The ubiquitin-proteasome system is responsible for the degradation of proteins and
plays a critical role in key cellular processes. While the constitutive proteasome
(cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily
induced during disease processes, and its inhibition is beneficial in the treatment
of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were
reported to selectively inhibit iPS over cPS, and the inhibitory activity of several
oxathiazolones against iPS was experimentally determined. However, the detailed mechanism
of the chemical reaction leading to irreversible iPS inhibition and the key selectivity
drivers are unknown, and separate characterization of the noncovalent and covalent
inhibition steps is not available for several compounds. Here, we investigate the
chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/
molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism
and to determine the rate-determining step of covalent complex formation. The modelled
binding mode and reaction mechanism are in line with the selective inhibition of iPS
versus cPS by oxathiazolones. The k(inact )value of several ligands was estimated
by constructing the potential of mean force of the rate-determining step by QM/MM
simulations coupled with umbrella sampling. The equilibrium constant K-i of the noncovalent
complex formation was evaluated by classical force field-based thermodynamic integration.
The calculated K-i and kinact values made it possible to analyse the contribution
of the noncovalent and covalent steps to the overall inhibitory activity. Compounds
with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS
owing to subtle differences in the binding modes that slightly affect K-i, the noncovalent
affinity, and importantly alter k(inact), the covalent reactivity of the bound compounds.
A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in
designing iPS selective inhibitors with improved drug-like properties. (C) 2021 The
Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational
and Structural Biotechnology.
