Defined oligogalacturonides have been reported to inhibit yeast α-glucosidase, but direct evidence against human N-terminal maltase-glucoamylase (NtMGAM) is lacking. We asked whether idealized GalA2 and GalA3 generate reproducible geometries in the acarbose-defined orthosteric site. Chain A of human NtMGAM structure 2QMJ was treated as a rigid, dry receptor. Vina-Carb 1.0 was the prespecified primary method and conventional AutoDock Vina 1.2.7 a diagnostic method used only to assess method dependence. Two representative conformers (cluster medoids) from short ligand-only explicit-solvent simulations per ligand were docked across ten fixed seeds. Top-five poses were subjected to prespecified active-site, clash, integrity, carbohydrate-torsion, recurrence, and cross-conformer criteria. Acarbose pose recovery qualified the search procedure. A qualifying acarbose pose was recovered in all ten Vina-Carb seeds within ranks 1−5; every representative occurred at rank 2, with heavy-atom RMSD of 0.718−1.153Å and 15−17 of 18 crystallographic contacts recovered. Across 80 jobs, 1590 poses were generated and 400 top-five poses analyzed. Vina-Carb retained 27/100 GalA2 poses, which formed one recurrent family spanning both conformers and all ten seeds, meeting the geometric and cross-conformer recurrence criteria. For GalA3, 29/100 poses qualified and formed three families spanning 9−10 seeds, but none crossed conformers, so the cross-conformer criterion was not met. Diagnostic Vina produced cross-conformer GalA3 families, indicating method dependence.GalA2 is prioritized as a reproducible orthosteric structural hypothesis for experimental testing, whereas GalA3 remains unresolved. These calculations do not demonstrate binding, inhibition, altered starch digestion, or glycemic effects; human-enzyme kinetics and orthogonal structural or biophysical evidence are required.
Cardiofaciocutaneous syndrome, CFC, is a rare developmental disorder classified among the RASopathies, which arise from mutations in genes regulating the Ras/MAPK signaling pathway - a key cascade controlling cell proliferation, differentiation, and survival. One of its subtypes, CFC type 4, results from pathogenic variants in MAP2K2 (MEK2) and accounts for approximately 7% of genetically confirmed CFC cases.While MEK1 has been extensively characterized both structurally and functionally, its paralog MEK2 remains less understood. The two kinases share nearly 80% sequence identity, suggesting that homologous mutations may exert comparable structural and regulatory effects. MEK2 Glu207Lys was selected for this study because its MEK1 analogue provides an experimentally grounded benchmark, and the associated charge reversal is predicted to disrupt the salt bridge anchoring the helix A, offering a mechanistically interpretable test case (a functionally analogous mutation, Glu203Lys in MEK1, has previously been shown to destabilize the regulatory helix A). However, no high-resolution crystal structure of MEK2 including this region is currently available.Here, we constructed a complete structural model of MEK2, based on the crystal structures of MEK2 and MEK1. The Glu207Lys mutation was introduced in silico, and molecular docking with clinically used MEK inhibitors was performed. Molecular dynamics simulations were then conducted for wild-type and mutant MEK2, as well as for MEK1, to assess mutation-induced changes in conformational dynamics and ligand interactions.Our findings provide mechanistic insight into the structural impact of the MEK2 Glu207Lys mutation on inhibitor binding, identifying trametinib as the compound predicted to be the most consistently effective against the mutant across all analyses, with mirdametinib and cobimetinib as reasonable but conformationally less stable alternatives. However, trametinib's lack of preference for MEK2 over MEK1 argues for a mutation- and isoform-selectivity-informed approach rather than a single universal inhibitor. Results obtained in the study enhance understanding of mutation-driven changes in kinase signaling and drug response, and may support the development of MEK2-selective therapies for RASopathies.
