Tag Archives: virtual screening

Virtual screening of lead flavonoids against DENV2

J. Pharm. Pharmacogn. Res., vol. 10, no. 4, pp. 660-675, July-August 2022.

Original Article

Flavonoids as potential inhibitors of dengue virus 2 (DENV2) envelope protein

[Flavonoides como posibles inhibidores de la proteína de la cubierta del virus del dengue 2 (DENV2)]

Rachel Raditya Renantha1, Alvin Richardo Liga1, Christy Bianca Tanugroho1, Lovine Xaviera Denovian1, Siti Lateefa Az Zahra Budiyanto2, Arli Aditya Parikesit2*

1Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav.88 Jakarta 13210 Indonesia.

2Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav.88 Jakarta 13210 Indonesia.

*E-mail: arli.parikesit@i3l.ac.id

Abstract

Context: Dengue viruses (DENVs) are the cause of dengue disease, which is one of the most frequent diseases caused by mosquito-borne viral infections. Currently, no specific treatment is available for dengue.

Aims: To identify the most promising inhibitors of dengue virus 2 (DENV2) envelope protein of DENV2 envelope protein from flavonoids compounds through computational methods.

Methods: Structures of 54 flavonoids were collected, then the compounds were screened based on Lipinski’s rules, and there were only 34 compounds that passed the screening. Then QSAR analysis was performed, followed by molecular docking analysis, ADMET evaluation, and molecular dynamics simulations to assess the stability of the protein.

Results: Based on the QSAR analysis, only 32 compounds were subjected to molecular docking analysis. Silymarin had the highest docking score, while juglanin had the lowest ACE score compared to positive controls. The ADMET evaluation showed silymarin and juglanin had good absorption and could not penetrate the blood-brain barrier. In contrast to silymarin which had negative results for the Ames test, carcinogenicity, skin sensitization, and eye irritation, juglanin was positive for Ames test and skin sensitization. Even though the molecular dynamic simulation of both ligands with DENV2 envelope protein showed unstable confirmation, it did not necessarily mean that the ligands cannot be used as inhibitors since the molecular docking results provide evidence of the ligands binding to the DENV2 envelope protein.

Conclusions: Based on the favorable results of QSAR analysis, molecular docking, and ADMET evaluation, juglanin and silymarin were chosen as the candidate with the most potential for DENV2 envelope protein inhibitors. However, further analyses such as in vitro and in vivo analyses are necessary to validate the result of this study.

Keywords: DENV-2; envelope protein; flavonoids; molecular docking; virtual screening.

Resumen

Contexto: Los virus del dengue (DENV) son los causantes de la enfermedad del dengue, que es una de las enfermedades más frecuentes causada por infecciones virales transmitidas por mosquitos. Actualmente, no se dispone de un tratamiento específico para el dengue.

Objetivos: Identificar los inhibidores más prometedores de la proteína de la envoltura del virus del dengue 2 (DENV2) de la proteína de la envoltura del DENV2 a partir de compuestos de flavonoides a través de métodos computacionales.

Métodos: Las estructuras de 54 flavonoides fueron recolectadas. Los compuestos se seleccionaron según las reglas de Lipinski y solo 34 compuestos pasaron la selección. Luego se realizó el análisis QSAR, seguido de análisis de acoplamiento molecular, evaluación ADMET y simulaciones de dinámica molecular para evaluar la estabilidad de la proteína.

Resultados: Según el análisis QSAR, solo 32 compuestos se sometieron a análisis de acoplamiento molecular. La silimarina obtuvo la puntuación de acoplamiento más alta, mientras que juglanina obtuvo la puntuación ACE más baja en comparación con los controles positivos. La evaluación ADMET mostró que la silimarina y la juglanina tenían una buena absorción y no podían penetrar la barrera hematoencefálica. En contraste con la silimarina que tuvo resultados negativos para la prueba de Ames, carcinogenicidad, sensibilización de la piel e irritación de los ojos, la juglanina fue positiva para la prueba de Ames y la sensibilización de la piel. Aunque la simulación de la dinámica molecular de ambos ligandos con la proteína de la cubierta de DENV2 mostró una confirmación inestable, no significa necesariamente que los ligandos no puedan usarse como inhibidores, ya que los resultados del acoplamiento molecular proporcionan evidencia de que los ligandos se unen a la proteína de la cubierta de DENV2.

Conclusiones: En base a los resultados favorables del análisis QSAR, el acoplamiento molecular y la evaluación ADMET, la juglanina y la silimarina fueron elegidas como las candidatas con mayor potencial para los inhibidores de la proteína de la envoltura de DENV2. Sin embargo, se necesitan más análisis, como análisis in vitro e in vivo, para validar el resultado de este estudio.

Palabras Clave: acoplamiento molecular; DENV-2; flavonoides; proteína de envoltura; proyección virtual.

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Citation Format: Renantha RR, Liga AR, Tanugroho CB, Denovian LX, Budiyanto SLAZ, Parikesit AA (2022) Flavonoids as potential inhibitors of dengue virus 2 (DENV2) envelope protein. J Pharm Pharmacogn Res 10(4): 660–675.
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