In silico study reveals existing drugs as α-glucosidase inhibitors: Structure-based virtual screening validated by experimental investigation

Mechanistic study on the inhibition of α-amylase and α-glucosidase using the extract of ultrasound-treated coffee leaves

BACKGROUND

Our previous studies have shown that ultrasound-treated γ-aminobutyric acid (GABA)-rich coffee leaves have higher angiotensin-I-converting enzyme inhibitory activity than their untreated counterpart. However, whether they have antidiabetic activity remains unknown. In this study, we aimed to investigate the inhibitory activities of coffee leaf extracts (CLEs) prepared with ultrasound (CLE-U) or without ultrasound (CLE-NU) pretreatment on α-amylase and α-glucosidase. Subsequently, we evaluated the binding interaction between CLE-U and both enzymes using multi-spectroscopic and in silico analyses.

RESULTS

Ultrasound pretreatment increased the inhibitory activities of CLE-U against α-amylase and α-glucosidase by 21.78% and 25.13%, respectively. CLE-U reversibly inhibits both enzymes, with competitive inhibition observed for α-amylase and non-competitive inhibition for α-glucosidase. The static quenching of CLE-U against both enzymes was primarily driven by hydrogen bond and van der Waals interactions. The α-helices of α-amylase and α-glucosidase were increased by 1.8% and 21.3%, respectively. Molecular docking results showed that the key differential compounds, including mangiferin, 5-caffeoylquinic acid, rutin, trigonelline, GABA, caffeine, glutamate, and others, present in coffee leaves interacted with specific amino acid residues located at the active site of α-amylase (ASP197, GLU233, and ASP300). The binding of α-glucosidase and these bioactive components involved amino acid residues, such as PHE1289, PRO1329, and GLU1397, located outside the active site.

CONCLUSION

Ultrasound-treated coffee leaves are potential anti-diabetic substances, capable of preventing diabetes by inhibiting the activities of α-amylase and α-glucosidase, thus delaying starch digestion. Our study provides valuable information to elucidate the possible antidiabetic capacity of coffee leaves through the inhibition of α-amylase and α-glucosidase activities. © 2023 Society of Chemical Industry.

Study of Genotoxicity, Activities on Caspase 8 and on the Stabilization of the Topoisomerase Complex of Isoeleutherin and Analogues

This study evaluated the genotoxicity of Ethanol Extract (EEEp), Dichloromethane Fraction (FDCMEp) and isoeleutherin isolated from Eleutherine plicata, using the micronucleus test and the impact of structural alterations on toxicity and molecular docking (topoisomerase II and DNA complex). The extract was obtained by maceration and fractionation in a chromatography column. The genotoxicity was evaluated by the micronucleus test in human hepatoma cells (HepG2). Isoeleutherin was the starting molecule in the search for analogues by structural similarity, using the ZINC and e-Molecules databases. Isoeleutherin and analogues were subjected to in silico toxicity prediction, and compounds free of toxicological risks (CP13, CP14, CP17 and isoeleutherin) were selected for molecular docking in Topoisomerase II (PDB: 1ZXM). In the micronucleus test, isoeleutherin was less genotoxic. Among the 22 isoeleutherin analogues there were variations in the toxicity profile. Molecular docking studies showed that the compounds have good complementarity in the active site with important hydrogens bonds. Therefore, the structural changes of isoeleutherin led to the obtaining of a molecule with a lower mutagenic potential, and the CP13 can be considered a prototype compound for the development of new molecules with pharmacological potential.

Spike protein recognizer receptor ACE2 targeted identification of potential natural antiviral drug candidates against SARS-CoV-2

Angiotensin-converting enzyme 2 (ACE2), also known as peptidyl-dipeptidase A, belongs to the dipeptidyl carboxydipeptidases family has emerged as a potential antiviral drug target against SARS-CoV-2. Most of the ACE2 inhibitors discovered till now are chemical synthesis; suffer from many limitations related to stability and adverse side effects. However, natural, and selective ACE2 inhibitors that possess strong stability and low side effects can be replaced instead of those chemicals' inhibitors. To envisage structurally diverse natural entities as an ACE2 inhibitor with better efficacy, a 3D structure-based-pharmacophore model (SBPM) has been developed and validated by 20 known selective inhibitors with their correspondence 1166 decoy compounds. The validated SBPM has excellent goodness of hit score and good predictive ability, which has been appointed as a query model for further screening of 11,295 natural compounds. The resultant 23 hits compounds with pharmacophore fit score 75.31 to 78.81 were optimized using in-silico ADMET and molecular docking analysis. Four potential natural inhibitory molecules namely D-DOPA (Amb17613565), L-Saccharopine (Amb6600091), D-Phenylalanine (Amb3940754), and L-Mimosine (Amb21855906) have been selected based on their binding affinity (−7.5, −7.1, −7.1, and −7.0 kcal/mol), respectively. Moreover, 250 ns molecular dynamics (MD) simulations confirmed the structural stability of the ligands within the protein. Additionally, MM/GBSA approach also used to support the stability of molecules to the binding site of the protein that also confirm the stability of the selected four natural compounds. The virtual screening strategy used in this study demonstrated four natural compounds that can be utilized for designing a future class of potential natural ACE2 inhibitor that will block the spike (S) protein dependent entry of SARS-CoV-2 into the host cell.