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2021 ; 39
(11
): 3924-3933
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Repurposing approved drugs as inhibitors of SARS-CoV-2?S-protein from molecular
modeling and virtual screening
#MMPMID32448085
de Oliveira OV
; Rocha GB
; Paluch AS
; Costa LT
J Biomol Struct Dyn
2021[Jul]; 39
(11
): 3924-3933
PMID32448085
show ga
Herein, molecular modeling techniques were used with the main goal to obtain
candidates from a drug database as potential targets to be used against
SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since
the end of 2019, became a challenge since there is not vaccine for this disease.
The first step in this investigation was to solvate the isolated S-protein in
water for molecular dynamics (MD) simulation, being observed a transition from
"up" to "down" conformation of receptor-binding domain (RBD) of the S-protein
with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more
exposed to the solvent and to the possible drugs due to its enhanced surface
area. From the equilibrated MD structure, virtual screening by docking
calculations were performed using a library contained 9091 FDA approved drugs.
Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved
drugs) with the binding energy below -8.1?kcal/mol were selected as potential
candidates to inhibit the SARS-CoV-2?S-protein, preventing the human cell
infection and their replication. For instance, the ivermectin drug (present in
our list of promise candidates) was recently used successful to control viral
replication in vitro. MD simulations were performed for the three best
ligands@S-protein complexes and the binding energies were calculated using the
MM/PBSA approach. Overall, it is highlighted an important strategy, some key
residues, and chemical groups which may be considered on clinical trials for
COVID-19 outbreak. [Formula: see text]Communicated by Ramaswamy H. Sarma.