Unraveling the allosteric mechanisms of prolyl endopeptidases for celiac disease therapy: Insights from molecular dynamics simulations.

Prolyl endopeptidases (PEP) from Sphingomonas capsulata (sc) and Myxococcus xanthus (mx) selectively degrade gluten peptides in vitro, offering a potential therapeutic strategy for celiac disease. However, the mechanisms governing the interaction of these enzymes with their substrates remain unclear. In this study, conventional molecular dynamics simulations with a microsecond timescale and targeted molecular dynamics simulations were performed to investigate the native states of mxPEP and scPEP enzymes, as well as their allosteric binding with a representative substrate, namely, Z-Ala-Pro-p-nitroanilide (pNA). The simulations reveal that the native scPEP is in an open state, while the native mxPEP is in a closed state. When pNA approaches a closed mxPEP, it binds to an allosteric pocket located at the first and second ß-sheet of the ß-propeller domain, inducing the opening of this enzyme. Neither enzyme is active in the open or partly-open states. Enzymatic activity is enabled only when the catalytic pocket in the closed state fully accommodates the substrates. The internal capacity of the catalytic pocket of PEP in the closed state determines the maximum size of the gluten peptides that the enzymes can catalyze. The present work provides essential molecular dynamics information for the redesign or engineering of PEP enzymes.

Correlation between the pKa and nuclear shielding of α-hydrogen of ketones.

The α-H acidity is an important chemical property of ketones that has attracted much research interest. Theoretical prediction of pKa for ketone α-H is significant. In this work, we theoretically studied the nuclear shielding of various α-Hs in a set of ketones and that of the corresponding enolic hydroxyl Hs in tautomeric enol forms. It has been demonstrated through linear regression analyses that the pKa values of these ketones correlate with both sets of the calculated nuclear shielding values. The correlation coefficient R2 of the linear correlation relationship is 0.90. The present work has provided a new approach to computationally evaluating the acidity of α-Hs in ketones, enabling us to semi-empirically predict the ketone α-H acidity from the calculated nuclear shielding values. Graphical AbstractExperimental pKa values in DMSO vs predicted pKa values calculated from 1H nuclear shielding for the hydroxyl hydrogens in the enol forms and for the α-Hs in the keto forms. The surrounding solvent effects were modelled by keto/enol-DMSO clusters and SMD solvent models.