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Natures Therapy for COVID-19: Targeting the Vital Non-Structural Proteins (NSP) from SARS-CoV-2 with Phytochemicals from Indian Medicinal Plants

preprint
revised on 16.07.2020 and posted on 16.07.2020 by Pratap Kumar Parida, Dipak Paul, Debamitra Chakravorty
Containing COVID-19 is still a global challenge. It has affected the "normal" world by
targeting its economy and health sector. Research is more focused on finding a cure to this
disease and is less concerned about other life threatening diseases like cancer. Thus we need to
develop a medical solution at the earliest. In this context the present work aimed to understand
the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained
from our previous work, following drug-likeness properties, against 6 non-structural-proteins
(NSP) from SARS-CoV-2. 100 ns molecular dynamics simulations were performed and
relative binding free energies were computed by MM/PBSA. Further, principal component
analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to
characterize protein–ligand interactions. Biological pathway enrichment analysis was also
carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-
CoV-2. The potential binding modes and favourable molecular interaction profile of 9
phytochemicals, majorly from Withania sominifera with lowest free binding energies, against
the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and
repurposed drugs with steroidal moieties in their chemical structures formed stable interactions
with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and
phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were
with the most significant p-value. To summarize this work, we suggest a global approach of
targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative
therapy for COVID-19. We also suggest that these phytochemicals need to be tested
experimentally to confirm their efficacy.

Funding

This work used resources services, and support provided via the COVID-19 HPC Consortium (https://covid19-hpc-consortium.org/), which is a unique private-public effort to bring together government, industry, and academic leaders who are volunteering free compute time and resources in support of COVID-19 research.

History

Email Address of Submitting Author

dc@noveltechsciences.com

Institution

Novel Techsciences (OPC) Private Limited, 37-B, Darga Road, 1st Floor, Kolkata - 700 017

Country

India

ORCID For Submitting Author

0000-0002-1520-0780

Declaration of Conflict of Interest

None

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