Dataset Information

Docking Characterization and in vitro Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2.

ABSTRACT: We report to use the main protease (M^pro) of SARS-Cov-2 to screen plant flavan-3-ols and proanthocyanidins. Twelve compounds, (-)-afzelechin (AF), (-)-epiafzelechin (EAF), (+)-catechin (CA), (-)-epicatechin (EC), (+)-gallocatechin (GC), (-)-epigallocatechin (EGC), (+)-catechin-3-O-gallate (CAG), (-)-epicatechin-3-O-gallate (ECG), (-)-gallocatechin-3-O-gallate (GCG), (-)-epigallocatechin-3-O-gallate (EGCG), procyanidin A2 (PA2), and procyanidin B2 (PB2), were selected for docking simulation. The resulting data predicted that all 12 metabolites could bind to M^pro. The affinity scores of PA2 and PB2 were predicted to be -9.2, followed by ECG, GCG, EGCG, and CAG, -8.3 to -8.7, and then six flavan-3-ol aglycones, -7.0 to -7.7. Docking characterization predicted that these compounds bound to three or four subsites (S1, S1', S2, and S4) in the binding pocket of M^pro via different spatial ways and various formation of one to four hydrogen bonds. In vitro analysis with 10 available compounds showed that CAG, ECG, GCG, EGCG, and PB2 inhibited the M^pro activity with an IC₅₀ value, 2.98 ± 0.21, 5.21 ± 0.5, 6.38 ± 0.5, 7.51 ± 0.21, and 75.3 ± 1.29 ?M, respectively, while CA, EC, EGC, GC, and PA2 did not have inhibitory activities. To further substantiate the inhibitory activities, extracts prepared from green tea (GT), two muscadine grapes (MG), cacao, and dark chocolate (DC), which are rich in CAG, ECG, GAG, EGCG, or/and PB2, were used for inhibitory assay. The resulting data showed that GT, two MG, cacao, and DC extracts inhibited the M^pro activity with an IC₅₀ value, 2.84 ± 0.25, 29.54 ± 0.41, 29.93 ± 0.83, 153.3 ± 47.3, and 256.39 ± 66.3 ?g/ml, respectively. These findings indicate that on the one hand, the structural features of flavan-3-ols are closely associated with the affinity scores; on the other hand, the galloylation and oligomeric types of flavan-3-ols are critical in creating the inhibitory activity against the M^pro activity.

SUBMITTER: Zhu Y

PROVIDER: S-EPMC7733993 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Docking Characterization and <i>in vitro</i> Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2.

Zhu Yue Y Xie De-Yu DY

Frontiers in plant science 20201130

We report to use the main protease (M<sup>pro</sup>) of SARS-Cov-2 to screen plant flavan-3-ols and proanthocyanidins. Twelve compounds, (-)-afzelechin (AF), (-)-epiafzelechin (EAF), (+)-catechin (CA), (-)-epicatechin (EC), (+)-gallocatechin (GC), (-)-epigallocatechin (EGC), (+)-catechin-3-O-gallate (CAG), (-)-epicatechin-3-O-gallate (ECG), (-)-gallocatechin-3-O-gallate (GCG), (-)-epigallocatechin-3-O-gallate (EGCG), procyanidin A2 (PA2), and procyanidin B2 (PB2), were selected for docking simul ...[more]

PMID: 33329667

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Project description:Bassia longifoliaKOENIG (= Madhuca longifolia (L.) is an evergreen tree that is widely distributed throughout Nepal, India, and Sri Lanka. The bark has various traditional uses: as a paste in the treatment of cuts and wounds or internally as a decoction that is given to diabetic patients. Chemical-analytical and pharmacological investigations regarding the bark are not sufficiently available. We focused on the isolation of flavan-3-ols from the methanolic extract and their contribution to the described traditional uses in wound healing and diabetes treatment. Therefore, an antibacterial assay and an α-glucosidase assay were performed. The isolation process was performed by a combination of Sephadex®-, MCI®-Gel-, and RP-18 chromatography. The structures of the isolated compounds were elucidated by 1H- and 13C-NMR-spectroscopy including COSY, ROESY, HSQC, and HMBC methods. Optical characterization was performed by polarimetry and circular dichroism. Two monomeric, seven dimeric, six trimeric, and one tetrameric flavan-3-ols were found including one dimer and three trimers with rare epiafzelechin units. Two compounds were isolated for the first time. A fraction containing higher oligomeric and polymeric proanthocyanidins (PAs) was examined by 13C NMR spectroscopy and revealed an average degree of polymerization of 8-9. PA with cis-configurated subunits predominated at 90 % and the presence of further monohydroxylated flavan-3-ols was revealed. Minimal inhibitory concentrations (MICs) were investigated by the serial microdilution broth assay with Staphylococcus aureus. The bacterial suspension was inoculated on agar plates for determining the MICs. The α-glucosidase assay was performed in 96 well plates with α-glucosidase from Bacillus stearothermophilus. For the detection of enzyme inhibition, p-nitrophenyl-α-d-glucopyranoside was used as a substrate and after incubation absorbance was measured at 405 nm. Antibacterial effects were only found for fractions enriched with PAs or containing higher oligomeric and polymeric flavan-3-ols. All tested substances showed high α-glucosidase inhibition. Whereby 4β→8 conjugated dimers and the monomers showed the lowest inhibition, procyanidin (PC) B5 as 4β→6 conjugated and cinnamtannin A2 as tetrameric flavan-3-ol showed the highest. PAs with epiafzelechin units are rarely found in nature but their reoccurring appearance in B. longifolia could be characteristic of this plant. For its traditional uses, the antibacterial activity of the PA-enriched fractions could contribute to the wound healing process when applied to the injured skin. Moreover, all tested substances and fractions showed α-glucosidase inhibition, which could also explain the use of a decoction in the treatment of diabetes. In conclusion, pharmacological investigations could provide scientific evidence for traditional uses of B. longifolia.

Dataset Information

Docking Characterization and in vitro Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2.

Publications

Docking Characterization and <i>in vitro</i> Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2.

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