Phylogenetic analysis, computer modeling and catalytic prediction of an Amazonian soil β-glucosidase against a soybean saponin

Abstract

Abstract Saponins are amphipathic glycosides with detergent properties present in vegetables. These compounds, when ingested, can cause difficulties in absorbing nutrients from food and even induce inflammatory processes in the intestine. There is already some evidence that saponins can be degraded by β-glucosidases of the GH3 family. In the present study, we evaluated, through computational tools, the possibility of a β-glucosidase (AMBGL17) obtained from a metagenomic analysis of the Amazonian soil, to catalytically interact with a saponin present in soybean. For this, the amino acid sequence of AMBGL17 was used in a phylogenetic analysis to estimate its origin and to determine its three-dimensional structure. The 3D structure of the enzyme was used in a molecular docking analysis to evaluate its interaction with soy saponin as a ligand. The results of the phylogenetic analysis showed that AMBGL17 comes from a microorganism of the phylum Chloroflexi, probably related to species of the order Aggregatinales. Molecular docking showed that soybean saponin can interact with the catalytic site of AMBGL17, with the amino acid GLY345 being important in this catalytic interaction, especially with a β-1,2 glycosidic bond present in the carbohydrate portion of saponin. In conclusion, AMBGL17 is an enzyme with interesting biotechnological potential in terms of mitigating the anti-nutritional and pro-inflammatory effects of saponins present in vegetables used for human and animal food.