J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1103-1116, November-December 2022.
DOI: https://doi.org/10.56499/jppres22.1485_10.6.1103
Original Article
Phyllanthus tenellus Roxb. and Kaempferia parviflora Wall. ex Baker compounds as inhibitors of SARS-CoV-2 main protease and RNA-dependent RNA polymerase: A molecular docking study
[Compuestos de Phyllanthus tenellus Roxb. y Kaempferia parviflora Wall. ex Baker como inhibidores de la proteasa principal del SARS-CoV-2 y de la ARN polimerasa dependiente de ARN: Un estudio de acoplamiento molecular]
Suhaina Supian*, Muhamad Aizuddin Ahmad, Lina Rozano, Machap Chandradevan, Zuraida Ab Rahman
Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Serdang 43400, Selangor, Malaysia.
*E-mail: suhaina@mardi.gov.my
Abstract
Context: The outbreak of a novel coronavirus, SARS-CoV-2 has caused an unprecedented COVID-19 pandemic. To put an end to this pandemic, effective antivirals should be identified or developed for COVID-19 treatment. However, specific and effective antivirals or inhibitors against SARS-CoV-2 are still lacking.
Aims: To evaluate bioactive compounds from Phyllanthus tenellus and Kaempferia parviflora as inhibitorsagainst two essential SARS-CoV-2 proteins, main protease (Mpro) and RNA-dependent RNA polymerase (RdRp), through molecular docking studies and to predict the drug-likeness properties of the compounds.
Methods: The inhibition potential and interaction of P. tenellus and K. parviflora compounds against Mpro and RdRp were assessed through molecular docking. The drug-likeness properties of the compounds were predicted using SwissADME and AdmetSAR tools.
Results: Rutin and ellagic acid glucoside from P. tenellus and 4-hydroxy-6-methoxyflavone and 5-hydroxy-3,7,4’-trimethoxyflavone from K. parviflora exhibited the highest binding conformations to Mpro by interacting with its substrate binding site that was predicted to halt the Mpro activity. As for RdRp, ellagitannin and rutin from P. tenellus and peonidin and 5,3’-dihydroxy-3,7,4’-trimethoxyflavone from K. parviflora were the best-docked compounds that bound to the RdRp catalytic domain (Asp760 and Asp761) and NTP-entry channel that were anticipated to stop RNA polymerization. However, in the context of drug developability, 4-hydroxy-6-methoxyflavone, 5-hydroxy-3,7,4’-trimethoxyflavone, peonidin and 5,3’-dihydroxy-3,7,4’-trimethoxyflavone from K. parviflora were highly potential to be oral active drugs compared to rutin, ellagic acid glucoside and ellagitannin from P. tenellus.
Conclusions: P. tenellus and K. parviflora compounds, particularly the aforementioned compounds, were suggested as potential inhibitors of SARS-CoV-2 Mpro and RdRp.
Keywords: antiviral; compounds; COVID-19; in silico; Kaempferia parviflora; Phyllanthus tenellus.
Resumen
Contexto: El brote de un nuevo coronavirus, el SARS-CoV-2, ha provocado una pandemia de COVID-19 sin precedentes. Para poner fin a esta pandemia, es necesario identificar o desarrollar antivirales eficaces para el tratamiento del COVID-19. Sin embargo, aún se carece de antivirales o inhibidores específicos y eficaces contra el SARS-CoV-2.
Objetivos: Evaluar compuestos bioactivos de Phyllanthus tenellus y Kaempferia parviflora como inhibidores contra dos proteínas esenciales del SARS-CoV-2, la proteasa principal (Mpro) y la ARN polimerasa dependiente del ARN (RdRp), mediante estudios de acoplamiento molecular y predecir las propiedades de similitud con los fármacos de los compuestos.
Métodos: El potencial de inhibición y la interacción de los compuestos de P. tenellus y K. parviflora contra la Mpro y la RdRp fueron evaluados mediante docking molecular. Las propiedades de semejanza de los compuestos se predijeron mediante las herramientas SwissADME y AdmetSAR.
Resultados: La rutina y el glucósido del ácido elágico de P. tenellus y la 4-hidroxi-6-metoxiflavona y la 5-hidroxi-3,7,4′-trimetoxiflavona de K. parviflora mostraron las conformaciones de unión más altas a Mpro al interactuar con su sitio de unión al sustrato que se predijo para detener la actividad de Mpro. En cuanto a la RdRp, la elagitanina y la rutina de P. tenellus y la peonidina y la 5,3′-dihidroxi-3,7,4′-trimetoxiflavona de K. parviflora fueron los compuestos mejor acoplados que se unieron al dominio catalítico de la RdRp (Asp760 y Asp761) y al canal de entrada NTP que se anticipó que detendría la polimerización del ARN. Sin embargo, en el contexto del desarrollo de fármacos, la 4-hidroxi-6-metoxiflavona, la 5-hidroxi-3,7,4′-trimetoxiflavona, la peonidina y la 5,3′-dihidroxi-3,7,4′-trimetoxiflavona de K. parviflora tendrían un gran potencial para ser fármacos activos por vía oral en comparación con la rutina, el glucósido de ácido elágico y la elagitanina de P. tenellus.
Conclusiones: Los compuestos de P. tenellus y K. parviflora, en particular los mencionados, fueron sugeridos como potenciales inhibidores de Mpro y RdRp del SARS-CoV-2.
Palabras Clave: antiviral; compuestos; COVID-19; in silico; Kaempferia parviflora; Phyllanthus tenellus.
Citation Format: Supian S, Ahmad MA, Rozano L, Chandradevan M, Ab Rahman Z (2022) Phyllanthus tenellus Roxb. and Kaempferia parviflora Wall. ex Baker compounds as inhibitors of SARS-CoV-2 main protease and RNA-dependent RNA polymerase: A molecular docking study. J Pharm Pharmacogn Res 10(6): 1103–1116. https://doi.org/10.56499/jppres22.1485_10.6.1103
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