| Literature DB >> 34345157 |
S A Syrbu1, A N Kiselev1,2, M A Lebedev1,2, Yu A Gubarev1, E S Yurina1, N Sh Lebedeva1.
Abstract
Novel porphyrin compounds containing benzothiazole, benzoxazole, and benzimidazole moieties have been prepared and their structures have been confirmed. Molecular docking of non-symmetric hetaryl-substituted porphyrins and chlorin e6 with SARS-CoV-2 helicase has been carried out. The affinity of hetaryl-substituted porphyrins to this protein has been found significantly higher than that of the drugs approved by the FDA and chlorin e6. The structure of the complexes of SARS-CoV-2 helicase with the considered macroheterocyclic compounds has been analyzed. Possible ways to inhibit and photoinactivate SARS-CoV helicase have been suggested basing on the localization of porphyrins and chlorin e6 in the helicase domains. © Pleiades Publishing, Ltd. 2021.Entities:
Keywords: SARS-CoV-2 virus; helicase; inactivation; inhibition; molecular docking; porphyrins
Year: 2021 PMID: 34345157 PMCID: PMC8323091 DOI: 10.1134/S1070363221060098
Source DB: PubMed Journal: Russ J Gen Chem ISSN: 1070-3632 Impact factor: 0.868
Affinity of helicase to potential inhibitors of SARS-CoV-2
| Compound | Affinity, kcal/mol | References |
|---|---|---|
| Vapreotide | ‒12.88 | [ |
| ‒12.30 | This study | |
| Cangrelor | ‒11.48 | [ |
| Atazanavir | ‒11.28 | [ |
| ‒11.20 | This study | |
| Nystatin | ‒11.10 | [ |
| ‒10.90 | This study | |
| Lopinavir | ‒10.71 | [ |
| Ivermectin | ‒10.70 | [ |
| Elbasvir | ‒10.50 | [ |
| Simeprevir | ‒10.42 | [ |
| Cepharanthine | ‒10.30 | [ |
| Ritonavir | ‒9.39 | [ |
| Chlorin е6, complex | ‒9.30 | This study |
| Grazoprevir | ‒9.15 | [ |
| Chlorin е6, complex | ‒9.00 | This study |
| Rilpivirine | ‒8.03 | [ |
| Favipiravir | ‒4.65 | [ |
Scheme
Scheme
Fig. 1. Molecular docking of 5-[4-(1-methyl-1,3-benzimidazol-2-yl)phenyl]-10,15,20-tris(1-methylpyridin-3-yl)porphyrin with SARS-Cov-2 helicase. (a) general view of the complex, (b) electrostatic potential of the complex surface, (c) structure of the complex.
Fig. 2. Amino acid surrounding in the radius of 4 Å from 5-[4-(1,3-benzothiazol-2-yl)phenyl]-10,15,20-tris(1-methylpyridin-3-yl)-porphyrin (a) and 5-[4-(1,3-benzoxazol-2-yl)phenyl]-10,15,20-tris(1-methylpyridin-3-yl)porphyrin (b) in the complex with SARS-CoV-2 helicase.
Structure description of helicase complexes with hetaryl-substituted porphyrins 1a–1c and chlorin е6
| Compound | Amino acid surrounding in the radius of 4 Å | Hydrogen bonds of the peripheral substituent in the
porphyrin with the amino acid residue of helicase ( |
|---|---|---|
| ASN177, ASN 179, GLU201, LYS202, | No | |
| ASN177, ASN179, GLU201, LYS202, ASP204, | No | |
| ASN177, LYS202, ASP204, | No | |
| Chlorin е6, complex | ASN177, ASN179, PRO406, PRO408, LEU412, THR413, LYS414, GLY415, THR416, LEY417, PHE422, ASP534, ASN557, ASN559, ARG560 | GLY415 (2.7), LEY417 (1.9), ASN557 (3.1), PRO408a (3.8) |
| Chlorin е6, complex | PRO284, GLY285, THR286, GLY287, LYS288, SER289, | GLY285 (1.6, 3.3), GLY538 (3.1), THR286 (2.9), GLY287 (2.0), LYS288 (1.7), HIS290 (1.5), SER289 (3.0) |
a Н-Bond with the N atom in the reactive site.
Fig. 3. Molecular docking of chlorin е6 with SARS-CoV-2 helicase. (a) general view of the complex, (b) electrostatic potential of the complex surface, (c) structure of the complex А, (d) structure of the complex B. Н-Bonds are shown with dashed line.