Abstract
The worldwide outbreak of the COVID-19 pandemic compelled scientists to develop new, highly effective therapeutic
approaches to fight it. Multitarget drugs have been proven to be effective in managing complex disorders. But designing
multitarget drugs is a great challenge. In this study, to prevent a lack of efficacy due to viral mutation escape, a multi
target agent against the COVID-19 virus was discovered. As crucial targets, RNA-dependent RNA polymerase (RdRp),
COVID-19 main protease (Mpro), and SARS-CoV-2 Nsp15 were selected. A pharmacophore model was developed using
the native ligands of the chosen targets. This model was used to screen the ZINC Drug Database for commercially
available compounds having similar features to the experimentally tested drugs. Pharmacophore-based virtual screening
yielded 1331 hits, which were further docked into the binding sites of selected proteins using PyRx AutoDock Vina.
Evaluation of docking results revealed that glisoxepide (Zn 00537804) has the highest binding scores for the three
target proteins. It showed binding free energies of 6.8, 6.2, and 7.8kcal/moltowardsSARS-CoV-2Mpro,Nsp15,and
RdRp, respectively. According to an in silico ADME study, glisoxepide follows Lipinski’s rule. The results of a molecular
dynamics simulation study and subsequent investigations showed that glisoxepide had good dynamics and stability
within the active sites of selected targets. The promise of glisoxepide as a potential treatment for SARS-CoV-2 still needs
to be further evaluated through experimental research.
approaches to fight it. Multitarget drugs have been proven to be effective in managing complex disorders. But designing
multitarget drugs is a great challenge. In this study, to prevent a lack of efficacy due to viral mutation escape, a multi
target agent against the COVID-19 virus was discovered. As crucial targets, RNA-dependent RNA polymerase (RdRp),
COVID-19 main protease (Mpro), and SARS-CoV-2 Nsp15 were selected. A pharmacophore model was developed using
the native ligands of the chosen targets. This model was used to screen the ZINC Drug Database for commercially
available compounds having similar features to the experimentally tested drugs. Pharmacophore-based virtual screening
yielded 1331 hits, which were further docked into the binding sites of selected proteins using PyRx AutoDock Vina.
Evaluation of docking results revealed that glisoxepide (Zn 00537804) has the highest binding scores for the three
target proteins. It showed binding free energies of 6.8, 6.2, and 7.8kcal/moltowardsSARS-CoV-2Mpro,Nsp15,and
RdRp, respectively. According to an in silico ADME study, glisoxepide follows Lipinski’s rule. The results of a molecular
dynamics simulation study and subsequent investigations showed that glisoxepide had good dynamics and stability
within the active sites of selected targets. The promise of glisoxepide as a potential treatment for SARS-CoV-2 still needs
to be further evaluated through experimental research.
Keywords
:Multi-target pharmacophore
and Nsp15
Anti-SARS-CoV-2 RdRp
Glisoxepide
Molecular docking
Molecular dynamics simulation
Mpro
Virtual screening