Mary Matyskiela

Complete subunit architecture of the proteasome regulatory particle.

The proteasome is the major ATP-dependent protease in eukaryotic cells, but limited structural information restricts a mechanistic understanding of its activities. The proteasome regulatory particle, consisting of the lid and base subcomplexes, recognizes and processes polyubiquitinated substrates. Here we used electron microscopy and a new heterologous expression system for the lid to delineate the complete subunit architecture of the regulatory particle from yeast. Our studies reveal the spatial arrangement of ubiquitin receptors, deubiquitinating enzymes and the protein unfolding machinery at subnanometre resolution, outlining the substrate’s path to degradation. Unexpectedly, the ATPase subunits within the base unfoldase are arranged in a spiral staircase, providing insight into potential mechanisms for substrate translocation through the central pore. Large conformational rearrangements of the lid upon holoenzyme formation suggest allosteric regulation of deubiquitination. We provide a structural basis for the ability of the proteasome to degrade a diverse set of substrates and thus regulate vital cellular processes.

Conformational switching of the 26S proteasome enables substrate degradation

The 26S proteasome is the major eukaryotic ATP-dependent protease, responsible for regulating the proteome through degradation of ubiquitin-tagged substrates. Its regulatory particle, containing the heterohexameric AAA+ ATPase motor and the essential deubiquitinase Rpn11, recognizes substrates, removes their ubiquitin chains and translocates them into the associated peptidase after unfolding, but detailed mechanisms remain unknown. Here we present the 26S proteasome structure from Saccharomyces cerevisiae during substrate degradation, showing that the regulatory particle switches from a preengaged to a translocation-competent conformation. This conformation is characterized by a rearranged ATPase ring with uniform subunit interfaces, a widened central channel coaxially aligned with the peptidase and a spiral orientation of pore loops that suggests a rapid progression of ATP-hydrolysis events around the ring. Notably, Rpn11 moves from an occluded position to directly above the central pore, thus facilitating substrate deubiquitination concomitant with translocation.

A novel cereblon modulator recruits GSPT1 to the CRL4(CRBN) ubiquitin ligase.

Immunomodulatory drugs bind to cereblon (CRBN) to confer differentiated substrate specificity on the CRL4CRBN E3 ubiquitin ligase. Here we report the identification of a new cereblon modulator, CC-885, with potent anti-tumour activity. The anti-tumour activity of CC-885 is mediated through the cereblon-dependent ubiquitination and degradation of the translation termination factor GSPT1. Patient-derived acute myeloid leukaemia tumour cells exhibit high sensitivity to CC-885, indicating the clinical potential of this mechanism. Crystallographic studies of the CRBN–DDB1–CC-885–GSPT1 complex reveal that GSPT1 binds to cereblon through a surface turn containing a glycine residue at a key position, interacting with both CC-885 and a ‘hotspot’ on the cereblon surface. Although GSPT1 possesses no obvious structural, sequence or functional homology to previously known cereblon substrates, mutational analysis and modelling indicate that the cereblon substrate Ikaros uses a similar structural feature to bind cereblon, suggesting a common motif for substrate recruitment. These findings define a structural degron underlying cereblon ‘neosubstrate’ selectivity, and identify an anti-tumour target rendered druggable by cereblon modulation.

Design Principles of a Universal Protein Degradation Machine

The 26S proteasome is a 2.5-MDa, 32-subunit ATP-dependent protease that is responsible for the degradation of ubiquitinated protein targets in all eukaryotic cells. This proteolytic machine consists of a barrel-shaped peptidase capped by a large regulatory particle, which contains a heterohexameric AAA+ unfoldase as well as several structural modules of previously unknown function. Recent electron microscopy (EM) studies have allowed major breakthroughs in understanding the architecture of the regulatory particle, revealing that the additional modules provide a structural framework to position critical, ubiquitin-interacting subunits and thus allow the 26S proteasome to function as a universal degradation machine for a wide variety of protein substrates. The EM studies have also uncovered surprising asymmetries in the spatial arrangement of proteasome subunits, yet the functional significance of these architectural features remains unclear. This review will summarize the recent findings on 26S proteasome structure and discuss the mechanistic implications for substrate binding, deubiquitination, unfolding, and degradation.

