A Practical Review of Proteasome Pharmacology

Abstract

The ubiquitin proteasome system (UPS) degrades individual proteins in a highly regulated fashion and is responsible for the degradation of misfolded, damaged, or unneeded cellular proteins. During the past 20 years, investigators have established a critical role for the UPS in essentially every cellular process, including cell cycle progression, transcriptional regulation, genome integrity, apoptosis, immune responses, and neuronal plasticity. At the center of the UPS is the proteasome, a large and complex molecular machine containing a multicatalytic protease complex. When the efficiency of this proteostasis system is perturbed, misfolded and damaged protein aggregates can accumulate to toxic levels and cause neuronal dysfunction, which may underlie many neurodegenerative diseases. In addition, many cancers rely on robust proteasome activity for degrading tumor suppressors and cell cycle checkpoint inhibitors necessary for rapid cell division. Thus, proteasome inhibitors have proven clinically useful to treat some types of cancer, especially multiple myeloma. Numerous cellular processes rely on finely tuned proteasome function, making it a crucial target for future therapeutic intervention in many diseases, including neurodegenerative diseases, cystic fibrosis, atherosclerosis, autoimmune diseases, diabetes, and cancer. In this review, we discuss the structure and function of the proteasome, the mechanisms of action of different proteasome inhibitors, various techniques to evaluate proteasome function in vitro and in vivo, proteasome inhibitors in preclinical and clinical development, and the feasibility for pharmacological activation of the proteasome to potentially treat neurodegenerative disease.

Fig. 1.

The ubiquitin proteasome pathway. (A) Simplified model of the ubiquitin conjugation system. (B) Primary steps involved in ubiquitinated substrate processing by the 26S proteasome.

Fig. 2.

Proteasome structure and function. (A) Structures (PDB 4r3o) and cartoon representation of 20S proteasome, highlighting the different β-subunit combinations found in tissue-specific proteasomes discussed in the text. (B) Structure of the 26S proteasome in complex with Ubp6 (PDB 5a5b). A cross-section of 20S proteasome reveals the C terminus of Rpt5 ATPase (dark orange) positioned in the inter-α-subunit pocket (asterisk). Proteolytic sites are marked with yellow stars. Labeled 19S subunits are discussed in the text. (C) 20S proteasomes (blue and gray) complexed with regulatory caps: PA28 homolog PA26 (PDB 1fnt), 19S (PDB 5gjr), and PA200 yeast homolog Blm10 (PDB 4v7o). 19S ATPases are dark orange, and non-ATPase subunits are light orange. PDB, Protein Data Bank.

Fig. 3.

Examples of cellular functions that depend on proteasome function. Important pathways dependent on proteasome function and exemplar substrates. Bax, bcl-2-like protein 4; Bim, bcl-2-like protein 11; Cdk, cyclin-dependent kinase; Drp1, dynamin-1-like protein; ERAD, endoplasmic-reticulum-associated protein degradation; E2F-1, target of retinoblastoma protein; Fis1, mitochondrial fission 1 protein; GABA, gamma-aminobutyric acid; JNK, C-Jun-amino-terminal kinase; Mfn, mitofusin; MHC-I, major histocompatibility complex-I; Miro, mitochondrial Rho GTPase; NF-κB, nuclear factor–κB; PKA, protein kinase A; PSD-95, postsynaptic density protein 95; Topo II, type II topoisomerase; Wnt, wingless-type.

Fig. 4.

Proteasome inhibitors and the β5 binding site. (A) Chemical structures of proteasome inhibitors that are FDA approved and/or are in clinical trials with pharmacophores shown in red. For ixazomib, the orally bioavailable prodrug (MLN9708) is shown, with the biologically active metabolite (MLN2238) highlighted in black and red for clarity. (B) X-ray crystallography structures of human 20S proteasomes in complex with carfilzomib (PDB 4r67), bortezomib (PDB 5lf3), and ixazomib (PDB 5lf7); yeast 20S in complex with marizomib (PDB 2fak); and the cryo-EM structure of human 26S in complex with oprozomib (PDB 5m32). PDB, Protein Data Bank.