Afnan M. Alnajeebi
The growing diabetes trend worldwide demands the identification of new α-glucosidase inhibitors for delaying postprandial hyperglycemia. However, the use of existing drugs is often limited by adverse effects, which has increased interest in natural products as safer alternative sources of α-glucosidase inhibitors. I. aquifolium was selected based on reports of flavonoid-rich phytochemistry, leading to the hypothesis that its major flavonoids could act as potential α-glucosidase inhibitors for the management of diabetes. Herein, the virtual α-glucosidase inhibitory potential of eight flavonoid-based phytochemicals of I. aquifolium extracts was investigated through an integrated in silico workflow, which includes molecular docking, DFT analysis, and ADMET profiling. Docking analysis identified IA- 2 (Rutin) and IA- 5 (Kaempferol-3-O-rhamnoglucoside) as the most potent ligands with binding affinities of - 9.59 kcal/mol and - 9.18 kcal/mol, respectively, closely approaching the standard acarbose (-10.96 kcal/mol). The re-docking RMSD of 2.1375 Å fell within the acceptable validation benchmark, supporting the reliability of the docking protocol. The second and third positions were occupied by IA- 1 (Quercetin) and IA- 3 (Quercetin-3-O-hexoside) as potential inhibitors, as they formed hydrogen bonds with hydrophobic contacts. DFT study suggested that all the flavonoids exhibited moderate to high dipole moments (4.88-7.36 Debye) along with the high HOMO-LUMO gaps. Additionally, IA- 7 (Apigenin) showed the highest electrophilicity (3.313) among all the phytochemicals. The pharmacokinetic evaluation of ligands by SwissADME and PkCSM suggested IA- 1 as the most potential hit, and it occupied the main drug-likeness parameters with a bioavailability score of 0.55, whereas low bioavailability scores (0.17) for IA- 2 and IA- 5 indicated their poor permeability through the membrane. The potential toxicity of the ligands through SwissADME predicted that all the ligands have renal and respiratory issues, but IA- 1 showed the highest potential of acute dermal toxicity. MD simulations supported the docking results by showing protein backbone RMSD stabilization at 2.0-2.4 Å and revealing that IA-2 and IA-5 form the most dynamically stable complexes (lowest ligand RMSD, compact Rg, persistent H bonds), while IA-3 and IA-1 display greater ligand flexibility, thereby prioritizing these compounds for experimental validation in a hypothesis-generating context. However, these computational findings do not replace experimental validation and should be interpreted as hypothesis-generating predictions. Overall, the study provides a hypothesis-generating framework, prioritizing IA-2 and IA-5 as potential α-glucosidase inhibitory candidates, with IA-1 emerging as a top-ranked ligand through pharmacokinetic parameters, required further experimental validation.