A Cereblon Modulator (CC-220) with Improved Degradation of Ikaros and Aiolos

The drugs lenalidomide and pomalidomide bind to the protein cereblon, directing the CRL4-CRBN E3 ligase toward the transcription factors Ikaros and Aiolos to cause their ubiquitination and degradation. Here we describe CC-220 (compound 6), a cereblon modulator in clinical development for systemic lupus erythematosis and relapsed/refractory multiple myeloma. Compound 6 binds cereblon with a higher affinity than lenalidomide or pomalidomide. Consistent with this, the cellular degradation of Ikaros and Aiolos is more potent and the extent of substrate depletion is greater. The crystal structure of cereblon in complex with DDB1 and compound 6 reveals that the increase in potency correlates with increased contacts between compound 6 and cereblon away from the modeled binding site for Ikaros/Aiolos. These results describe a new cereblon modulator which achieves greater substrate degradation via tighter binding to the cereblon E3 ligase and provides an example of the effect of E3 ligase binding affinity with relevance to other drug discovery efforts in targeted protein degradation.

Obtaining 3 Å Resolution Structures of Biomedical Targets at 200 keV

Increasingly, electron microscopes coupled with direct electron detectors are being used to determine the structures of macromolecular complexes at resolutions that were historically only attainable by X-ray crystallography. In order to maximize the efficacy of atomic models determined from cryo-electron microscopy densities in structure-based drug design, the resolution of the targeted structure should be such that coordinated ions and ordered water molecules are visible. Generally, such details become visible in the 2 to 3 Å resolution range. Despite the advent of high-speed direct detectors, which enable correction of beamor stage-induced movements of the sample during acquisition while simultaneously mitigating the damaging effects of radiation [1], single particle cryo-EM structures in the 2 to 3 Å resolution range have thus far only been collected using high-end 300 keV microscopes. Unfortunately, access to these high-end instruments is not only expensive, but also limited at most institutes due to heavy usage. Often times, mid-range 200 keV instruments are also installed alongside high-end 300 keV microscopes, and these mid-range microscopes are primarily used to screen sample conditions and determine preliminary reconstructions to serve as initial models for higher resolution data collection at 300 keV. Since the purchase cost and service contracts for these mid-range 200 keV instruments are lower than 300 keV microscopes, the ability to solve high-resolution structures at 200 keV could lead to substantial savings in academia and industry, as well as lessening the demand on the 300 keV instruments.

Abstract SY37-02: Ligand-directed degradation of GSPT1 by a novel cereblon modulator drives potent antitumor effects

The protein cereblon is part of the CRL4-CRBN E3 ubiquitin ligase complex, and has been shown to be the molecular target for the drugs lenalidomide and pomalidomide. These drugs bind to the surface of cereblon, triggering the recruitment of substrate proteins to the ligase complex where they can be ubiquitinated and subsequently degraded by the proteosome. By this mechanism, lenalidomide and pomalidomide cause the degradation of the zinc finger transcription factors Ikaros and Aiolos, which mediate the antimyeloma activity of these compounds. Here we describe the discovery of CC-885, a novel cereblon modulator with potent and broad-spectrum antiproliferative activity against a panel of tumor cell lines. Acute myeloid leukemia (AML) cell lines and patient-derived AML cells show particular sensitivity to CC-885 treatment. CC-885 achieves this activity by causing the degradation of G1 to S phase transition 1 (GSPT1), a translation termination factor required for the release of nascent peptides from the ribosome. A crystal structure of cereblon in complex with the ligase adapter protein DDB1, as well as CC-885 and GSPT1, reveals that GSPT1 interacts with both CC-885 and the surface of cereblon. The principal molecular feature on GSPT1 that binds to cereblon is a beta-hairpin incorporating a glycine residue that docks against CC-885. Surprisingly, we found evidence that a similar molecular feature mediates Ikaros recruitment, even though there is no common structural fold or sequence homology other than the key glycine residue. We thereby define the common molecular feature, or degron, shared by the known cereblon neomorphic substrates. We further describe a novel therapeutic target, GSPT1, with promise in cancer such as AML. These results further show that cereblon-mediated protein degradation can be directed against new proteins and that this mechanism enables the targeting of multiple protein classes that may be considered undruggable with conventional approaches. Citation Format: Mary Matyskiela, Gang Lu, Takumi Ito, Barbra Pagarigan, Chin-Chu Lu, Karen Miller, Wei Fang, Nai-Yu Wang, Derek Nguyen, Jack Houston, Gilles Carmel, Tam Tran, Mariko Riley, Lyn9Al Nosaka, Gabriel Lander, Svetlana Gaidarova, Shuichan Xu, Alexander Ruchelman, Hiroshi Handa, James Carmichale, Thomas O. Daniel, Brian E. Cathers, Antonia Lopez-Girona, Philip Chamberlain. Ligand-directed degradation of GSPT1 by a novel cereblon modulator drives potent antitumor effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr SY37-02. doi:10.1158/1538-7445.AM2017-SY37-02