Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome

Abstract

The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor.

Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors

“…The reaction of the Thr1 residue of the proteasome with several ligands has been investigated, and varying protonation states of the active site residues have been proposed [42] . The nucleophilic attack of Thr1 Oγ is accompanied by proton transfer either to the Nε of Lys33 [43] , [44] or to the terminal amine of Thr1 [45] , [46] .…”