Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar;23(1):23-36.
doi: 10.4314/ahs.v23i1.4.

Investigation of antiviral substances in Covid 19 by Molecular Docking: In Silico Study

Erkan Oner  1 , Ilter Demirhan  2 , Meral Miraloglu  3 , Serap Yalin  1 , Ergul Belge Kurutas  4
Affiliations

Investigation of antiviral substances in Covid 19 by Molecular Docking: In Silico Study

Erkan Oner et al. Afr Health Sci. 2023 Mar.

Abstract

Aims: This paper aimed to investigate the antiviral drugs against Sars-Cov-2 main protease (MPro) using in silico methods.

Material and method: A search was made for antiviral drugs in the PubChem database and antiviral drugs such as Bictegravir, Emtricitabine, Entecavir, Lamivudine, Tenofovir, Favipiravir, Hydroxychloroquine, Lopinavir, Oseltamavir, Remdevisir, Ribavirin, Ritonavir were included in our study. The protein structure of Sars-Cov-2 Mpro (PDB ID: 6LU7) was taken from the Protein Data Bank (www.rcsb. Org) system and included in our study. Molecular docking was performed using AutoDock/Vina, a computational docking program. Protein-ligand interactions were performed with the AutoDock Vina program. 3D visualizations were made with the Discovery Studio 2020 program. N3 inhibitor method was used for our validation.

Results: In the present study, bictegravir, remdevisir and lopinavir compounds in the Sars-Cov-2 Mpro structure showed higher binding affinity compared to the antiviral compounds N3 inhibitor, according to our molecular insertion results. However, the favipiravir, emtricitabine and lamuvidune compounds were detected very low binding affinity. Other antiviral compounds were found close binding affinity with the N3 inhibitor.

Conclusion: Bictegravir, remdevisir and lopinavir drugs showed very good results compared to the N3 inhibitor. Therefore, they could be inhibitory in the Sars Cov-2 Mpro target.

Keywords: Antiviral Drugs; Molecular Docking; Sars-CoV-2 Main Protease.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Covid 19 Structure .
Figure 2
Figure 2
Status of N3 inhibitor with Sars-Cov-2 MPro inhibitor before reconfirmation (red), status of N3 inhibitor after insertion (yellow)
See this image and copyright information in PMC

References

    1. Park SE. Epidemiology, virology, and clinical features of severe acute respiratory syndrome - coronavirus-2 (SARS-CoV-2; Coronavirus Disease-19) Clinical and Experimental Pediatrics. 2020;63(4):119–124. - PMC - PubMed
    1. Lai CC, Wang CY, Wang YH, et al. Global epidemiology of coronavirus disease 2019 (COVID19): disease incidence, daily cumulative index, mortality, and their association with country healthcare resources and economic status. International Journal of Antimicrobial Agents. 2020 Mar 19;:105946. doi: 10.1016/j.ijantimicag.2020.105946. - DOI - PMC - PubMed
    1. WHO - World Health Organization [homepage on Internet], author Coronavirus disease (COVID-2019) situation report 198. 2020. [updated 2020 Aug 5; cited 2020 Aug 5]. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situatio....
    1. Kampf G, Todt D, Pfaender S, Steinmann E. Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents. Journal of Hospital Infection. 2020;104(3):246–251. - PMC - PubMed
    1. Bourouiba L. Turbulent gas clouds and respiratory pathogen emissions: potential implications for reducing transmission of COVID-19. JAMA. 2020;323(18):1837–1838. - PubMed