Caffeine and caffeine-containing pharmaceuticals as promising inhibitors for 3-chymotrypsin-like protease of SARS-CoV-2

Amin O Elzupir, Amin O Elzupir

Abstract

In December 2019, a new coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the outbreak of a pulmonary disease called COVID-19, which killed thousands of people worldwide. Therefore, the necessity to find out the potential therapeutic pharmaceuticals is imperious. This study investigates the inhibitory effect of SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) using caffeine and caffeine-containing pharmaceuticals (3CPs) based on molecular dynamics simulations and free energy calculations by means of molecular mechanics-Poisson-Boltzmann surface area (MMPBSA) and molecular mechanics-generalized-Born surface area (MMGBSA). Of these 3CPs, seven drugs approved by the US-Food and Drug Administration have shown a good binding affinity to the catalytic residues of 3CLpro of His41 and Cys145: caffeine, theophylline, dyphylline, pentoxifylline, linagliptin, bromotheophylline and istradefylline. Their binding affinity score ranged from -4.9 to -8.6 kcal/mol. The molecular dynamic simulation in an aqueous solution of docked complexes demonstrated that the 3CPs conformations bound to the active sites of 3CLpro during 200 ns molecular dynamics simulations. The free energy of binding also confirms the stability of the 3CPs-3CLpro complexes. To our knowledge, this in silico study shows for the first time very inexpensive drugs available in large quantities that can be potential inhibitors against 3CLpro. In particular, the repurposing of linagliptin, and caffeine are recommended for COVID-19 treatment after in vitro, in vivo and clinical trial validation.Communicated by Ramaswamy H. Sarma.

Keywords: 3-chymotrypsin-like protease; COVID-19; Coronavirus SARS-CoV-2; caffeine-containing pharmaceuticals; molecular dynamics.

Conflict of interest statement

The author declares that he has no conflict of interest.

Figures

Scheme 1.
Scheme 1.
Chemical structures of (a) pyridone and (b) 4-pyrimid-dione
Figure 1.
Figure 1.
Crystal structure of 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 (PDB ID: 6Y2E) and ligands docked with 3CLpro and its contact sites with HIS41, CYS145 and GLU166. (a) Remdesivir; (b) linagliptin; (c) istradefylline; (d) dyphylline; (e) caffeine; (f) bromotheophylline; (g) pentoxifylline; (h) theophylline. Hydrocarbon skeleton cyan, nitrogen atoms are blue, oxygens red.
Figure 2.
Figure 2.
The RMSD values of the simulated complexes of 3CLpro and ligands throughout the 200 ns of production runs.
Figure 3.
Figure 3.
The RMSF values of the simulated complexes of 3CLpro and ligands throughout the 200 ns of production runs.
Figure 4.
Figure 4.
(a) Remdesivir, (b) linagliptin, (c) dyphylline, (d) caffeine, (e) istradefylline, (f) bromotheophylline, (g) pentoxifylline, and (h) theophylline at 1 ns, 133 ns, and 200 ns throughout the production runs.

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