The angiotensin-converting enzyme 2 (ACE2) and main protease (MPro), are the putative drug candidates for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, we performed 3D-QSAR pharmacophore modeling and screened 1,264,479 ligands gathered from Pubchem and Zinc databases. Following the calculation of the ADMET properties, molecular docking was carried out. Moreover, the
de novo
ligand design was performed. MD simulation was then applied to survey the behavior of the ligand-protein complexes. Furthermore, MMPBSA has utilized to re-estimate the binding affinities. Then, a free energy landscape was used to find the most stable conformation of the complexes. Finally, the hybrid QM-MM method was carried out for the precise calculation of the energies.
The Hypo1 pharmacophore model was selected as the best model. Our docking results indicate that the compounds ZINC12562757 and 112,260,215 were the best potential inhibitors of the ACE2 and MPro, respectively. Furthermore, the Evo_1 compound enjoys the highest docking energy among the designed
de novo
ligands. Results of RMSD, RMSF, H-bond, and DSSP analyses have demonstrated that the lead compounds preserve the stability of the complexes’ conformation during the MD simulation. MMPBSA data confirmed the molecular docking results. The results of QM-MM showed that Evo_1 has a stronger potential for specific inhibition of MPro, as compared to the 112,260,215 compound.
The angiotensin-converting enzyme 2 (ACE2) and main protease (MPro), are
the putative drug candidates for the severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2). In this study, we performed 3D-QSAR
pharmacophore modeling and screened 1264479 ligands gathered from
Pubchem and Zinc databases. Following the calculation of the ADMET
properties, molecular docking was carried out. Moreover, de novo ligand
design was performed. MD simulation was then applied to survey the
behavior of the ligand-protein complexes. Furthermore, MMPBSA was
utilized to re-estimate the binding affinities. Then, a free energy
landscape was used to find the most stable conformation of the
complexes. Finally, the hybrid QM-MM method was carried out for the
precise calculation of the energies. The Hypo1 pharmacophore model was
selected as the best model. Our docking results indicate that the
compounds ZINC12562757 and 112260215 were the best potential inhibitors
of the ACE2 and MPro, respectively. Furthermore, the Evo_1 compound
enjoys the highest docking energy among the designed de novo ligands.
Results of RMSD, RMSF, H-bond and DSSP analyses have demonstrated that
the lead compounds preserve the stability of the complexes’ conformation
during the MD simulation. MMPBSA data confirmed the molecular docking
results. The results of QM-MM showed that Evo_1 has a stronger
potential for specific inhibition of MPro, as compared to the 112260215
compound. In conclusion, our results showed that the de novo designed
Evo_1 compound has the potential to be used as a drug for the treatment
of COVID-19; however, further in vitro and in vivo validations are
required.
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