Robert Huber (2018) - The Proteasome, Structure, Mechanism, Ligand-Binding, and Application in Drug Design and Development

Robert Huber (2018)

The Proteasome, Structure, Mechanism, Ligand-Binding, and Application in Drug Design and Development

Robert Huber (2018)

The Proteasome, Structure, Mechanism, Ligand-Binding, and Application in Drug Design and Development

Abstract

The proteasome plays a key role in archaeal and eukaryotic cells by proteolysis of incorrectly folded, non-functional proteins (in archaea and eukaryotes), and of ubiquitin-labelled signalling proteins (in eukaryotes) and antigenic proteins (in vertebrates with an adaptive immune system). The eukaryotic proteasome is composed of two components, the regulatory cap and the core particle (CP), which harbours the active sites. Its activity is controlled by sequestration of the substrate-binding active sites inside the barrel-shaped architecture of the CP equipped with entry gates at both ends, which are closed in the latent state and opened induced by cofactors leading to activity.

My presentation focuses on CP which has been extensively characterized in structure by x-ray crystallography (Groll, M., Ditzel, L., Löwe, J., Stock, D., Bochtler, M., Bartunik, H. D. and Huber, R. (1997). "Structure of 20S proteasome from yeast at 2.4 Å resolution." Nature 386, 463-471.) and by in vitro and in vivo functional studies.
It consists of 28 subunits arranged in 4 stacked hetero-heptameric rings, alpha1-7, beta1-7, beta1-7, alpha1-7. The assembly of CP commences sequentially with the formation of the alpha rings onto which beta subunits affix in a defined order and is followed by autolytic cleavage of the N-terminal pro-peptides thus exposing the N-terminal Thr residues of three of the seven beta subunits (1,2,5), which are enzymatically active. (Groll, M., Heinemeyer, W., Jäger, S., Ullrich, T., Bochtler, M., Wolf, D. H. and Huber, R. (1999. "The catalytic sites of 20S proteasomes and their role in subunit maturation: A mutational and crystallographic study." Proc. Natl. Acad. Sci. USA 96, 10976-10983.)

Access of the active sites for substrate requires opening of the entry gates formed by the entangled N-terminal segments of the seven alpha units. Mutation of a single residue in alpha3 generates a constitutively active enzyme. (Groll, M., Bajorek, M., Köhler, A., Moroder, L., Rubin, D. M., Huber, R., Glickman, M. H. and Finley, D. (2000). "A gated channel into the proteasome core particle." Nature Struct. Biol. 7, 1062-1067.)

The enzyme mechanism proceeds via formation of a tetrahedral adduct of the threonine hydroxyl group with the carbonyl carbon of the scissile peptide assisted by invariant lysine33 and aspartate17 residues, continues with acyl enzyme formation and peptide bond cleavage, and finishes by water mediated ester hydrolysis and liberation of the products.
The majority of the specific ligands discovered and developed for the proteasome target the threonine nucleophile by aldehyde-, lactone-, boronic acid-, epoxyketone-, unsaturated amide- head groups (war heads) covalently. Noncovalent ligands of different chemistries have also been found. Natural compound libraries appear to be a rich source. (Groll, M., Huber, R. and Moroder, L. (2009). "The persisting challenge of selective and specific proteasome inhibition." Journal of Peptide Science 15, 58-66.)

Research in proteasome inhibitors is strongly encouraged by the discovery of the proteasome as a drug target for leukemic cells and haematological tumors. Three proteasome inhibitors have been developed, are clinically applied, and commercially very successful.
Vertebrates have three different CPs. The constitutive proteasome (cCP) is ubiquitous in all tissues, whereas the immunoproteasome (iCP) is found predominantly in lymphocytes. cCP and iCP differ by a unique set of catalytic subunits beta1,2,5 displaying modified substrate binding pockets and enzymatic specificities and activities.
Selective inhibitors of the immunoproteasome have gained interest offering new strategies for autoimmune disorders, inflammation, rheumatoid arthritis, and certain types of cancer, and promise/show reduced side effects such as peripheral neuropathy.
(Arciniega, M., Beck, P., Lange, O.F., Groll, M. and Huber, R. (2014). "Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding." PNAS vol.111 no.26, 9479-9484; Huber, E.M. and Groll, M. (2012) “Inhibitors for the immune- and constitutive proteasome: current and future trends in drug development” Angew.Chem. Int. Ed. 51, 8708-8720; Cromm, P.M. and Crews, C.M. (2017). “The proteasome in modern drug discovery: second life of a highly valuable drug target”, ACS Cent. Sci. 3(8), 830-838.)

Various lines of development based on different chemical scaffolds are pursued in Academia and Industry (www.Proteros.com; www.lead-discovery.com) guided by high resolution crystal structures and give hope for new therapeutic options for diseases with high medical need.

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