Target Class Approach to Develop DUB Inhibitors

ASPIRE Award (ASPIRE I: 2019-2020; ASPIRE II: 2021-PRESENT)

Sara Buhrlage, PhD (Principal) and Jarrod Marto, PhD, Dana-Farber Cancer Institute

Sara Buhrlage, PhD

Jarrod Marto, PhD

Deubiquitinases (DUBs) catalyze the removal of ubiquitin from proteins. Proteins tagged with ubiquitin are marked for shuttling to the cell’s waste disposal system, known as the proteasome. Inactivation of specific DUBs could, therefore, lead to the degradation of proteins that keep cancer cells alive. DUBs function as part of the ubiquitin-proteasome system (UPS), and although they represent a class of highly specific protein targets whose inhibition could be therapeutic, there are currently no approved DUB-targeting drugs. Dr. Sara Buhrlage of the Dana-Farber Cancer Institute is working with her team on a target class approach to develop tool molecules and drug candidates that inhibit DUBs, utilizing novel chemoproteomic methods to characterize a focused library of covalent probe compounds. Non-specific drugs targeting the UPS have worked in lymphoma and multiple myeloma, both of which have approved UPS-based drugs. However, these inhibitors target the broader function of the UPS and often lead to toxicity. Targeting specific DUBs could provide the desired therapeutic benefit while alleviating toxic side effects. This work will also provide a framework for future target class approaches to inhibiting other types of enzymes.

published research

Magin RS, Liu X, Felix A, Bratt AS, Chan WC, Buhrlage SJ. Small molecules as tools for functional assessment of deubiquitinating enzyme function. Cell Chem Biol. 2021.

Varca AC, Casalena D, Chan WC, Hu B, Magin RS, Roberts RM, Liu X, Zhu H, Seo HS, Dhe-Paganon S, Marto JA, Auld D, Buhrlage SJ. Identification and validation of selective deubiquitinase inhibitors. Cell Chem Biol. 2021.

Chan WC, Sharifzadeh S, Buhrlage SJ, Marto JA. Chemoproteomic methods for covalent drug discovery. Chem Soc Rev. 2021.

Varca AC, Casalena D, Auld D, Buhrlage SJ. Identification of deubiquitinase inhibitors via high-throughput screening using a fluorogenic ubiquitin-rhodamine assay. STAR Protoc. 2021.

Zhu H, Ficarro SB, Alexander WM, Fleming LE, Adelmant G, Zhang T, Willetts M, Decker J, Brehmer S, Krause M, East MP, Gray NS, Johnson GL, Kruppa G, Marto JA. PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors. Anal Chem. 2021.

Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Anal Chem. 2022.

Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ. Accelerating inhibitor discovery for deubiquitinating enzymes. Nat Commun. 2023.

Sahu I, Zhu H, Buhrlage SJ, Marto JA. Proteomic approaches to study ubiquitinomics. Biochim Biophys Acta Gene Regul Mech. 2023.