In-silico study of volatile compounds and COVID-19

J. Pharm. Pharmacogn. Res., vol. 10, no. 3, pp. 469-485, May-June 2022.

Original Article

Volatile compounds from Phyla scaberrima (Juss. ex Pers.) Moldenke and Dysphania ambrosioides (L.) Mosyakin & Clemants as possible SARS-CoV-2 protease inhibitors: Identification and in-silico study

[Compuestos volátiles de Phyla scaberrima (Juss. ex Pers.) Moldenke y Dysphania ambrosioides (L.) Mosyakin & Clemants como posibles inhibidores de proteasas de SARS-CoV-2: Identificación y estudio in-silico]

Neyder Contreras-Puentes1*, Manuel Salas-Moreno2,3, Lina Mosquera-Chaverra2, Leonomir Córdoba-Tovar4, Antistio Alviz-Amador5

1GINUMED, Medicine, Corporation University Rafael Nuñez, Cartagena D.T y C, Colombia.

2Faculty of Naturals Sciences, Biology Department, Biosistematic Research Group, Technological University of Chocó, Quibdó, Colombia.

3Analytical Chemistry and Biomedicine Group. Exacts and Natural Sciences Faculty. University of Cartagena. Cartagena, Colombia.

4Research Group Natural Resources and Environmental Toxicology, Technological University of Chocó, Quibdó, Colombia.

 5Pharmacology and Therapeutics Group, University of Cartagena, Cartagena D.T y C., Colombia.

*E-mail: neyder.contreras@curnvirtual.edu.co

Abstract

Context: COVID-19 is a pandemic that has affected the entire population, characterized by multisystemic involvement. With around 130 million cases of infection and more than 2.5 million deaths globally. However, the development of a low-efficacy treatment has led to the study of natural products as possible therapeutic alternatives against SARS-CoV-2.

Aims: To identify volatile compounds present in two plants in the Colombian Pacific and carry out in-silico studies to search for promising inhibitory molecules against SARS-CoV-2 proteases.

Methods: This research carried out the identification of metabolites of two plants identified in the Colombian Pacific, called P. scaberrima (Juss. ex Pers.) Moldenke y D. ambrosioides (L.) Mosyakin & Clemants. Ethanolic extracts were obtained by rotary-evaporation and determinated by GC-MS. Subsequently, in-silico studies were carried out by molecular docking against Mpro and PLpro using Autodock-vina 1.1. Also, a prediction of ADMET properties using SwissADME and GUSAR-Online server was performed.

Results: Thus, 15 volatile compounds with similarities greater than 85% were identified from both extracts, mostly sesquiterpenic and monoterpenic compounds. The compounds that showed the highest affinity against Mpro were α-amorphene and phytol for PLpro. Likewise, these were contrasted with co-crystallized molecules such as boceprevir and VIR2-251 as control structures. Finally, the predictions of ADMET properties showed values consistent with the literature.

Conclusions: Therefore, the follow-up of in-silico studies with these plants from Colombian pacific are considered as possible tools in the search for active molecules against proteases linked to virus.

Keywords: Dysphania ambrosioides; GC-MS/MS; molecular docking; Phyla scaberrima; SARS-CoV-2.

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Resumen

Contexto: COVID-19 es una pandemia que ha afectado a toda la población mundial, caracterizada por compromisos multisistémicos. Con alrededor de 130 millones de casos de infección y más de 2,5 millones de muertes en todo el mundo. Sin embargo, el desarrollo de un tratamiento de baja eficacia ha llevado al estudio de productos naturales como posibles alternativas terapéuticas frente al SARS-CoV-2.

Objetivos: Identificar compuestos volátiles presentes en dos plantas del Pacifico colombiano y realizar estudios in-silico para la búsqueda de promisorias moléculas inhibidoras contra proteasas de SARS-CoV-2.

Métodos: En esta investigación se realizó la identificación de metabolitos de dos plantas identificadas en el Pacífico colombiano, llamadas P. scaberrima (Juss. ex Pers.) Moldenke y D. ambrosioides (L.) Mosyakin & ClemantsSe obtuvieron extractos etanólicos, preconcentrados con evaporación rotatoria y se determinaron por GC-MS. Posteriormente, se realizaron estudios in-silico mediante acoplamiento molecular contra Mpro y PLpro utilizando Autodock-vina. Además, prediciendo las propiedades de ADMET mediante SwissADME y GUSAR-Online.

Resultados: Se identificaron 15 compuestos volátiles con similitudes superiores al 85% de ambos extractos, en su mayoría compuestos sesquiterpénicos y monoterpénicos. Los compuestos que mostraron la mayor afinidad contra Mpro fue α-amorfeno y fitol para PLpro. Asimismo, se contrastaron con moléculas co-cristalizadas como boceprevir y VIR2-251 como estructuras control. Finalmente, en las predicciones de propiedades ADMET mostraron valores consistentes con la literatura.

Conclusiones: Se consideró el seguimiento de estudios in-silico con estas plantas del Pacífico colombiano como posibles herramientas en la búsqueda de moléculas activas frente a proteasas ligadas al virus.

Palabras Clave: acoplamiento molecular; Dysphania ambrosioides; GC-MS/MS; Phyla scaberrima; SARS-CoV-2.

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Citation Format: Contreras-Puentes N, Salas-Moreno MH, Mosquera-Chaverra L, Córdoba-Tovar L, Alvíz-Amador AA (2022) Volatile compounds from Phyla scaberrima (Juss. ex Pers.) Moldenke y Dysphania ambrosioides (L.) Mosyakin & Clemants as possible SARS-CoV-2 protease inhibitors: Identification and in-silico study. J Pharm Pharmacogn Res 10(3): 469–485.
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