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Article

In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer

by
Muruganantham Bharathi
1,
Bhagavathi Sundaram Sivamaruthi
1,2,*,
Periyanaina Kesika
1,2,
Subramanian Thangaleela
1,* and
Chaiyavat Chaiyasut
1,*
1
Innovation Center for Holistic Health, Nutraceuticals and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
2
Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand
*
Authors to whom correspondence should be addressed.
Appl. Sci. 2022, 12(2), 665; https://doi.org/10.3390/app12020665
Submission received: 29 November 2021 / Revised: 24 December 2021 / Accepted: 1 January 2022 / Published: 11 January 2022
(This article belongs to the Special Issue Artificial Intelligence Computing and Applications for COVID-19)

Abstract

In October 2020, the SARS-CoV-2 B.1.617 lineage was discovered in India. It has since become a prominent variant in several Indian regions and 156 countries, including the United States of America. The lineage B.1.617.2 is termed the delta variant, harboring diverse spike mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD), which may heighten its immune evasion potentiality and cause it to be more transmissible than other variants. As a result, it has sparked substantial scientific investigation into the development of effective vaccinations and anti-viral drugs. Several efforts have been made to examine ancient medicinal herbs known for their health benefits and immune-boosting action against SARS-CoV-2, including repurposing existing FDA-approved anti-viral drugs. No efficient anti-viral drugs are available against the SARS-CoV-2 Indian delta variant B.1.617.2. In this study, efforts were made to shed light on the potential of 603 phytocompounds from 22 plant species to inhibit the Indian delta variant B.1.617.2. We also compared these compounds with the standard drug ceftriaxone, which was already suggested as a beneficial drug in COVID-19 treatment; these compounds were compared with other FDA-approved drugs: remdesivir, chloroquine, hydroxy-chloroquine, lopinavir, and ritonavir. From the analysis, the identified phytocompounds acteoside (−7.3 kcal/mol) and verbascoside (−7.1 kcal/mol), from the plants Clerodendrum serratum and Houttuynia cordata, evidenced a strong inhibitory effect against the mutated NTD (MT-NTD). In addition, the phytocompounds kanzonol V (−6.8 kcal/mol), progeldanamycin (−6.4 kcal/mol), and rhodoxanthin (−7.5 kcal/mol), from the plant Houttuynia cordata, manifested significant prohibition against RBD. Nevertheless, the standard drug, ceftriaxone, signals less inhibitory effect against MT-NTD and RBD with binding affinities of −6.3 kcal/mol and −6.5 kcal/mol, respectively. In this study, we also emphasized the pharmacological properties of the plants, which contain the screened phytocompounds. Our research could be used as a lead for future drug design to develop anti-viral drugs, as well as for preening the Siddha formulation to control the Indian delta variant B.1.617.2 and other future SARS-CoV-2 variants.
Keywords: delta variant B.1.617.2; Clerodendrum serratum; Houttuynia cordata; Siddha; mutated NTD; anti-viral drug delta variant B.1.617.2; Clerodendrum serratum; Houttuynia cordata; Siddha; mutated NTD; anti-viral drug

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MDPI and ACS Style

Bharathi, M.; Sivamaruthi, B.S.; Kesika, P.; Thangaleela, S.; Chaiyasut, C. In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. Appl. Sci. 2022, 12, 665. https://doi.org/10.3390/app12020665

AMA Style

Bharathi M, Sivamaruthi BS, Kesika P, Thangaleela S, Chaiyasut C. In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. Applied Sciences. 2022; 12(2):665. https://doi.org/10.3390/app12020665

Chicago/Turabian Style

Bharathi, Muruganantham, Bhagavathi Sundaram Sivamaruthi, Periyanaina Kesika, Subramanian Thangaleela, and Chaiyavat Chaiyasut. 2022. "In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer" Applied Sciences 12, no. 2: 665. https://doi.org/10.3390/app12020665

APA Style

Bharathi, M., Sivamaruthi, B. S., Kesika, P., Thangaleela, S., & Chaiyasut, C. (2022). In Silico Screening of Potential Phytocompounds from Several Herbs against SARS-CoV-2 Indian Delta Variant B.1.617.2 to Inhibit the Spike Glycoprotein Trimer. Applied Sciences, 12(2), 665. https://doi.org/10.3390/app12020665

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