| Literature DB >> 35608787 |
Prajakta Kulkarni1, Sriram Padmanabhan2.
Abstract
PURPOSE: In the wake of SARS-CoV-2's global spread, human activities from health to social life to education have been affected. Favipiravir and Molnupiravir exhibited novel hexokinase inhibition and we discuss advantages of this property in their COVID-19 inhibition potential.Entities:
Keywords: 2 Deoxy D glucose; COVID-19; Favipiravir; Hexokinase; Molecular docking; Molnupiravir
Mesh:
Substances:
Year: 2022 PMID: 35608787 PMCID: PMC9128636 DOI: 10.1007/s10529-022-03259-6
Source DB: PubMed Journal: Biotechnol Lett ISSN: 0141-5492 Impact factor: 2.716
Fig. 1Hexokinase inhibition potential of Favipiravir and Molnupiravir. All values are mean ± SD, n = 3. ****P < 0.001 for favipiravir (adjusted P value < 0.0001), *P < 0.05 for Molnupiravir (adjusted P value 0.0124) when compared to 2-deoxy-2-glucose (2DG)
Comparison between Favipiravir, Molnupiravir, 2DG and Remdesivir
| Drug | Property | References | |
|---|---|---|---|
| 1 | |||
| Docking energy with Human HK-II | First report | This study | |
| Hexokinase II inhibition, 0.12 mM | 55% | This study | |
| RdRp inhibition | 67.61 μM | Zhao et al. ( | |
| Half life | 2.5 to 5.5 h | Painter et al. ( | |
| Inhibition of SARS-CoV-2 in vitro, EC50 | > 100 μM | Rabie ( | |
| 2 | |||
| Docking energy with Human HK-II | First report | This study | |
| Hexokinase II inhibition, 0.3 mM | ~ 10% | This study | |
| RdRp inhibition | 0.22 μM | Zhao et al. ( | |
| Half life | 1–1.75 h | Painter et al. ( | |
| Inhibition of SARS-CoV-2 in vitro, EC50 | 8.8 μM | Wang et al. ( | |
| 3 | |||
| Docking energy with Human HK-II | Reported | Gao et al. ( | |
| Hexokinase II inhibition, 1 mM | 21% | This study | |
| RdRp inhibition | Not available | ||
| Half life | 1.5 h | Dwarakanath and Jain, | |
| Inhibition of SARS-CoV-2 in vitro, EC50 | 0.7 mM | Bhatt et al. ( | |
| 4 | |||
| Docking energy with Human HK-II | First report | This study | |
| Hexokinase II inhibition, 1 mM | Not done | This study | |
| RdRp inhibition | 0.67 μM | Zhao et al. ( | |
| Half life | 1 h | Tempestilli et al. ( | |
| Inhibition of SARS-CoV-2 in vitro, EC50 | 23.88 μM | Rabie ( | |
| 5 | |||
| Docking energy with Human HK-II | First report | This study | |
| Hexokinase II inhibition, 1 mM | Not done | This study | |
| RdRp inhibition | Not available | ||
| Anti-viral agent | Yes | Rabie ( | |
| Inhibition of SARS-CoV-2 in vitro, EC50 | 0.48 μM | Rabie ( | |
Detailed binding energy and intermolecular energy of all the possible HK II (PDB ID = 2NZT) docked with selected drugs
| Ligand | (ΔGbind)a | No. of H bonds | Interacting residues | Final intermolecular energy (kcal/mol) | (ΔGdesolv)c | (ΔGelec)b | (ΔGtor)d |
|---|---|---|---|---|---|---|---|
| 2-DG | − 3.40 | 02 (H1 = 2.52 Å, H2 = 2.43 Å) | LYS:147(H1), PRO:149, GLU:79(H2) | − 3.52 | − 3.42 | − 0.09 | + 2.68 |
| T-705 | − 4.68 | 04 (H1 = 2.65 Å, H2 = 3.03 Å, H3 = 2.81 Å, H4 = 2.25 Å) | MET:119(H1), ILE:114(H2), GLY:87, PHE:90(H3), ASN:89(H4) | − 4.57 | − 4.48 | − 0.08 | + 0.30 |
| EIDD-2801 | − 3.12 | 03 (H1 = 2.82 Å), (H2 = 2.12 Å), (H3 = 2.54 Å) | THR:336(H1), SER:340(H2), SER:415(H3), GLY:299, LYS:337 | − 5.80 | − 5.79 | − 0.02 | + 2.68 |
| Cyan 20 | − 5.84 | 03 (H1 = 1.89 Å), (H2 = 2.79 Å), (H3 = 2.33 Å), | LEU:734(H1), ARG:779(H2, THR:784(H3, MET:748 | − 6.43 | − 6.27 | − 0.17 | + 0.60 |
| Remdesivir | − 2.21 | 02 (H1 = 1.74 Å, H2 = 3.08 Å) | SER:506, LYS:510(H1), LYS:618(H2) | − 5.74 | − 5.53 | − 0.21 | + 5.07 |
2DG- 2 Deoxy d glucose, T-705- Favipiravir, EIDD-2801 Molnupiravir, Cyan 20 Cyanorona
aΔGbind = Net predicted binding Energy, (kcal/mol)
bΔGelec = electrostatic energy (kcal/mol)
cΔGdesolv = desolvation energy (kcal/mol)
dΔGtor = torsional free energy (kcal/mol)
