Improved Electrophile Design for Exquisite Covalent Molecule Selectivity

Area of Science:

• Medicinal Chemistry
• Chemical Biology
• Pharmacology

Background:

• Covalent inhibitors are effective therapeutics but face challenges due to off-target reactivity.
• Strategies to improve selectivity often involve modifying the reactivity of electrophilic warheads.

Purpose of the Study:

• To develop a novel, warhead-independent method for enhancing covalent inhibitor selectivity.
• To investigate if increasing steric bulk on electrophilic warheads can improve selectivity without compromising on-target reactivity.

Main Methods:

• Utilized the Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib scaffold for proof-of-concept.
• Synthesized and tested a tert-butyl (t-Bu) fumarate ester analogue.
• Employed chemical proteomic techniques to assess protein targets and reactivity.
• Compared the selectivity and downstream effects of the t-Bu analogue against Ibrutinib.

Main Results:

• The t-Bu fumarate analogue significantly reduced time-dependent and abolished time-independent off-target reactivity.
• A t-Bu fumarate probe analogue identified only 7 protein targets, compared to 247 for an alkyne analogue.
• The t-Bu inhibitor demonstrated 70% greater selectivity for BTK, with fewer downregulated proteins (8 vs. 107).

Conclusions:

• Increasing steric bulk of electrophilic warheads is a viable strategy to enhance covalent inhibitor selectivity.
• This approach offers a complementary method to existing strategies for optimizing covalent therapeutics.
• Electrophilic structure optimization can lead to more selective covalent inhibitors with improved therapeutic profiles.