Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV‑2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein

Umifenovir (Arbidol)
has been reported to exhibit some degree of
efficacy in multiple clinical trials for the treatment of COVID-19
as a monotherapy. It has also demonstrated synergistic inhibition
of SARS-CoV-2 with other direct-acting antivirals such as Remdesivir.
A computational approach was used to identify the most favorable binding
site to the SARS-CoV-2 Spike S2 segment and to perform virtual screening.
Compounds selected from modeling were evaluated in a live SARS-CoV-2
infection assay. An Arbidol (ARB) derivative with substitutions at
both the C-4 and C-6 positions was found to exhibit a modest improvement
in activity and solubility properties in comparison to ARB. However,
all of the derivatives were found to only be partial inhibitors, rather
than full inhibitors in a virus-induced cytopathic effect-based assay.
The binding mode is also corroborated by parallel modeling of a series
of oleanolic acid trisaccharide saponin fusion inhibitors shown to
bind to the S2 segment. Recently determined experimental structures
of the Spike protein allowed atomic resolution modeling of fusion
inhibitor binding as a function of pH, and the implications for the
molecular mechanism of direct-acting fusion inhibitors targeting the
S2 segment are discussed.