Covalent ATG4B Inhibitors for Treatment of Cancer

NU2025-186

INVENTORS

• Karl Scheidt*
• Claire Trudeau
• Shiyuan Cheng

SHORT DESCRIPTION

The invention introduces a novel class of peptidyl covalent reversible ketoamide inhibitors designed to target the cysteine protease ATG4B.

BACKGROUND

Glioblastoma (GBM) is an aggressive and highly malignant tumor of the central nervous system, characterized by significant intra-tumor heterogeneity and a dismal prognosis, with a median survival rate of only 13.5 months after diagnosis. Current standard of care for GBM includes radiation therapy and temozolomide (TMZ) chemotherapy. Paradoxically, these treatments have been found to induce autophagy, a cellular degradation process that enables normal cells to respond to stress but can also promote tumor survival and therapy resistance. This autophagy-mediated resistance is mediated by activation of ATG4B, a cysteine protease, highlighting the enzyme as a promising therapeutic target for GBM.

ATG4B is a cysteine protease responsible for LC3 cleavage and processing. LC3-II is bound to phosphidylethanolamine (PE) allowing it to seal the isolation membrane and form the autophagosome. ATG4B is also responsible for dilipidation of LC3-II, allowing for the autophagosome to bind to the lysosome. ATG4B inhibition can inhibit autophagy at two different stages.

ABSTRACT

Northwestern researchers have developed a series of novel inhibitors to ATG4B featuring a ketoamide electrophilic warhead. This scaffold was initially identified from a screen of covalent reversible and irreversible small molecules designed to mimic the native substrate of ATG4B, and represents a promising approach due to its reversibility, which avoids challenges due to off-target irreversible engagement observed with other ATG4B tool compounds. The development of a convergent synthesis methodology allowing for modular chemical modifications was used to create a series of ketoamide compounds for analyses of structure activity relationship. Through this work, a lead early discovery compound was identified, which demonstrates potent and selective biochemical ATG4B inhibition. This compound reduces glioblastoma stem cell tumor sphere formation in vitro and significantly decreases tumor burden and extends survival in mice with orthotopically xenografted brain tumors, suggesting the potential for ATGB4 inhibitors to overcome autophagy-mediated treatment resistance in GBM.

APPLICATIONS

• Drug development for GBM – inhibition of autophagy to overcome resistance mechanisms to current therapies
• Treatment for other cancers – inhibition of ATG4B is broadly applicable to other cancers where autophagy contributes to tumor survival
• Chemical probes for studying ATG4B biology and autophagy pathways in cancer

ADVANTAGES

• Overcoming treatment resistance in GBM – inhibiting autophagy disrupts tumor survival mechanism observed in GBM cells exposed to radiation and TMZ
• Potential for combination therapy with existing treatments to enhance efficacy
• Enhanced specificity for targeting autophagy – specific targeting of ATG4B may reduce adverse events and increase therapeutic efficacy compared to other autophagy inhibitors

IP STATUS

A provisional patent application has been filed.