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Multi-target potential of Indian phytochemicals against SARS-CoV-2: A docking, molecular dynamics and MM-GBSA approach extended to Omicron B.1.1.529.
Roshni, Jency; Vaishali, R; Ganesh, K S; Dharani, N; Alzahrani, Khalid J; Banjer, Hamsa Jameel; Alghamdi, Ali H; Theyab, Abdulrahman; Ahmed, Shiek Ssj; Patil, Shankargouda.
  • Roshni J; Department of Medical Biotechnology, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam 603103, India. Electronic address: jencyroshni@gmail.com.
  • Vaishali R; Department of Medical Biotechnology, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam 603103, India. Electronic address: vaishalir967@gmail.com.
  • Ganesh KS; Department of Medical Biotechnology, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam 603103, India. Electronic address: ganeshkumar1742001@gmail.com.
  • Dharani N; Department of Medical Biotechnology, Chettinad Hospital & Research Institute (CHRI), Chettinad Academy of Research and Education (CARE), Kelambakkam 603103, India. Electronic address: lakshmi.dharani007@gmail.com.
  • Alzahrani KJ; Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia. Electronic address: h.banjer@tu.edu.sa.
  • Banjer HJ; Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia. Electronic address: ak.jamaan@tu.edu.sa.
  • Alghamdi AH; Department of Biology, Faculty of Science, Albaha University, Albaha 7738-65799, Saudi Arabia. Electronic address: aayfan@bu.edu.sa.
  • Theyab A; College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh, 11533, Saudi Arabia; Department of Laboratory Medicine, Security Forces Hospital, Mecca, Saudi Arabia. Electronic address: aalshehri@sfhm.med.sa.
  • Ahmed SS; Multi-omics and Drug Discovery Lab, Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute (CHRI), Chettinad Academy of Research and Education(CARE), Kelambakkam 603103, India. Electronic address: shiekssjahmed@gmail.com.
  • Patil S; Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan 45412, Saudi Arabia. Electronic address: dr.ravipatil@gmail.com.
J Infect Public Health ; 15(6): 662-669, 2022 May 13.
Article in English | MEDLINE | ID: covidwho-1945691
ABSTRACT

BACKGROUND:

SARS-CoV-2, an emerged strain of corona virus family became almost serious health concern worldwide. Despite vaccines availability, reports suggest the occurrence of SARS-CoV-2 infection even in a vaccinated population. With frequent evolution and expected multiple COVID-19 waves, improved preventive, diagnostic, and treatment measures are required. In recent times, phytochemicals have gained attention due to their therapeutic characteristics and are suggested as alternative and complementary treatments for infectious diseases. This present study aimed to identify potential inhibitors against reported protein targets of SARS-CoV-2.

METHODOLOGY:

We computationally investigated potential SARS-CoV-2 protein targets from the literature and collected druggable phytochemicals from Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT) database. Further, we implemented a systematic workflow of molecular docking, dynamic simulations and generalized born surface area free-energy calculations (MM-GBSA).

RESULTS:

Extensive literature search and assessment of 1508 articles identifies 13 potential SARS-CoV-2 protein targets. We screened 501 druggable phytochemicals with proven biological activities. Analysis of 6513(501 *13) docked phytochemicals complex, 26 were efficient against SARS-CoV-2. Amongst, 4,8-dihydroxysesamin and arboreal from Gmelina arborea were ranked potential against most of the targets with binding energy ranging between - 10.7 to - 8.2 kcal/mol. Additionally, comparative docking with known drugs such as arbidol (-6.6 to -5.1 kcal/mol), favipiravir (-5.5 to -4.5 kcal/mol), hydroxychloroquine (-6.5 to -5.1 kcal/mol), and remedesivir (-8.0 to -5.3 kcal/mol) revealed equal/less affinity than 4,8-dihydroxysesamin and arboreal. Interestingly, the nucleocapsid target was found commonly inhibited by 4,8-dihydroxysesamin and arboreal. Molecular dynamic simulation and Molecular mechanics generalized born surface area (MM-GBSA)calculations reflect that both the compounds possess high inhibiting potential against SARS-CoV-2 including the recently emerged Omicron variant (B.1.1.529).

CONCLUSION:

Overall our study imparts the usage of phytochemicals as antiviral agents for SARS-CoV-2 infection. Additional in vitro and in vivo testing of these phytochemicals is required to confirm their potency.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Systematic review/Meta Analysis Topics: Traditional medicine / Vaccines / Variants Language: English Journal: J Infect Public Health Journal subject: Communicable Diseases / Public Health Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Systematic review/Meta Analysis Topics: Traditional medicine / Vaccines / Variants Language: English Journal: J Infect Public Health Journal subject: Communicable Diseases / Public Health Year: 2022 Document Type: Article