Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation

Lemma, Betsegaw; Zhang, Di; Vamisetti, Ganga B.; Wentz, Bryan G.; Suga, Hiroaki; Brik, Ashraf; Lubkowski, Jacek; Fushman, David

doi:10.1038/s41467-023-43025-4

Title: Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation

Journal Article · 08 November 2023 · Nature Communications

DOI: https://doi.org/10.1038/s41467-023-43025-4 · OSTI ID:2470181

Lemma, Betsegaw ^[1]; Zhang, Di ^[2]; Vamisetti, Ganga B. ^[3];

^[1];

^[4];

^[3]; Lubkowski, Jacek ^[2];

^[1]

Univ. of Maryland, College Park, MD (United States)
National Cancer Institute, Frederick, MD (United States)
Technion-Israel Institute of Technology, Haifa (Israel)
Univ. of Tokyo (Japan)

Post-translational modification of proteins with polyubiquitin chains is a critical cellular signaling mechanism in eukaryotes with implications in various cellular states and processes. Unregulated ubiquitin-mediated protein degradation can be detrimental to cellular homeostasis, causing numerous diseases including cancers. Recently, macrocyclic peptides were developed that selectively target long Lysine-48-linked polyubiquitin chains (tetra-ubiquitin) to inhibit ubiquitin-proteasome system, leading to attenuation of tumor growth in vivo. However, structural determinants of the chain length and linkage selectivity by these cyclic peptides remained unclear. Here, we uncover the mechanism underlying cyclic peptide’s affinity and binding selectivity by combining X-ray crystallography, solution NMR, and biochemical studies. We found that the peptide engages three consecutive ubiquitins that form a ring around the peptide and determined requirements for preferential selection of a specific trimer moiety in longer polyubiquitin chains. The structural insights gained from this work will guide the development of next-generation cyclic peptides with enhanced anti-cancer activity.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2470181

Journal Information:: Nature Communications, Journal Name: Nature Communications Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation

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