Are Non-Structural Proteins From SARS-CoV-2 the Target of Hydroxychloroquine? An in Silico Study

Ériky Fernandes  Guimarães Silva; Bruna Fernandes; Luan Gabriel Pinto; Angélica De Fátima Marcuss; Anderson  Dillmann Groto; Kádima  Nayara Teixeira

doi:10.18502/acta.v61i2.12533

Ériky Fernandes Guimarães Silva Campus Toledo, Universidade Federal do Paraná, Toledo, Brazil
Bruna Fernandes Campus Toledo, Universidade Federal do Paraná, Toledo, Brazil
Luan Gabriel Pinto Campus Toledo, Universidade Federal do Paraná, Toledo, Brazil
Angélica De Fátima Marcuss Campus Toledo, Universidade Federal do Paraná, Toledo, Brazil
Anderson Dillmann Groto Campus Toledo, Universidade Federal do Paraná, Toledo, Brazil
Kádima Nayara Teixeira Campus Toledo, Universidade Federal do Paraná, Toledo, Brazil

DOI: https://doi.org/10.18502/acta.v61i2.12533

Keywords: Betacoronavirus; Coronavirus infections; Viral proteins; Hydroxychloroquine; Computational biology; Computer simulation

Abstract

COVID-19 is caused by SARS-CoV-2 which has structural and non-structural proteins (NSP) essential for infection and viral replication. There is a possible binding of SARS-CoV-2 to the beta-1 chain of hemoglobin in red blood cells and thus, decreasing the oxygen transport capacity. Since hydroxychloroquine (HCQ) can accumulate in red cells, there is a chance of interaction of this drug with the virus. To analyze possible interactions between SARS-CoV-2 NSP and hemoglobin with the HCQ using molecular docking and implications for the infected host. This research consisted of a study using bioinformatics tools. The files of the protein structures and HCQ were prepared using the AutoDock Tools software. These files were used to perform molecular docking simulations by AutoDock Vina. The binding affinity report of the generated conformers was analyzed using PyMol software, as well as the chemical bonds formed. The results showed that HCQ is capable of interacting with both SARS-CoV-2 NSP and human hemoglobin. The HCQ/NSP3 conformer, HCQ/NSP5, HCQ/NSP7-NSP8-NSP12, HCQ/NSP9, HCQ/NSP10-NSP16 showed binding affinity. In addition, the interaction between HCQ and hemoglobin resulted in polar bonds. Interaction between SARS-CoV-2 NSP and HCQ indicates that this drug possibly acts by preventing the continuity of infection.