Immunoproteasome and Non-Covalent Inhibition: Exploration by Advanced Molecular Dynamics and Docking Methods.

Giulia Culletta,Maria Zappalà,Roberta Ettari,Anna Maria Almerico,Marco Tutone

doi:10.3390/molecules26134046

Giulia Culletta, Maria Zappalà + Show 3 more

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https://doi.org/10.3390/molecules26134046

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Abstract

The selective inhibition of immunoproteasome is a valuable strategy to treat autoimmune, inflammatory diseases, and hematologic malignancies. Recently, a new series of amide derivatives as non-covalent inhibitors of the β1i subunit with Ki values in the low/submicromolar ranges have been identified. Here, we investigated the binding mechanism of the most potent and selective inhibitor, N-benzyl-2-(2-oxopyridin-1(2H)-yl)propanamide (1), to elucidate the steps from the ligand entrance into the binding pocket to the ligand-induced conformational changes. We carried out a total of 400 ns of MD-binding analyses, followed by 200 ns of plain MD. The trajectories clustering allowed identifying three representative poses evidencing new key interactions with Phe31 and Lys33 together in a flipped orientation of a representative pose. Further, Binding Pose MetaDynamics (BPMD) studies were performed to evaluate the binding stability, comparing 1 with four other inhibitors of the β1i subunit: N-benzyl-2-(2-oxopyridin-1(2H)-yl)acetamide (2), N-cyclohexyl-3-(2-oxopyridin-1(2H)-yl)propenamide (3), N-butyl-3-(2-oxopyridin-1(2H)-yl)propanamide (4), and (S)-2-(2-oxopyridin-1(2H)-yl)-N,4-diphenylbutanamide (5). The obtained results in terms of free binding energy were consistent with the experimental values of inhibition, confirming 1 as a lead compound of this series. The adopted methods provided a full dynamic description of the binding events, and the information obtained could be exploited for the rational design of new and more active inhibitors.

Highlights

Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Abstract: The selective inhibition of immunoproteasome is a valuable strategy to treat autoimmune, inflammatory diseases, and hematologic malignancies
Introduction with regard to jurisdictional claims in Protein turnover is essential for cellular function and homeostasis; in eukaryotic cells, the ubiquitin-proteasome system (UPS) is the central non-lysosomal pathway devoted to protein degradation
The main class of covalent immunoproteasome inhibitors is that of peptide derivatives bearing an electrophile warhead able to interact with the nucleophilic hydroxyl group of catalytic Thr1

Summary

Introduction

Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Abstract: The selective inhibition of immunoproteasome is a valuable strategy to treat autoimmune, inflammatory diseases, and hematologic malignancies. A new series of amide derivatives as non-covalent inhibitors of the β1i subunit with Ki values in the low/submicromolar ranges have been identified. The covalent irreversible inhibition of a human enzyme is not always desirable in medicinal chemistry, as it can be responsible for potential toxicity due to off-target binding Another drawback is that a single mutation in the catalytic amino acid (i.e., Thr1) could cause a loss of activity and acquired resistance. Other compounds are N,C-capped dipeptides, such as PKS2279 and PKS2252, in which the insertion of a β-amino acid markedly reduces the inhibitory potency against constitutive proteasomes, yet maintain potent inhibitory activity against immunoproteasomes [11]. Some of us identified a panel of selective non-covalent inhibitors of the β1i and/or β5i subunits, characterized by a 2(1H)-pyridone scaffold linked to an amide function [12]. Methods.InIn particular, binding mode ofnon-covalent the non-covalent ofmolecular molecular docking particular, thethe binding mode of the amideamide derivatives

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