis, DFT, and Molecular Dynamics Simulations by Md. Golam Mortuza, Md Abul Hasan Roni, Ajoy Kumer, Suvro Biswas, Md. Abu Saleh, Shirmin Islam, Samia Sadaf, Fahmida Akther

“…Molecular dynamics simulations (MDS) with a time step of up to 100 ns were used to confirm that the three docked complexes were more stable. It was found that the most prevalent and active binding sites that limit Mpro’sactivity are PHE294, ARG298, and GLN110. …”
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ZnO Nanoparticle-Assisted Synthesis of Thiazolo[3,2-α]Pyrimidine Analogs: Antibacterial and Antioxidant Activity, In Silico Molecular Docking, and ADMET Prediction Study by Demis Zelelew, Milkyas Endale, Yadessa Melaku, Taye B. Demissie, Japheth O. Ombito, Rajalakshmanan Eswaramoorthy

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Telomerase inhibiting phytochemicals derived from Blumea eriantha for cancer treatment: A comprehensive computational analysis by Rahil Ummar Faruk Abbu, Shaik Mohammad Abdul Fayaz, Divyashree M S, Raghu Chandrashekhar H, Prasanna Kumar Reddy Gayam, Archana Mahadev Rao

Subjects: “…Molecular docking…”
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Naringenin inhibits lipid accumulation by activating the AMPK pathway in vivo and vitro by Xiaoyu Cai, Songxue Wang, Huali Wang, Suwen Liu, Guishan Liu, Huibin Chen, Ji Kang, Hao Wang

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Curcumin: Synthesis optimization and in silico interaction with cyclin dependent kinase by Ahmed Mahmood, Abdul Qadir Muhammad, Imtiaz Shafiq Muhammad, Muddassar Muhammad, Hameed Abdul, Nadeem Arshad Muhammad, Asiri Abdullah M.

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Effector proteins of Funneliformis mosseae BR221: unravelling plant-fungal interactions through reference-based transcriptome analysis, in vitro validation, and protein‒protein docking studies by Pratima Vasistha, Pushplata Prasad Singh, Divya Srivastava, Leena Johny, Sadhana Shukla

“…In silico prediction using a pathogen-host interaction database suggested four of the 163 effectors could be crucial in establishing AM fungi-host interactions. Protein–protein docking analysis revealed interactions between these potential effectors and plant proteins known to be differentially expressed during mycorrhizal association, such as defensins, aquaporins, and PTO proteins. …”
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Molecular Docking, Dynamics Simulations, ADMET, and DFT Calculations: Combined In Silico Approach to Screen Natural Inhibitors of 3CL and PL Proteases of SARS-CoV-2 by Sugumar Mohanasundaram, Porkodi Karthikeyan, Venkatesan Sampath, M. Anbazhagan, Sundramurthy Venkatesa Prabhu, Jamal M. Khaled, Muthu Thiruvengadam

“…Violaxanthin and naringin occupied the subsequent position in the docking score table with 3CL and PL proteases, respectively. …”
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A Diversified Spectrometric and Molecular Docking Technique to Biophysical Study of Interaction between Bovine Serum Albumin and Sodium Salt of Risedronic Acid, a Bisphosphonate for Skeletal Disorders by M. Manjushree, Hosakere D. Revanasiddappa

“…The subdomain IIIA of BSA involved with RSN interaction was authenticated from molecular docking analysis.…”
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3D-QSAR, design, molecular docking and dynamics simulation studies of novel 6-hydroxybenzothiazole-2-carboxamides as potentially potent and selective monoamine oxidase B inhibitors by Dong Xie, Dong Xie, Yongzheng Tian, Li Cao, Penghang Guo, Penghang Guo, Zhibiao Cai, Jie Zhou

“…Among them, compound 31.j3 exhibited the highest predicted IC50 value and obtained the highest score in the molecular docking test. MD simulation results showed that compound 31.j3 was stable in binding to the MAO-B receptor, and the RMSD values fluctuated between 1.0 and 2.0 Å, indicating its conformational stability. …”
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Evaluation of Melongosides as Potential Inhibitors of NS2B-NS3 Activator-Protease of Dengue Virus (Serotype 2) by Using Molecular Docking and Dynamics Simulation Approach by Partha Biswas, Ommay Hany Rumi, Dhrubo Ahmed Khan, Md Nasir Ahmed, Nusratun Nahar, Rownak Jahan, Md Nazmul Hasan Zilani, Tridib K Paul, Anamul Hasan, Tohmina Afroze Bondhon, Khoshnur Jannat, Md Nazmul Hasan, Mohammed Rahmatullah

