Comprehensive Chemoproteomics Unveils Selective HMG-CoA Synthase 1 Inhibitors for Targeting Mevalonate Metabolism in...

Area of Science:

• Chemical Biology
• Proteomics
• Enzyme Inhibition

Background:

• Target validation is crucial for developing selective covalent inhibitors, but traditional methods struggle with off-target reactivity and distinguishing binder occupancy.
• HMG-CoA synthase 1 (HMGCS1), a key enzyme in the mevalonate pathway, is an underexplored target for chemical probes.

Purpose of the Study:

• To develop and validate a comprehensive chemoproteomic framework for assessing covalent inhibitor selectivity and engagement.
• To characterize CNP7, a novel covalent inhibitor targeting HMGCS1, and explore its biological effects and therapeutic potential.

Main Methods:

• Integrated orthogonal chemoproteomic methods, including traditional enrichment and complementary scavenging proteomics, to analyze on- and off-target profiles.
• Developed CNP7, a cyanopyrrolidine inhibitor, and assessed its selectivity using comprehensive chemoproteomics.
• Determined the cryo-electron microscopy (cryo-EM) structure of CNP7 bound to HMGCS1.
• Measured HMG-CoA levels and global protein deprenylation following CNP7 treatment.

Main Results:

• The proposed chemoproteomic framework effectively distinguishes high- and low-occupancy binders by analyzing de-enriched fractions.
• CNP7 selectively covalently modifies HMGCS1's catalytic cysteine, confirmed by cryo-EM structure and chemoproteomics.
• CNP7 treatment rapidly reduced HMG-CoA levels and induced global protein deprenylation.
• CNP7 demonstrated distinct cell line-specific anticancer activity compared to statins, suggesting pathway node-specific vulnerabilities.

Conclusions:

• The integrated chemoproteomic approach provides unbiased, comprehensive target engagement insights for covalent inhibitors.
• CNP7 is a potent and selective HMGCS1 inhibitor with potential therapeutic applications in cancer.
• This framework advances chemical biology and drug development by enabling rigorous characterization of covalent inhibitors.