Discovery of Novel Prebiotic Carbohydrates and Sugar Mimics of BlMsmE, a Solute-Binding Protein of the ABC Transporter from Bacillus licheniformis

Discovery of the new alpha-glucosidase inhibitor with therapeutic potential in type 2 diabetes mellitus by a novel high-throughput virtual screening and free energy evaluation

Type 2 diabetes can cause a variety of complications, significantly affecting people's health. Given their ability to suppress carbohydrate digestion, alpha-glucosidase inhibitors are effective treatments for diabetes. However, the current approved glucosidase inhibitors' side effects of abdominal discomfort limit their use. We used the compound Pg3R from the natural fruit berry as a reference, screening against a large database of 22 million compounds to identify potential health-friendly alpha-glucosidase inhibitors. Ligand-based screening enables us to identify 3968 ligands that exhibit structural similarity compared to the natural compound. These lead hits were used for LeDock, and their binding free energies were evaluated by MM/GBSA. Among the top-scoring candidates, ZINC263584304 exhibited the strongest binding affinity to alpha-glucosidase, with a "low-fat" structural characteristic. Its recognition mechanism was further investigated by microsecond MD simulations and free energy landscapes, exhibiting novel conformational changes during the binding process. Our study provided a novel alpha-glucosidase inhibitor with the potential to treat type 2 diabetes.

High-throughput virtual screening and microsecond MD simulations to identify potential sugar mimic of the solute-binding protein BlAXBP of the ABC transporter from Bifidobacterium animalis subsp. Lactis

Xylotetraose is a prebiotic oligosaccharide can be utilized by the ABC transporter of the gut microbiota Bifidobacteria. BlAXBP is the solute binding protein of the ABC transporter, and its complex with xylotetraose has been solved by X-ray crystallography. Here, we have identified novel sugar mimic of BlAXBP by applying a high-throughput virtual screening of ZINC database containing a huge library with ∼22 M compounds. To begin with, we identified 18,571 ligands by a ligand-based virtual screening. Further, a total of 3968 compounds were selected for molecular docking due to their Tanimoto coefficient's value were larger than a cutoff of 0.08. The molecular mechanics-generalized born surface area was used to evaluate the binding free energies, and the top 10 ligands with free energies below an energy threshold of -35.22 kcal/mol were selected. ZINC13783511 formed the most stable complex with BlAXBP and its recognition mechanism were further explored by microsecond MD simulations in explicit solvent. Free energy landscapes were used to evaluate conformational changes of BlAXBP in its ligand free and binding states. Collectively, this work identified potential novel sugar mimics to BlAXBP, providing novel atomic-level understanding of the binding mechanism.