“…However, the 200 ns molecular dynamic simulation experiment indicates significant stability of the protein-ligand interactions with the RMSD values of 2.5 Å, thus suggesting a better docking position and no disruption of the protein-ligand structure. …”
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Methicillin-Resistant Staphylococcus aureus: Docking-Based Virtual Screening and Molecular Dynamics Simulations to Identify Potential Penicillin-Binding Protein 2a Inhibitors from Natural Flavonoids by Motahareh Masumi, Fatemeh Noormohammadi, Fatemeh Kianisaba, Fatemeh Nouri, Mohammad Taheri, Amir Taherkhani

“…The binding affinity of 46 natural flavonoids to the SauPBP2a active site was examined via molecular docking analysis. The stability of docked poses associated with the top-ranked flavonoids was tested by performing molecular dynamics (MD) in 10 nanoseconds (ns) computer simulations. …”
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Effective anti-inflammatory phenolic compounds from dandelion: identification and mechanistic insights using UHPLC-ESI-MS/MS, fluorescence quenching and anisotropy, molecular docking and dynamics simulation by Hui Zou, Tingting Ben, Ping Wu, Geoffrey I.N. Waterhouse, Yilun Chen

“…This novel study identifies the effective anti-inflammatory phenolic compounds in dandelion and provides mechanistic insights into their interactions with receptor proteins (toll‐like receptor 4, TLR4; co‐receptor myeloid differentiation protein-2, MD-2) using UHPLC-ESI-MS/MS, lipopolysaccharide (LPS)-stimulated THP-1 cell line, fluorescence quenching and anisotropy, molecular docking (single ligand and multi-ligand docking) and molecular dynamics simulation. …”
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Potential of Co(II) and Cd(II) chelates of N′-(3-fluorobenzoyl)benzo[d]thiazole-2-carbohydrazide: Structural aspects, binding interactions, biological and molecular docking studies by K. Srilaxmi, B. Sireesha

“…Cytotoxicity of the compounds was performed for Hela and MCF cell lines by MTT assay. Molecular docking studies carried out using Auto Dock 4.2 program revealed HL and Co(II)-MFBBTCH docking at the minor groove, and Cd(II)-MFBBTCH was docked at the major groove with hydrogen bonding.…”
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Multi-stage structure-based virtual screening approach combining 3D pharmacophore, docking and molecular dynamic simulation towards the identification of potential selective PARP-1 inhibitors by Mahmoud A. El Hassab, Wagdy M. Eldehna, Ghaneya S. Hassan, Sahar M. Abou-Seri

“…The retrieved compounds were docked into the active site of PARP-1 where only 5 compounds MWGS-1-5 achieved a favorable docking score than the reference IV (-16.8 Kcal/mol). …”
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Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation by Arwansyah Arwansyah, Sitti Rahmawati, Siti Nuryanti, Yenni Yusuf, Hartono, Abdur Rahman Arif

“…To confirm Citroxanthin's binding site, re-docking simulations and k-means clustering analysis were conducted. …”
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Chemical reactivity of alliin and its molecular interactions with the M proteasepro of SARS-CoV-2 by López-Orozco Wendolyne, Mendoza-Huizar Humberto Luis, Álvarez-Romero Giaan Arturo, Torres-Valencia Jesús Martín, Sanchez-Zavala Maricruz

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Prediction of ADMET profile and anti-inflammatory potential of chamuangone by Sompot Jantarawong, Puripat Wathanaphanit, Pharkphoom Panichayupakaranant, Yutthana Pengjam

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In silico and in vitro evaluation of potential agonistic and antagonistic estrogenic and androgenic activities of pure cyanotoxins, microcystin-LR and cylindrospermopsin by Antonio Casas-Rodríguez, Antonio Cascajosa-Lira, María Puerto, Ana María Cameán, Angeles Jos

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