Baylor College of Medicine researchers have developed a powerful new tool for pharmaceutical analysis which provides a comprehensive, unbiased view of how covalent inhibitors interact with proteins throughout a cell.
The innovative new method, called COOKIE-Pro (Covalent Occupancy Kinetic Enrichment via Proteomics), was recently described in a publication in the journal Nature Communications. COOKIE-Pro promises to accelerate covalent inhibitor design, providing a streamlined method to ensure effective, safe drugs by analyzing binding strength and reaction speed.
"Covalent inhibitors, which include well-known drugs like aspirin and the cancer therapeutic ibrutinib, are highly effective because they form a strong, permanent bond with their target protein," said Dr. Jin Wang, director of the Center for NextGen Therapeutics and Michael E. DeBakey, M.D. Endowed Professor in Pharmacology at Baylor. "However, this strength can be a double-edged sword; these drugs can also bind to unintended off-target proteins, potentially leading to unwanted side effects."
Optimizing covalent inhibitors has proven challenging in the past, requiring a delicate balance between affinity and reactivity. Until now, measuring this balance across the cellular protein landscape has been limited, hindering covalent inhibitor development.
"The challenge was getting a clear, complete picture," added Hanfeng Lin, graduate student in the Wang lab. "We knew we needed to measure both affinity and reactivity, but doing it for one protein takes time, let alone thousands. COOKIE-Pro gives us a comprehensive map in which we can see for the first time, not just if a drug binds off-target, but how well and how fast, which is critical information for drug designers."
The team validated the method using spebrutinib and ibrutinib, two well-studied drugs, ultimately finding that the method not only produced accurate, reproducible results, but also uncovered new insights.
"The ultimate goal is rational drug design," said Wang. "A drug might appear potent because it binds quickly, but if that is simply because it has a 'hot' reactive group, it might cause side effects by binding everywhere. COOKIE-Pro allows us to separate that intrinsic reactivity from true binding affinity. We can now help chemists prioritize compounds that are potent because they bind specifically to the right target, not just because they are broadly reactive. This is a crucial step toward creating the next generation of highly selective and safer covalent medicines."