8RHK

Yeast 20S proteasome in complex with a linear oxindole epoxyketone (compound 6)

This is a non-PDB format compatible entry.

Summary for 8RHK

• Entry DOI: 10.2210/pdb8rhk/pdb
• Descriptor: Proteasome subunit alpha type-2, Proteasome subunit beta type-4, Proteasome subunit beta type-5, ... (20 entities in total)
• Functional Keywords: proteasome, epoxomicin, tmc-95a, carfilzomib, binding analysis, hydrolase
• Biological source: Saccharomyces cerevisiae (brewer's yeast); More
• Total number of polymer chains: 34
• Total formula weight: 736163.60

Authors

Goetz, M.G.,Godwin, K.,Price, R.,Dorn, R.,Merrill-Steskal, G.,Hansen, H.,Klemmer, W.,Produturi, G.,Rocha, M.,Palmer, M.,Molacek, L.,Strater, Z.,Groll, M. (deposition date: 2023-12-15, release date: 2024-05-01)

Primary citation

Gotz, M.G.,Godwin, K.,Price, R.,Dorn, R.,Merrill-Steskal, G.,Klemmer, W.,Hansen, H.,Produturi, G.,Rocha, M.,Palmer, M.,Molacek, L.,Strater, Z.,Groll, M.
Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome.
Acs Med.Chem.Lett., 15:533-539, 2024

PubMed Abstract: Peptide macrocycles have recently gained attention as protease inhibitors due to their metabolic stability and specificity. However, the development of peptide macrocycles with improved binding potency has so far been challenging. Here we present macrocyclic peptides derived from the clinically applied proteasome inhibitor carfilzomib with an oxindole group that mimics the natural product TMC-95A. Fluorescence kinetic activity assays reveal a high potency of the oxindole group (IC = 0.19 μM) compared with agents lacking this motif. X-ray structures of the ligands with the β5-subunit of the yeast 20S proteasome illustrate that the installed macrocycle forces strong hydrogen bonding of the oxindole group with β5-Gly23NH. Thus, the binding of our designed oxindole epoxyketones is entropically and enthalpically favored in contrast to more flexible proteasome inhibitors such as carfilzomib.

PubMed: 38628795
DOI: 10.1021/acsmedchemlett.4c00017

Experimental method

X-RAY DIFFRACTION (2.8 Å)