ArticleJournal of biomolecular structure & dynamics2022
The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach.
Article in Journal of biomolecular structure & dynamics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 38 citations in OpenAlex.
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- Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics.Journal of molecular structure · 2023Article
- Inhibitory effects and mechanisms of proanthocyanidins against enterovirus 71 infection.Virus research · 2023Article
- Phenolic Fraction from Peanut (Food and bioprocess technology · 2023Review
- Agathisflavone, a natural biflavonoid that inhibits SARS-CoV-2 replication by targeting its proteases.International journal of biological macromolecules · 2022Article
- Bioactive compounds as potential angiotensin-converting enzyme II inhibitors against COVID-19: a scoping review.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2022Article
- Natural Inhibitors Targeting the Localization of Lipoprotein System inInternational journal of molecular sciences · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Screening of Botanical Drugs against SARS-CoV-2 Entry Reveals Novel Therapeutic Agents to Treat COVID-19.Viruses · 2022Article
- Targeting autophagy with natural products to prevent SARS-CoV-2 infection.Journal of traditional and complementary medicine · 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
- Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019.Current opinion in colloid & interface science · 2021Review
- Article
- Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning.Computers in biology and medicine · 2021Article
- Natural Products for the Prevention and Control of the COVID-19 Pandemic: Sustainable Bioresources.Frontiers in pharmacology · 2021Review
- Potentials of Antitussive Traditional Persian Functional Foods for COVID-19 TherapyFrontiers in pharmacology · 2021Review
- Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PLCurrent research in pharmacology and drug discovery · 2021Article
- ACE2 Interaction Networks in COVID-19: A Physiological Framework for Prediction of Outcome in Patients with Cardiovascular Risk Factors.Journal of clinical medicine · 2020Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors. Communicated by Ramaswamy H. Sarma.
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