ArticleJournal of biomolecular structure & dynamics2021
A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2.
Article in Journal of biomolecular structure & dynamics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
143 citing papers in PubMed, 345 citations in OpenAlex.
- Dual targeting of IGF-1R and K-RAS with natural phytochemicals for lung cancer therapy: an in-silico study.Journal, genetic engineering & biotechnology · 2026Article
- Investigating the Structural and Functional Consequences of Pathogenic SNPs on Human VEGFA Dimer: Insights from Molecular Dynamics Study.ACS omega · 2025Article
- Scopoletin: A Validated Protector against Cerulein-induced Acute Pancreatitis & Associated Lung Injury by Regulating PPAR- γ "A Multidimensional Approach".Molecular biotechnology · 2025Article
- Licoisoflavone B and glabridin from Glycyrrhiza glabra as potent nucleoprotein antagonists of Lassa virus: insights from molecular docking, dynamics simulation, PCA, and DFT studies.Journal, genetic engineering & biotechnology · 2025Article
- Phytochemical-based nanosystems: recent advances and emerging application in antiviral photodynamic therapy.Nanomedicine (London, England) · 2025Review
- Research Progress on the Structure and Function, Immune Escape Mechanism, Antiviral Drug Development Methods, and Clinical Use of SARS-CoV-2 MMolecules (Basel, Switzerland) · 2025Review
- Repurposing of approved drugs towards Nipah virus treatment: an in silico docking, molecular dynamics simulation and a MM/GBSA approach.In silico pharmacology · 2025Article
- Article
- Article
- Article
- Phytochemical Analysis, Computational Study, and in vitro Assay ofJournal of experimental pharmacology · 2025Article
- In silico evaluation and therapeutic targeting of LVDD9B protein for WSSV inhibition: molecular and ecological insights for aquaculture solutions.In silico pharmacology · 2025Article
- Plausible mechanism of drug resistance and side-effects of COVID-19 therapeutics: a bottleneck for its eradication.Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences · 2024Review
- Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis.Journal of biological engineering · 2024Article
- In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (MPathogens (Basel, Switzerland) · 2024Article
- Probing the function of C-terminal region of recombinant α-amylase BmaN1 fromMicrobiology spectrum · 2024Article
- Modified oxymatrine as novel therapeutic inhibitors against Monkeypox and Marburg virus through computational drug design approaches.Journal of cellular and molecular medicine · 2024Article
- InBiochemistry and biophysics reports · 2024Article
- Discovery of novel BRD4-BD2 inhibitors via in silico approaches: QSAR techniques, molecular docking, and molecular dynamics simulations.Molecular diversity · 2024Article
- Article
83 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The main protease of SARS-CoV-2 is one of the important targets to design and develop antiviral drugs. In this study, we have selected 40 antiviral phytochemicals to find out the best candidates which can act as potent inhibitors against the main protease. Molecular docking is performed using AutoDock Vina and GOLD suite to determine the binding affinities and interactions between the phytochemicals and the main protease. The selected candidates strongly interact with the key Cys145 and His41 residues. To validate the docking interactions, 100 ns molecular dynamics (MD) simulations on the five top-ranked inhibitors including hypericin, cyanidin 3-glucoside, baicalin, glabridin, and α-ketoamide-11r are performed. Principal component analysis (PCA) on the MD simulation discloses that baicalin, cyanidin 3-glucoside, and α-ketoamide-11r have structural similarity with the apo-form of the main protease. These findings are also strongly supported by root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and solvent accessible surface area (SASA) investigations. PCA is also used to find out the quantitative structure-activity relationship (QSAR) for pattern recognition of the best ligands. Multiple linear regression (MLR) of QSAR reveals the
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.