Molecular docking of cyanine and squarylium dyes with SARS-CoV-2 proteases NSP3, NSP5 and NSP12

Abstract

Background: The outbreak and continued spread of coronavirus infection (COVID-19) sets the goal of finding new tools and methods to develop analytical procedures and tests to detect, study infection and prevent morbidity.

Methods: The noncovalent binding of cyanine and squarylium dyes of different classes (60 compounds in total) with the proteases NSP3, NSP5, and NSP12 of SARS-CoV-2 was studied by the method of molecular docking.

Results: The interaction energies and spatial configurations of dye molecules in complexes with NSP3, NSP5, and NSP12 have been determined.

Conclusion: A number of anionic dyes showing lower values of the total energy E_tot could be recommended for practical research in the development of agents for the detection and inactivation of the coronavirus.

Graphical abstract

Keywords

SARS-CoV-2 / proteases / polymethine dyes / squarylium dyes / noncovalent interaction / molecular docking

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The Author(s) 2021. Published by Higher Education Press.