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1.
Turkish Journal of Chemistry ; 47(2):329-345, 2023.
Article in English | Web of Science | ID: covidwho-20233008

ABSTRACT

The coronavirus disease, COVID-19, is the major focus of the whole world due to insufficient treatment options. It has spread all around the world and is responsible for the death of numerous human beings. The future consequences for the disease survivors are still unknown. Hence, all contributions to understand the disease and effectively inhibit the effects of the disease have great importance. In this study, different thioxanthone based molecules, which are known to be fluorescent compounds, were selectively chosen to study if they can inhibit the main protease of SARS-CoV-2 using various computational tools. All candidate ligands were optimized, molecular docking and adsorption, distribution, metabolism, excretion, and toxicity (ADMET) studies were conducted and subsequently, some were subjected to 100 ns molecular dynamics simulations in conjunction with the known antiviral drugs, favipiravir, and hydroxychlo-roquine. It was found that different functional groups containing thioxanthone based molecules are capable of different intermolecular interactions. Even though most of the studied ligands showed stable interactions with the main protease, para-oxygen-di-acetic acid functional group containing thioxanthone was found to be a more effective inhibitor due to the higher number of intermolecular inter-actions and higher stability during the simulations.

2.
Structural Chemistry ; : 21, 2022.
Article in English | Web of Science | ID: covidwho-1926060

ABSTRACT

Coronavirus disease-2019 (COVID-19), a global pandemic, has currently infected more than 247 million people around the world. Nowadays, several receptors of COVID-19 have been reported, and few of them are explored for drug discovery. New mutant strains of COVID-19 are emerging since the first outbreak of disease and causing significant morbidity and mortality across the world. Although, few drugs were approved for emergency uses, however, promising drug with well-proven clinical efficacy is yet to be discovered. Hence, researchers are continuously attempting to search for potential drug candidates targeting the well-established enzymatic targets of the virus. The present study aims to discover the antiviral compounds as potential inhibitors against the five targets in various stages of the SARS-CoV-2 life cycle, i.e., virus attachments (ACE2 and TMPRSS2), viral replication, and transcription (M-pro, PLpro and RdRp), using the most reliable molecular docking and molecular dynamics method. The ADMET study was then carried out to determine the pharmacokinetics and toxicity of several compounds with the best docking results. To provide a more effective mechanism for demonstrating protein-ligand interactions, molecular docking data were subjected to a molecular dynamic (MD) simulation at 300 K for 100 ns. In terms of structural stability, structure compactness, solvent accessible surface area, residue flexibility, and hydrogen bond interactions, the dynamic features of complexes have been compared.

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