Paralog-dependent isogenic cell assay cascade generates highly selective SLC16A3 inhibitors

Area of Science:

• Pharmacology and Drug Discovery
• Molecular Biology and Genetics
• Membrane Transport Proteins

Background:

• Solute carrier (SLC) membrane transporters are crucial drug targets but remain largely underexploited due to challenges in developing specific chemical screening assays.
• Functional redundancies among SLCs complicate the identification of selective inhibitors, hindering pharmacological intervention.
• Targeting SLCs offers significant therapeutic potential, yet requires innovative approaches for drug development.

Purpose of the Study:

• To develop a novel, reliable chemical screening assay for identifying inhibitors of solute carrier (SLC) membrane transporters, specifically targeting SLC16A3.
• To leverage synthetic lethality between paralogous SLCs to create a selective screening system.
• To discover and characterize a potent and selective inhibitor for SLC16A3.

Main Methods:

• Development of the paralog-dependent isogenic cell assay (PARADISO) using five isogenic cell lines exploiting synthetic lethality between SLC16A1 and SLC16A3.
• Screening of a diversity-oriented library of approximately 90,000 compounds using the PARADISO system.
• Hit optimization and characterization of the identified SLC16A3 inhibitor, slCeMM1, including chemoproteomic analysis for proteome-wide selectivity.

Main Results:

• The PARADISO screening strategy successfully identified potent inhibitors for SLC16A3.
• The developed compound, slCeMM1, demonstrated high potency and paralog selectivity for SLC16A3.
• Chemoproteomics confirmed slCeMM1's selectivity at the proteome-wide level, validating its utility as a chemical probe.

Conclusions:

• The PARADISO assay provides a robust framework for developing specific cell-based drug discovery assays for SLC transporters.
• The discovery of slCeMM1 validates the PARADISO approach and offers a valuable tool for studying SLC16A3 function.
• This study paves the way for overcoming challenges in the pharmacological exploitation of SLC membrane transporters.