Development of Novel Amides as Noncovalent Inhibitors of Immunoproteasomes

Abstract

The development of immunoproteasome‐selective inhibitors is a promising strategy for treating hematologic malignancies, autoimmune and inflammatory diseases. In this context, we report the design, synthesis, and biological evaluation of a new series of amide derivatives as immunoproteasome inhibitors. Notably, the designed compounds act as noncovalent inhibitors, which might be a promising therapeutic option because of the lack of drawbacks and side effects associated with irreversible inhibition. Among the synthesized compounds, we identified a panel of active inhibitors with Ki values in the low micromolar or sub‐micromolar ranges toward the β5i and/or β1i subunits of immunoproteasomes. One of the active compounds was shown to be the most potent and selective inhibitor with a Ki value of 21 nm against the single β1i subunit. Docking studies allowed us to determine the mode of binding of the molecules in the catalytic site of immunoproteasome subunits.

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

“…The folded conformation assumed by the ligand in pose 2 seemed to represent an intermediate conformation. Concerning previous studies [ 12 ], two pi-stacking interactions and van der Waals contacts between the rings and the residues Thr1, Val20, Phe31, Lys33, Leu45, Ser46, and Ala52 were identified ( Figure 5 ).…”

“…For these reasons, the attention was focused on non-covalent immunoproteasome inhibitors. In this context, a series of amide derivative β1i subunit inhibitors with K i values in the low micromolar or submicromolar range have been recently identified [ 12 ]. The use of computational approaches could characterize the binding process of these inhibitors—in particular, the use of advanced molecular dynamics approaches able to explore the dynamic features of the protein/ligand complex could overcome the limitations of semiflexible molecular docking methods in which the protein target is treated as a rigid body.…”

“…In the recent past, most of these studies made use of molecular docking methods. In particular, the binding mode of the non-covalent amide derivatives 1 and 2 was investigated at this level [ 12 ], while, to the best of our knowledge, the most accurate computational investigations were performed just on the β1i subunit ( Figure 2 A,B) and the peptide α′,β′-epoxyketone UK101 ( Figure 2 C) using molecular dynamics (MD) simulations. The observed selectivity of UK101 for the β1i subunit is rationalized by the requirement for both a linear hydrocarbon chain at the N-terminus and a bulky group at the C-terminus of the inhibitor [ 13 ].…”

“…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]. Recently, 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]. N-Benzyl-2-(2-oxopyridin-1(2H)-yl)propanamide (1) proved to be the most potent and selective inhibitor, with a Ki = 21 nM against the β1i subunit.…”

Recent insights how combined inhibition of immuno/proteasome subunits enables therapeutic efficacy

“…Furthennore, the recently described non-covalent amide derivate proteasome inhibitors simultaneously target multiple proteasome subunits, and, therefore bear the potential to be effective in solid tumors [89]. Amide derivates targeting the ß5i and ß2i have been shown to induce cell cycle arrest in mul tip le myeloma MM.IR cells [90].…”