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. File list (2)download file view on ChemRxiv supporting.pdf (58.70 MiB) download file view on ChemRxiv manuscript.pdf (30.98 MiB)

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Inhibition studies on the human 20S proteasome: molecular insights from a computational approach

“…Moreover, just a few attempts were done to study the system using advanced computational techniques. [196][197][198][199][200][201][202] These studies can be classified by the size of the model employed and the computational approach used by the researchers to solve particular problems. Previous studies have been based on two main types of potentials: Mata and co-workers 196,197 reported their results based on QMcluster calculations, and hybrid QM/MM potentials were used with different approaches.…”

“…[196][197][198][199][200][201][202] These studies can be classified by the size of the model employed and the computational approach used by the researchers to solve particular problems. Previous studies have been based on two main types of potentials: Mata and co-workers 196,197 reported their results based on QMcluster calculations, and hybrid QM/MM potentials were used with different approaches. Mihalovits et al 198 reported potentials of mean force (PMFs) results corrected by QM-cluster calculations at a higher level of theory; Wei et al [199][200][201] use the FEP methodology for their reported results; and Saha et al 202 use the empirical valence bond (EVB) methodology for obtaining their results.…”

“…[203][204][205][206] Afterwards, corrections computed from frequency analysis under the rigid-rotor harmonic approximation at the same level of theory were applied. Another study involving QM-cluster model by Mata and coworkers 197 was designed to model the acid-base equilibria of the β2 active site with a substrate model, the inhibitors with the epoxy-and boronic-acid warheads. Additionally, in this study, replica-exchange constant pH molecular mechanics simulations with a larger model consisting of one subunit in the β2 active site and the inhibitor were reported.…”