“…Moreover, Ni(II) complex [Ni(L) 2 ] (1) shows better result than HL and Cu(II) complex [Cu(L) 2 ] (2) when docked against the proteins SARS-CoV-2 than HIV-1 virus (PDB ID: 7BZ5 and 6MQA ). The binding affinities of the studied new Schiff base ligand and their metal complexes were found to be better than other metal complexes reported using molecular docking techniques [ 68 , 69 ]. Figure 9 The docked nickel(II) complex [Ni(L 2 )] ( 1 ) inside the HIV-1 virus (PDB ID: 6MQA ) with its focused view for interacting residues around the docked complex.…”
“…Moreover, Ni(II) complex [Ni(L) 2 ] (1) shows better result than HL and Cu(II) complex [Cu(L) 2 ] (2) when docked against the proteins SARS-CoV-2 than HIV-1 virus (PDB ID: 7BZ5 and 6MQA ). The binding affinities of the studied new Schiff base ligand and their metal complexes were found to be better than other metal complexes reported using molecular docking techniques [ 68 , 69 ]. Figure 9 The docked nickel(II) complex [Ni(L 2 )] ( 1 ) inside the HIV-1 virus (PDB ID: 6MQA ) with its focused view for interacting residues around the docked complex.…”
“…DFT calculations with the well-known B3LYP exchange-correlation functional [33] were performed to optimize the tautomers and isomers of FAV drug, NTs, and encapsulated FAV/NTs. B3LYP is a consistently used function when studying similar nanostructures [4,15,34]. A moderate size basis set (6-31G(d,p)) was employed along with B3LYP functional.…”
Favipiravir (FAV) (6-fluoro-3-oxo-3,4-dihydropyrazine-2-carboxamide) is one of the most effective antiviral drugs which is cited for action against RNA-viral infections of COVID-19. In this study, Density Functional Theory (DFT) calculations were used to investigate three nanotubes (NTs) with FAV drug as delivery systems. The encapsulated systems (ESs) consisting of FAV drug inside carbon-carbon, aluminum nitride, and boron nitride. At B3LYP-D/6-31G(d,p) and CPCM/B3LYP-D/6-31G(d,p), the optimization of NTs, FAV and its tautomeric forms, and six ESs were investigated in gas and water environments. Five tautomeric forms of FAV were investigated, two keto forms (K1 and K2) and three enol forms ( (E1, E2, and E3). The results revealed that E3 and K2 isomeric forms represented the most stable structures in both media; thus, these two forms were encapsulated into the NTs. The stability and the synthesis feasibility of NTs have been proven by calculating their interaction energies. Noncovalent interactions (NCIs) were investigated in the ESs to show the type of NCI with the molecular voids. The binding energies, thermochemical parameters, and recovery times were investigated to understand the mechanism of FAV encapsulation and release. The encapsulated AlNNT systems are more favorable than those of BNNTs and CNTs in gas and aqueous environments with much higher binding energies. The quantum theory of atoms in molecules (QTAIM) and recovery time analysis revealed the easier releasing of E3 from AlNNT over K2 form. Based on molecular docking simulations, we found that E3 and K2 FAV forms showed a high level of resistance to SARS-CoV-6M3M/6LU7/6W9C proteases.
“…DFT calculations with the well-known B3LYP exchange–correlation functional [ 36 ] were performed to optimize the tautomers and isomers of FAV drug, NTs, and encapsulated FAV/NTs. B3LYP is a consistently used function when studying similar nanostructures [ 4 , 17 , 37 ]. A moderate size basis set (6-31G(d,p)) was employed along with B3LYP functional.…”
Favipiravir (FAV) (6-fluoro-3-oxo-3,4-dihydropyrazine-2-carboxamide) is one of the most effective antiviral drugs which is cited for action against RNA-viral infections of COVID-19. In this study, density functional theory (DFT) calculations were used to investigate three nanotubes (NTs) with FAV drug as delivery systems. The encapsulated systems (ESs) consist of FAV drug inside carbon–carbon, aluminum nitride, and boron nitride. At B3LYP-D/6-31G(d,p) and CPCM/B3LYP-D/6-31G(d,p), the optimization of NTs, FAV, and its tautomeric forms and six ESs was investigated in gas and water environments. Five tautomeric forms of FAV were investigated, two keto forms (K1 and K2) and three enol forms (E1, E2, and E3). The results revealed that E3 and K2 isomeric forms represented the most stable structures in both media; thus, these two forms were encapsulated into the NTs. The stability and the synthesis feasibility of NTs have been proven by calculating their interaction energies. Non-covalent interactions (NCIs) were investigated in the ESs to show the type of NCI with the molecular voids. The binding energies, thermochemical parameters, and recovery times were investigated to understand the mechanism of FAV encapsulation and release. The encapsulated AlNNT systems are more favorable than those of BNNTs and CNTs in gas and aqueous environments with much higher binding energies. The quantum theory of atoms in molecules (QTAIM) and recovery time analysis revealed the easier releasing of E3 from AlNNT over K2 form. Based on molecular docking simulations, we found that E3 and K2 FAV forms showed a high level of resistance to SARS-CoV-6M3M/6LU7/6W9C proteases.
Supplementary Information
The online version contains supplementary material available at 10.1007/s11224-023-02182-4.
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