The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening

Wu, Yang‐Chang; Chen, Guan-Yu; Tang, Yao; Ahmed, Azaj; Pan, Yi-Cheng; Yang, Juan-Cheng

doi:10.1101/2020.06.25.170639

Cited by 4 publications

(2 citation statements)

References 80 publications

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“…RBD was solvated in 5% v/v ratio of the probe to water with each probe. Tleap in AMBER18 (Case et al, 2020) was used for simulation setup. Hydrogens were added, and disulfide bonds and histidine protonation were assigned.…”

Section: Mixmd Simulationsmentioning

confidence: 99%

Screening of Natural Products Targeting SARS-CoV-2–ACE2 Receptor Interface – A MixMD Based HTVS Pipeline

et al. 2020

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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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Section: Mixmd Simulationsmentioning

confidence: 99%

Screening of Natural Products Targeting SARS-CoV-2–ACE2 Receptor Interface – A MixMD Based HTVS Pipeline

et al. 2020

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“…In silico studies of small molecules including those of natural compounds of plant origin have been screened and confirm to directly inhibit this important protein of SARS-Cov-2 (Zhang et al, 2020;Chen et al, 2020;Wen et al, 2007). Although drug development against coronavirus (Covid-19) has poses great challenge to scientist.…”

Section: Introductionmentioning

confidence: 99%

SARS-COV-2 Spike Glycoprotein as Inhibitory Target for Insilico Screening of Natural Compounds

Omoboyowa

Balogun

Chukwudozie

et al. 2021

Preprint

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Coronavirius disease 2019 (Covid-19) pandemic caused by SARS-Cov-2 has raised global health concern without approved drug for management of this lie threatening disease. The aim of this study was to predict the inhibitory potential of quercetin-3-o-rutinoside against SARS-Cov-2 spike glycoprotein. Targeting the SARS-Cov-2 spike protein from angiotensin converting enzyme 2 complex (pdb: 6lzg) is gaining importance. In this study, in silico computational relationship between plant-derived natural drug and spike glycoprotein was predicted. The results were evaluated based on glide (Schrodinger) dock score. Among the five (5) screened compounds, quercetin-3-o-rutinoside has the best docking score (-9.296) with the target. Molecular dynamic (MD) simulation study was performed for 1000ps to confirm the stability behavior of the spike protein and quercetin-3-o-rutinoside complex. The MD simulation study validated the stability of quercetin-3-o-rutinoside in the spike protein binding pocket as potent inhibitor.

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Natural products as a therapy to combat against SARS-CoV-2 virus infection

Malviya

Parihar

Parihar³

et al. 2022

Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV-2 Infection

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The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening

Cited by 4 publications

References 80 publications

Screening of Natural Products Targeting SARS-CoV-2–ACE2 Receptor Interface – A MixMD Based HTVS Pipeline

Screening of Natural Products Targeting SARS-CoV-2–ACE2 Receptor Interface – A MixMD Based HTVS Pipeline

SARS-COV-2 Spike Glycoprotein as Inhibitory Target for Insilico Screening of Natural Compounds

Natural products as a therapy to combat against SARS-CoV-2 virus infection

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