Polymethine Dyes as Probes for Detecting the SARS-COV-2 Coronavirus: In silico Molecular Docking Study

• Published in: Russian journal of physical chemistry. B Vol. 15; no. 1; pp. 25 - 32
• Main Authors: Pronkin, P. G., Tatikolov, A. S.
• Format: Journal Article
• Language: English
• Published: Moscow Pleiades Publishing 2021; Springer Nature B.V
• Subjects: Chemistry; Chemistry and Materials Science; Coronaviruses; Dyes; Molecular docking; Physical Chemistry; Quantum Chemistry; Severe acute respiratory syndrome coronavirus 2; Spectroscopy; Structure of Chemical Compounds; Structure of Chemical Compounds, Quantum Chemistry, Spectroscopy; Viral diseases; polymethine dyes; molecular docking; SARS-CoV-2 coronavirus; non-covalent interaction; spike protein
• ISSN: 1990-7931; 1990-7923
• DOI: 10.1134/S1990793121010267

The noncovalent interaction between various polymethine dyes (45 compounds in total) and a spike protein (S), one of the main structural component of the SARS-CoV-2 coronavirus, is studied in silico (molecular docking) to develop effective probes to detect the virus. The interaction energies and the spatial configurations of the complexes of the dye molecules with S are found. We showed that cationic polymethine dyes and neutral squarylium dyes do not form stable complexes with S. Some anionic dyes having negative total energies
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may be recommended for practical research.