Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles

Area of Science:

• Chemical Biology
• Medicinal Chemistry
• Proteomics

Background:

• Covalent ligands are crucial chemical probes and therapeutic agents.
• An expanded range of cysteine-reactive electrophiles is needed for advanced proteome profiling.
• Cyclopropane-based electrophiles offer a new avenue for chemical probe development.

Purpose of the Study:

• To develop a novel class of strain-enabled electrophiles based on cyclopropanes.
• To expand the repertoire of cysteine-reactive electrophiles for proteome profiling.
• To identify and validate new ligandable cysteine residues and their functional implications.

Main Methods:

• Development of cyclopropane-based strain-enabled electrophiles.
• Proteome profiling using the novel electrophiles.
• Fragment-based ligand discovery (FBLD) to identify reactive fragments.
• Biochemical assays to confirm covalent binding and functional impact.

Main Results:

• Identification of C163 in lactate dehydrogenase A (LDHA) and C88 in adhesion regulating molecule 1 (ADRM1) as ligandable residues.
• Discovery of fragment Y-35 exhibiting strong reactivity towards C66 of thioredoxin domain-containing protein 12 (TXD12).
• Demonstration that covalent binding of Y-35 to TXD12 impacts downstream signaling, leading to anti-survival and anti-proliferative effects.
• Validation of dicarbonitrile-cyclopropane as an electrophilic warhead for developing dual covalent inhibitors targeting GSTO1.

Conclusions:

• Novel cyclopropane-based electrophiles expand the toolkit for cysteine-reactive probe development.
• The identified ligandable residues in LDHA and ADRM1 offer new targets for modulating protein function.
• TXD12 and its interaction with Y-35 highlight a novel pathway for anti-cancer effects.
• Dicarbonitrile-cyclopropane-based inhibitors show promise in overcoming drug resistance.