Discovery of α-Glucosidase Inhibitors from Paenibacillus sp. JNUCC 31 via Genome Mining, Metabolite Profiling, and In Silico Analysis

The increasing prevalence of type 2 diabetes has driven an increasing demand for safe and effective α-glucosidase inhibitors (AGIs). Paenibacillus spp., known producers of diverse secondary metabolites, remain underexplored as AGI sources. This study aims to evaluate the biosynthetic potential and α-glucosidase inhibitory activity of Paenibacillus sp. JNUCC 31. Genomic annotation of the strain JNUCC 31 revealed multiple biosynthetic gene clusters associated with secondary metabolite biosynthesis. Metabolic profiling initially identified anteiso-C15:0 (57.32%) as the dominant fatty acid via GC-MS. Subsequently, the ethyl acetate extract from fermented cultures, which exhibited the highest α-glucosidase inhibitory activity (52.4 ± 0.7%), was purified and five known compounds were isolated: adenosine, uridine, 4-hydroxybenzaldehyde, dibutyl phthalate (DBP), and 1-acetyl-β-carboline. Among these, adenosine, uridine, and DBP have been previously reported as α-glucosidase inhibitors. Enzyme kinetics confirmed that uridine functions as a competitive inhibitor, while adenosine and DBP act via a mixed-type inhibition mechanism. Molecular docking and molecular dynamics simulations demonstrated stable binding of these active compounds to human maltase-glucoamylase (MGAM, PDB ID: 2QMJ) and microbial isomaltase (PDB ID: 3A4A). MM/GBSA analysis indicated favorable binding free energies (−14.18 to −36.5 kcal/mol), with key residues such as Trp406 (MGAM), Tyr158 and Gln279 (isomaltase) playing major roles in binding stabilization. Collectively, these findings highlight the strain JNUCC 31 as a promising microbial source of antidiabetic lead compounds.