Covalent Inhibitors Against VCPIP1, a Deubiquitinating Enzyme with Critical Roles in Pancreatic Adenocarcinoma and Botulinum Neurotoxin Intoxication

Project Overview

• Deubiquitinating enzymes (DUBs) are emerging drug targets that regulate protein degradation Dysregulation of DUBs is observed in several clinical settings, including breast and pancreatic cancers, as well as in Alzheimer’s and Parkinson’s disease, making them attractive therapeutic targets.
• Scientists at Dana-Farber have developed a powerful discovery platform for DUB inhibitors and identified several promising tools and lead compounds, including for the emerging target, valosin containing protein interacting protein 1 (VCPIP1).
• Dana-Farber Cancer Institute is looking for the right partner to collaborate to further develop the VCPIP1 inhibitors and to jointly continue the validation of the emerging VCPIP1 target.

Technology

Deubiquitinating enzymes (DUBs) are emerging drug targets that regulate protein degradation by cleaving ubiquitin and ubiquitin-like modifications from proteins. DUBs also coordinate cellular localization of proteins and modulate protein-protein interactions within the ubiquitin-proteasome system (UPS). Dysregulation of DUBs is observed in several clinical settings, including breast and pancreatic cancers, as well as in Alzheimer’s and Parkinson’s disease, making them attractive therapeutic targets. However, developing selective DUB inhibitors has been hindered by poor selectivity of early compounds and limited understanding of DUB biology.

Valosin Containing Protein Interacting Protein 1 (VCPIP1) is a gene that encodes the deubiquitinating enzyme VCIP135 that plays a critical role in DNA repair and the reassembly of the Golgi apparatus and endoplasmic reticulum following mitosis. VCPIP1 is necessary for VCP-mediated reassembly of Golgi stacks after mitosis and participates in the formation of transitional endoplasmic reticulum (tER). VCPIP1 has a regulatory role in controlling protein levels of botulism toxin serotype A. VCPIP1 deubiquitinates and prevents degradation of Botulinum neurotoxin A light chain (LC) by the proteasome, allowing the toxin to build up and cause stronger, faster nerve damage. Additionally, clinical data revealed that VCPIP1 is elevated in pancreatic adenocarcinoma (PAAD) and correlated with poor survival in PAAD patients.

VCPIP1, like most DUBs, is annotated as cysteine proteases have unique structural features surrounding the catalytic site, suggesting that they can be selectively targeted with small molecule inhibitors. However, the field struggled in gaining pharmacologic traction and the early generation of DUB inhibitors were found to be multitargeted. Recently, the first selective inhibitors have been developed for a small subset of DUBs, but the larger class remains challenging. Previous technologies inadequately cover the DUB family and fail to discern structure–activity relationships (SAR) necessary for selective inhibitor design. Thus, a dedicated platform to develop selective DUB inhibitors, including VCPIP1, would enable therapeutic targeting of this class of important enzymes.

Dr. Sara Buhrlage at Dana-Farber is a world leader in the development of DUB-focused inhibitors. Her laboratory has established a powerful discovery platform for DUB inhibitors and has identified several promising tools and lead compounds, including for the emerging target, VCPIP1.

Demonstrating the power of the discovery platform, the initial VCPIP hit molecule was developed into a selective covalent inhibitor with an IC50 of 70 nM after limited SAR. This compound selectively binds the native enzyme with little to no activity against other DUBs and shows promising cell-based activity. Thus, our inhibitor provides an exceptional opportunity to further understand the biological functions of VCPIP1 and provides a starting point for subsequent therapeutic development.

More generally, Dr. Buhrlage’s covalent library consists of compounds diversified to target multiple regions around DUB catalytic sites. The library, informed by diverse DUB inhibitor chemotypes and structural analyses, was synthesized via combinatorial assembly of noncovalent building blocks, linkers, and electrophilic warheads designed to engage unique features of DUB active sites. This library was paired with activity-based protein profiling (ABPP) coupled with quantitative mass spectrometry for primary screening. The team assesses compound selectivity against DUBs in their native environment, enabling simultaneous hit identification and SAR deconvolution across the DUB family.

The team has identified hits and selective leads against multiple additional DUB family members demonstrating the platform’s capability to rapidly generate potent, selective inhibitors across multiple DUB subfamilies.

Team Members: Sara Buhrlage, PhD, Jarrod Marto, PhD

Applications

Therapeutic development: discovery of selective DUB inhibitors for treating diseases linked to DUB dysregulation, such as cancer and neurodegenerative diseases. 

Chemical biology tools: provision of chemical probes to advance understanding of DUB biology and the ubiquitin-proteasome system, aiding exploration of DUB functions and substrates.

Target validation: rigorous validation of DUBs as drug targets through selective inhibition.

Opportunities

Dana-Farber Cancer Institute is looking for the right partner to collaborate to further develop the VCPIP1 inhibitors and to jointly continue the validation of the emerging VCPIP1 target.

Team Members

Sara Buhrlage, PhD

Principal Investigator, Cancer Biology, Dana-Farber

Associate Professor, Biological Chemistry and Molecular Pharmacology, Harvard Medical School

Sara's Bio

Jarrod Marto, PhD

Professor of Chemistry (School of Arts & Sciences), Professor of Biochemistry & Molecular Genetics (School of Medicine) University of Virginia

Jarrod's Bio