Journal Article

Enumeration of olive derived lignan, pinoresinol for activity against recent Omicron variant spike protein for structure-based drug design, DFT, molecular dynamics simulations, and MMGBSA studies

Alkhamiss, Abdullah Saleh, Aljohani, Abdullah S. M., Alghsham, Ruqaih S., Saleh, Fayez M., Alosaimi, Manal E., Alkhalil, Samia S., Shater, Abdullah F., Alosaimi, Shoruq E., Almohaimeed, Hailah M., Mohammedsaleh, Zuhair M., Al Abdulmonem, Waleed, Soliman, Mona H.

2024

Overview

The coronavirus disease 2019 (COVID-19) was first found in Wuhan, China, in December 2019. Because the virus spreads quickly, it quickly became a global worry. Coronaviridae is the family that contains both SARS-CoV-2 and the viruses that came before (i.e., MERS-CoV and SARS-CoV). Recent sources portray that the COVID-19 virus has affected 344,710,576 people worldwide and killed about 5,598,511 people in the last 2 years. The B.1.1.529 strain, later called “Omicron,” was named a Variant of Concern on November 24, 2021. The SARS-CoV-2 virus has gone through a never-ending chain of changes that have never happened before. As a result, it has many different traits. Most of these changes have occurred in the spike protein, where antibodies bind. Because of these changes, the Omicron type is very contagious and easy to pass on. There have been a lot of studies done to try to figure out this new challenge in the COVID-19 strains race, but there is still a lot that needs to be explained. This study focuses on virtual screening, docking, and molecular dynamic analysis; we aimed to identify therapeutic candidates for the SARS-CoV-2 variant Omicron based on their ability to inhibit non-structural proteins. We investigate the prediction of the properties of a substantial database of drug molecules obtained from the OliveNet™ database. Compounds that did not exhibit adequate gastrointestinal absorption and failed the Lipinski test are not considered for further research. The filtered compounds were coupled with our primary target, SARS-CoV-2 Omicron spike protein. We focused on SARS-CoV-2 Omicron spike protein and filtering potent olive compounds. Pinoresinol, the most likely candidate, is bound best (− 8.5 kcal/mol). Pinoresinol’s strong interaction with the active site made the complex’s dynamic structure more resilient. MD simulations explain the protein–ligand complex’s stability and function. Pinoresinol may be a promising SARS-CoV-2 Omicron spike protein receptor lead drug, and additional research may assist the scientific community. Graphical Abstract

• Publisher: Springer Berlin Heidelberg,Springer,Springer Nature B.V
• Subject: active sites / Analysis / Animal Genetics and Genomics / Biomedical and Life Sciences / China / Coronaviruses / COVID-19 / COVID-19 infection / COVID-19 vaccines / Cytotoxicity / drug design / Drug development / drugs / Enumeration / family / genetics / Health aspects / Human Genetics / Human Genetics • Original Paper / intestinal absorption / Life Sciences / Ligands / Lignans / Microbial Genetics and Genomics / Molecular docking / Molecular dynamics / Mutation / olives / Pandemics / people / Pharmacokinetics / Plant Genetics and Genomics / prediction / Protein binding / Protein structure / Proteins / psychological stress / Severe acute respiratory syndrome coronavirus 2 / Severe acute respiratory syndrome-related coronavirus / Simulation methods / Spike protein / Structural proteins / therapeutics / Viral diseases / Viruses