Fig. 2Molecular docking of Favipiravir binding with Hexokinase II (PDB ID: 2NZT) shows 3D model of the interactions and the 2D interaction patterns and H-bond interactions. The polypeptide chain of HK II is folded into three structural domains, one of which is predominantly alpha-helical (red spiral) and two of which each contain a beta-pleated sheet (cyan blue) flanked by alpha-helices. The green string represents the turns of coils. Panel A shows the interaction of the ligand (Favipiravir) with protein HK II; Panel B is 3D Favipiravir with surrounding amino acids of HK II; Panel C is Favipiravir with HK II (hydrophobicity surface) at the active binding site; Panel D shows the 2D view of interaction type of Favipiravir with surrounding amino acids of HK II
Fig. 3Molecular docking of Crystal structure of human hexokinase II (PDB ID: 2NZT) binding with Molnupiravir shows 3D model of the interactions and the 2D interaction patterns and H-bond interaction. The polypeptide chain of HK II is folded into three structural domains, one of which is predominantly alpha-helical (red spiral) and two of which each contain a beta-pleated sheet (cyan blue) flanked by alpha-helices. The green string represents the turns of coils. Panel A shows the interaction of the ligand (Molnupiravir) with protein HK II; Panel B is Molnupiravir DG with surrounding amino acids of HK II; Panel C is Molnupiravir with HK II (hydrophobicity surface) at the active binding site; Panel D shows the 2D view of interaction type of Molnupiravir with surrounding amino acids of HK II
Fig. 4Molecular docking of 2-Deoxy-d-Glucose binding with Hexokinase II (PDB ID: 2NZT) shows 3D model of the interactions and the 2D interaction patterns and H-bond interaction. The polypeptide chain of HK II is folded into three structural domains, one of which is predominantly alpha-helical (red spiral) and two of which each contain a beta-pleated sheet (cyan blue) flanked by alpha-helices. The green string represents the turns of coils. Panel A shows the interaction of the ligand (2DG) with protein HK II; Panel B is 3D 2 DG with surrounding amino acids of HK II; Panel C is 2 DG with HK II (hydrophobicity surface) at the active binding site; Panel D shows the 2D view of interaction type of 2DG with surrounding amino acids of HK II
Fig. 5Molecular docking of Remdesivir binding with Hexokinase II (PDB ID: 2NZT) shows 3D model of the interactions and the 2D interaction patterns and H-bond interactions. The polypeptide chain of HK II is folded into three structural domains, one of which is predominantly alpha-helical (red spiral) and two of which each contain a beta-pleated sheet (cyan blue) flanked by alpha-helices. The green string represents the turns of coils. Panel A shows the interaction of the ligand (Remdesivir with protein HK II; Panel B is 3D Remdesivir with surrounding amino acids of HK II; Panel C is Remdesivir with HK II (hydrophobicity surface) at the active binding site; Panel D shows the 2D view of interaction type of Remdesivir with surrounding amino acids of HK II
Fig. 6Molecular docking of Cyan 20 binding with Hexokinase II (PDB ID: 2NZT) shows 3D model of the interactions and the 2D interaction patterns and H-bond interaction. The polypeptide chain of HK II is folded into three structural domains, one of which is predominantly alpha-helical (red spiral) and two of which each contain a beta-pleated sheet (cyan blue) flanked by alpha-helices. The green string represents the turns of coils. Panel A shows the interaction of the ligand (Cyan 20) with protein HK II; Panel B is 3D Cyan 20 with surrounding amino acids of HK II; Panel C is Cyan 20 with HK II (hydrophobicity surface) at the active binding site; Panel D shows the 2D view of interaction type of Cyan 20 with surrounding amino acids of HK II