Pipecolic esters as minimized templates for proteasome inhibition

Abstract

Allosteric regulators of clinically important enzymes are gaining popularity as alternatives to competitive inhibitors.

New Peptide-Based Pharmacophore Activates 20S Proteasome

“…As we have established previously, AFM collects images of single, native proteasome particles at nanometer resolution. The particles exhibit a well discernible gate area, assuming dynamic "open", closed" or "intermediate" positions, corresponding to the gate conformations detected by cryoEM [20,25,39,46]. These observations prompted us to search with AFM for structural consequences of (5) binding to the proteasome.…”

“…Certain anchoring peptides are known to interact with the α face in trans, most notably C-terminal "tails" of Rpt ATPase subunits of the 19S complex bearing the "HbYX" (hydrophobic-Y-any amino acid) C-terminal motif [38]. The 10-residue Rpt-derived C-terminal "tail" peptides ("Rpt peptides") can be used as competitors with the Rpt subunits or with small allosteric ligands [19,38,39]. Importantly, the Rpt peptides interject between the subunits with their C-termini, whereas TAT peptides, according to the modeling, use their N-termini for this purpose.…”

“…These observations prompted us to search with AFM for structural consequences of (5) binding to the proteasome. The latent core is known to preferentially remain in the closed-gate conformation, accounting for about three-quarters of particles detected by cryoEM or AFM, with less than 10% assuming the fully open-gate position [20,25,39]. In contrast, treatment with 1 µM of (5) resulted in a dramatic shift in partition of conformations toward more abundant, over 40%, open-gate proteasomes, and less prominent, below 30%, closed-gate particles (Figure 8).…”

“…[20]. In contrast, allosteric small-molecule or peptide inhibitors docking in the α face pockets suppressed the open-gate conformers [20,39]. The apparent strong stabilization of the open-gate conformation by (5) would be expected to promote catalysis by easing the rate-limiting obstacle of a closed gate.…”

“…TAT peptides may join other allosteric ligands in providing powerful tools for studying proteasome allostery. [20,39]). In the presence of 1μM of (5) 43% of core proteasomes assumed the open-gate conformation at any given time of AFM probing.…”