Analysis of polyphenolic metabolites from in vitro gastrointestinal digested soft fruit extracts identify malvidin-3-glucoside as an inhibitor of PTP1B

Protein-tyrosine phosphatase 1B (PTP1B, EC 3.1.3.48) is an important regulator of insulin signalling. Herein, we employed experimental and computational biology techniques to investigate the inhibitory properties of phenolics, identified from four in vitro gastrointestinal digested (IVGD) soft fruits, on PTP1B. Analysis by LC-MS/MS identified specific phenolics that inhibited PTP1B in vitro. Enzyme kinetics identified the mode of inhibition, while dynamics, stability and binding mechanisms of PTP1B-ligand complex were investigated through molecular modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. IVGD extracts and specific phenolics identified from the four soft fruits inhibited PTP1B (P < 0.0001) activity. Among the phenolics tested, the greatest inhibition was shown by malvidin-3-glucoside (P < 0.0001) and gallic acid (P < 0.0001). Malvidin-3-glucoside (Ki = 3.8 µg/mL) was a competitive inhibitor and gallic acid (Ki = 33.3 µg/mL) a non-competitive inhibitor of PTP1B. Malvidin-3-glucoside exhibited better binding energy than gallic acid and the synthetic inhibitor Dephostatin (-7.38 > -6.37 > -5.62 kcal/mol) respectively. Principal component analysis demonstrated malvidin-3-glucoside PTP1B-complex occupies more conformational space where critical WPD-loop displayed a higher degree of motion. MM/PBSA binding free energy for malvidin-3-glucoside to PTP1B was found to be higher than other complexes mediated by Van der Waals energy rather than electrostatic interaction for the other two inhibitors (-80.32 ± 1.25 > -40.64 ± 1.43 > -21.63 ± 1.73 kcal/mol) respectively. Altogether, we have established novel insights into the specific binding of dietary phenolics and have identified malvidin-3-glucoside as an PTP1B inhibitor, which may be further industrially developed for the treatment of type-2 diabetes.

Keywords: Binding energy; Docking; Malvidin-3-glucoside; Molecular dynamic simulation; PTP1B; Phenolic; Principal component analysis.