Computational Design of Lysine Targeting Covalent Binders Using Rosetta

Area of Science:

• Medicinal Chemistry
• Computational Chemistry
• Chemical Biology

Background:

• Covalent chemical probes targeting proteins are valuable tools for research and drug discovery.
• While cysteine-targeting probes are common, lysine-targeting probes present unique chemical challenges.
• Developing computational methods for lysine-targeting covalent binder design is an unmet need.

Purpose of the Study:

• To develop and validate computational methods for designing lysine-targeting covalent small-molecules from noncovalent precursors.
• To address the challenges associated with lysine's pKa and flexibility in covalent binder design.
• To prospectively validate the designed computational protocols and assess their broad applicability.

Main Methods:

• Developed two computational strategies: a 'ligand-side' approach and a 'protein-side' approach.
• The 'ligand-side' method involves derivatizing known binders with electrophiles and docking.
• The 'protein-side' method involves modifying the target lysine and finding complementary ligand vectors.

Main Results:

• Retrospective application showed high success rates: ligand-side (80-86%) and protein-side (56-82%).
• Prospective validation yielded a novel MKK7 inhibitor with confirmed covalent lysine binding via mass spectrometry and crystallography.
• Computational methods identified over 200 potential kinase targets for covalent inhibition.

Conclusions:

• The developed computational protocols are effective for designing lysine-targeting covalent small-molecules.
• These methods facilitate the discovery of novel covalent inhibitors and chemical probes.
• The approach has broad implications for drug discovery, particularly in kinase inhibitor development.