Developing and Discovering Covalent Inhibitors through Fragmentation-First Experimentation

Abstract Iterative chemical innovation plays an essential role in the study and treatment of disease. In an aging population and with antimicrobial resistance on the rise we could not be more dependent on state-of-the-art medicines to battle cancer and infectious disease. However, despite nearly two centuries of important progress in chemical synthesis the cycle time for discovering new medicines lies far behind the pace of evolutionarily acquired resistance. The existential threat posed by this lack of synthetic agility requires bold new strategies which contract the time for data collection and chemical optimization. The research described in this proposal leverages a conceptually novel framework which dramatically simplifies access to small molecules and the processes to impact prioritize their reactions with biomacromolecules. In fragmentation-first experimentation the fundamental fragmentation patterns which underlie chemical reagents define precise barcodes for scrutinizing the outputs of high-throughput chemical synthesis. In contrast to existing strategies which require per-product customized protocols, this approach connects chemical reaction analysis directly to the synthetic origin of a chemical product. The net effect is a dramatic reduction in opportunity cost associated with making new chemical matter and a concomitant contraction of the cycle time for new discoveries. The net effect is a shift in focus away from making molecules and toward finding new functions. Empowered by high- content access to chemical matter we will unify these approaches with methods to directly study the reactions of small molecules with proteins and bacteria ribosomes to identify more effective covalent inhibitors. Parallelized interrogation of biological targets will provide detailed structure interactivity data to iteratively inform molecular designs. A unifying feature of these approaches are that small molecules can be directly utilized to determine their biological activity without purification, thereby eliminating another slow step in the molecule making process. If successful, our proposed research program will dramatically shorten the timeline for developing reactive small organic molecules (covalent inhibitors) and reduce the material burden for exploring their structure reactivity relationships. Fundamental new characteristics in the design of reactive small molecules uncovered throughout the course of our investigations will contribute to our ability to innovate on the molecular scale.