Computational study on the affinity of potential drugs to SARS-CoV-2 main protease. (20th July 2022)

• Record Type: Journal Article
• Authors: Martín, Verónica; Sanz-Novo, Miguel; León, Iker; Redondo, Pilar; Largo, Antonio; Barrientos, Carmen
• Is Part Of: Journal of physics. Volume 34:Number 29(2022)
• Publication Date: 2022-07-20
• Subjects: molecular docking -- dexamethasone -- betamethasone -- chloroquine -- hydroxychloroquine -- SARS-CoV-2 main protease; Condensed matter -- Periodicals; Matière condensée -- Périodiques; Vaste stoffen; Vloeistoffen; Natuurkunde; Electronic journals; Computer network resources; 530.4105
• DOI: 10.1088/1361-648X/ac6c6c
• Languages: English
• ISSNs: 0953-8984

Abstract

Abstract: Herein, we report a computational investigation of the binding affinity of dexamethasone, betamethasone, chloroquine and hydroxychloroquine to SARS-CoV-2 main protease using molecular and quantum mechanics as well as molecular docking methodologies. We aim to provide information on the anti-COVID-19 mechanism of the abovementioned potential drugs against SARS-CoV-2 coronavirus. Hence, the 6w63 structure of the SARS-CoV-2 main protease was selected as potential target site for the docking analysis. The study includes an initial conformational analysis of dexamethasone, betamethasone, chloroquine and hydroxychloroquine. For the most stable conformers, a spectroscopic analysis has been carried out. In addition, global and local reactivity indexes have been calculated to predict the chemical reactivity of these molecules. The molecular docking results indicate that dexamethasone and betamethasone have a higher affinity than chloroquine and hydroxychloroquine for their theoretical 6w63 target. Additionally, dexamethasone and betamethasone show a hydrogen bond with the His41 residue of the 6w63 protein, while the interaction between chloroquine and hydroxychloroquine with this amino acid is weak. Thus, we confirm the importance of His41 amino acid as a target to inhibit the SARS-CoV-2 Mpro activity.