ArticleFrontiers in chemistry2020
Screening of Natural Products Targeting SARS-CoV-2-ACE2 Receptor Interface - A MixMD Based HTVS Pipeline.
Article in Frontiers in chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 14 citations in OpenAlex.
- Uncovering hidden druggable sites: computational approaches to allosteric and cryptic pocket discovery-from molecular dynamics to AI.Journal of computer-aided molecular design · 2026Review
- Mixed-Solvent MD suite: modular tools for building and analyzing mixed-solvent molecular dynamics systems.Journal of computer-aided molecular design · 2026Article
- Virtual Screening Strategy to Identify Retinoic Acid-Related Orphan Receptor γt Modulators.Molecules (Basel, Switzerland) · 2023Article
- Analysis and Identification of Bioactive Compounds of Cannabinoids in Silico for Inhibition of SARS-CoV-2 and SARS-CoV.Biomolecules · 2022Article
- The battle between host and SARS-CoV-2: Innate immunity and viral evasion strategies.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Review
- Plastic Antibodies Mimicking the ACE2 Receptor for Selective Binding of SARS-CoV-2 Spike.Advanced materials interfaces · 2022Article
- Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants.European journal of microbiology & immunology · 2022Article
- Virtual screening and in vitro validation of natural compound inhibitors against SARS-CoV-2 spike protein.Bioorganic chemistry · 2022Article
- Structure based Drug Designing Approaches in SARS-CoV-2 Spike Inhibitor Design.Current topics in medicinal chemistry · 2022Review
- Screening S protein - ACE2 blockers from natural products: Strategies and advances in the discovery of potential inhibitors of COVID-19.European journal of medicinal chemistry · 2021Review
- Antcins fromPlants (Basel, Switzerland) · 2021Article
- Recent efforts for drug identification from phytochemicals against SARS-CoV-2: Exploration of the chemical space to identify druggable leads.Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association · 2021Article
- Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents.IEEE/ACM transactions on computational biology and bioinformaticsArticle
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The COVID-19 pandemic, caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a severe global health crisis now. SARS-CoV-2 utilizes its Spike protein receptor-binding domain (S-protein) to invade human cell through binding to Angiotensin-Converting Enzyme 2 receptor (ACE2). S-protein is the key target for many therapeutics and vaccines. Potential S-protein-ACE2 fusion inhibitor is expected to block the virus entry into the host cell. In many countries, traditional practices, based on natural products (NPs) have been in use to slow down COVID-19 infection. In this study, a protocol was applied that combines mixed solvent molecular dynamics simulations (MixMD) with high-throughput virtual screening (HTVS) to search NPs to block SARS-CoV-2 entry into the human cell. MixMD simulations were employed to discover the most promising stable binding conformations of drug-like probes in the S-protein-ACE2 interface. Detected stable sites were used for HTVs of 612093 NPs to identify molecules that could interfere with the S-protein-ACE2 interaction. In total, 19 NPs were selected with rescoring model. These top-ranked NP-S-protein complexes were subjected to classical MD simulations for 300 ns (3 replicates of 100 ns) to estimate the stability and affinity of binding. Three compounds, ZINC000002128789, ZINC000002159944 and SN00059335, showed better stability in all MD runs, of which ZINC000002128789 was predicted to have the highest binding affinity, suggesting that it could be effective modulator in RBD-ACE2 interface to prevent SARS-CoV-2 infection. Our results support that NPs may provide tools to fight COVID-19.
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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.