Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV‑2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic

Despite the development of vaccines
against the severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) virus, there is an urgent need
for efficient drugs to treat infected patients. An attractive drug
target is the human transmembrane protease serine 2 (TMPRSS2) because
of its vital role in the viral infection mechanism of SARS-CoV-2 by
activation of the virus spike protein (S protein). Having in mind
that the information derived from quantum mechanics/molecular mechanics
(QM/MM) studies could be an important tool in the design of transition-state
(TS) analogue inhibitors, we resorted to adiabatic QM/MM calculations
to determine the mechanism of the first step (acylation) of proteolytic
cleavage of the S protein with atomistic details. Acylation occurred
in two stages: (i) proton transfer from Ser441 to His296 concerted
with the nucleophilic attack of Ser441 to the substrate’s P1-Arg
and (ii) proton transfer from His296 to the P1′-Ser residue
concerted with the cleavage of the ArgP1-SerP1′ peptide bond,
with a Gibbs activation energy of 17.1 and 15.8 kcal mol–1, relative to the reactant. An oxyanion hole composed of two hydrogen
bonds stabilized the rate-limiting TS by 8 kcal mol–1. An analysis of the TMPRSS2 interactions with the high-energy, short-lived
tetrahedral intermediate highlighted the limitations of current clinical
inhibitors and pointed out specific ways to develop higher-affinity
TS analogue inhibitors. The results support the development of more
efficient drugs against SARS-CoV-2 using a human target, free from
resistance development.