Sonchus arvensis L. against SARS-CoV-2 infection

J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1126-1138, November-December 2022.

DOI: https://doi.org/10.56499/jppres22.1489_10.6.1126

Original Article

Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein

[Simulación molecular de compuestos de la fracción de n-hexano de las hojas de Sonchus arvensis L. como antivirales del SARS-CoV-2 a través de la actividad inhibidora dirigida a la proteína viral estratégica]

Dwi Kusuma Wahyuni1,2*, Sumrit Wacharasindhu3, Wichanee Bankeeree2, Hunsa Punnapayak2, Hery Purnobasuki1, Junairiah1, Arif NM Ansori4, Viol Dhea Kharisma1,5, Arli Aditya Parikesit6, Listyani Suhargo1*, Sehanat Prasongsuk1,2*

1Department of Biology, Faculty of Science and Technology, Universitas Airlangga Surabaya, East Java, 60115, Indonesia.

2Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.

3Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok,10330, Thailand.

4Professor Nidom Foundation, Surabaya, East Java, 60115, Indonesia.

5Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik, East Java, 61171, Indonesia.

6Department of Bioinformatics, School of Life Science, Indonesia International Institute for Life Sciences, Jakarta, 13210, Indonesia.

*E-mail: dwi-k-w@fst.unair.ac.id (DKW), listyani-s@fst.unair.ac.id (LS), sehanat.p@chula.ac.th (SP)

Abstract

Context: COVID-19 was caused by the spread and transmission of SARS-CoV-2 at the end of 2019 until now. The problem comes when antiviral drugs have not yet been found and patients infected with SARS-CoV-2 can trigger a cytokine storm condition due to the effects of viral replication. Indonesia has various kinds of medicinal plants, such as Sonchus arvensis L., which are used as medicinal plants.

Aims: To analyze the activity of the inhibitor as SARS-CoV-2 antiviral agents from n-hexane fractions of S. arvensis leaves.

Methods: The sample was collected from GC-MS analysis, PubChem, and Protein Databank database, then drug-likeness identification using Lipinski Rule of Five server and bioactive prediction of bioactive compounds as inhibitor activity was conducted by Molinspiration server. Furthermore, the docking simulation was performed using PyRx 0.9.9 software to determine the binding activity, molecular interaction by Discovery Studio software to identify position and interaction type, 3D molecular visualization by PyMol 2.5. software, and dynamic by CABS-flex 2.0 server to predict interaction stability.

Results: α-Amyrin and β-amyrin from n-hexane fractions of S. arvensis leaves had activity as SARS-CoV-2 inhibitors through interactions on helicase, RdRp, Mpro, and RBD-Spike, both compounds had more negative binding affinity than control drug and can produce stable chemical bond interactions in the ligand-protein complexes. However, the results were merely computational, so they must be validated through an in vivo and in vitro research approach.

Conclusions: Sonchus arvensis L. leaves were predicted to have SARS-CoV-2 antiviral through inhibitor activity by α-amyrin and β-amyrin.

Keywords: antiviral; bioinformatics; SARS-CoV-2; Sonchus arvensis L.

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Resumen

Contexto: La propagación y la transmisión del SARS-CoV-2 han sido causadas por el COVID-19 desde finales de 2019 hasta ahora. El problema surge cuando aún no se han encontrado medicamentos antivirales y los pacientes infectados por el SARS-CoV-2 pueden desencadenar una condición de tormenta de citocinas debido a los efectos de la replicación viral. Indonesia tiene varios tipos de plantas medicinales, como Sonchus arvensis L., que se utilizan como plantas medicinales.

Objetivos: Analizar la actividad inhibidora de SARS-CoV-2 de fracciones de n-hexano de las hojas de S. arvensis.

Métodos: La muestra se recogió del análisis GC-MS, PubChem y la base de datos Protein Databank, luego se identificó la similitud de los fármacos utilizando el servidor Lipinski Rule of Five y se realizó la predicción de los compuestos bioactivos como actividad inhibidora mediante el servidor Molinspiration. Además, se realizó la simulación de acoplamiento mediante el software PyRx 0.9.9 para determinar la actividad de unión, la interacción molecular mediante el software Discovery Studio para identificar la posición y el tipo de interacción, la visualización molecular 3D mediante el software PyMol 2.5. y la dinámica mediante el servidor CABS-flex 2.0 para predecir la estabilidad de la interacción.

Resultados: La α-amirina y la β-amirina de las fracciones de n-hexano de las hojas de S. arvensis tuvieron actividad como inhibidores del SARS-CoV-2 a través de las interacciones en la helicasa, RdRp, Mpro y RBD-Spike, ambos compuestos tuvieron más afinidad de unión negativa que el fármaco de control y pueden producir interacciones de enlace químico estables en los complejos ligando-proteína. Sin embargo, los resultados fueron meramente computacionales, por lo que deben ser validados mediante un enfoque de investigación in vivo e in vitro.

Conclusiones: Se predijo que las hojas de S. arvensis tienen actividad antiviral contra el SARS-CoV-2 a través de la actividad inhibidora de la α-amirina y la β-amirina.

Palabras Clave: antiviral; bioinformática; SARS-CoV-2; Sonchus arvensis L.

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Citation Format: Wahyuni DK, Wacharasindhu S, Bankeeree W, Punnapayak H, Parikesit AA, Kharisma VD, Ansori ANM, Suhargo L, Prasongsuk S (2022) Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein. J Pharm Pharmacogn Res 10(6): 1126–1138. https://doi.org/10.56499/jppres22.1489_10.6.1126
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