Background: The discovery of a novel strain of coronavirus in 2019 (COVID-19) has
triggered a series of tragic events in the world with thousands of deaths recorded daily. Despite the huge
resources committed to the discovery of vaccines against this highly pathogenic virus, scientists are still
unable to find suitable treatments for the disease. Understanding the structure of coronavirus proteins
could provide a basis for the development of cheap, potent and, less toxic vaccines.
Objective: This study was therefore designed to model coronavirus spike (S) glycoprotein and envelope
(E) protein as well as to carry out molecular docking of potential drugs to the homologs and coronavirus
main protease (Mpro).
Methods: Homology modeling of coronavirus spike (S) glycoprotein and envelope (E) protein was carried
out using sequence deposited in the Uniprot database. The topological features of the model’s catalytic
site were evaluated using the CASTp server. Compounds reported as potential drugs against
COVID-19 were docked to S glycoprotein, E protein, and coronavirus main protease (Mpro) to determine
the best ligands and the mode of interaction.
Results: Homology modeling of the proteins revealed structures with 91-98% sequence similarity with
PDB entries. The catalytic site of the modeled proteins contained conserved residue involved in ligand
binding. In addition, remdesivir, lopinavir, and ritonavir have a high binding affinity for the three proteins
studied interacting with key residues in the protein’s catalytic domain.
Conclusion: Results from the study revealed that remdesivir, lopinavir, and ritonavir are inhibitors of
key coronavirus proteins and therefore qualify for further studies as a potential treatment for coronavirus.