Expanding the biological diversity of chemical probes to ligand the 'dark' proteome

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Identifying and exploring new biologically-relevant chemical space is a major challenge, central to both chemical biology and medicinal chemistry. Access to high quality chemical probes dramatically influences the scope of experimentally-investigated biomedical science and is crucial for validating novel targets. Small molecule drugs continue to dominate our collective ability to treat disease, yet identifying new biologically-relevant chemical space is hampered by the dominance of a narrow reaction toolkit. With the advent of reactive fragments, and the powerful companion technology of chemical proteomics, we now envision the prospect of mapping biological coverage systematically in a native cellular context. In this project, we will develop connective reactions that enable the one-pot, plate-based synthesis of diverse sets of distinctive reactive fragments (RFs). The synthetic approach will contrast starkly with the typical multi-step synthesis of fully-functionalised probes; as well as the simple amide coupling chemistry that generally drives direct-to-biology experimentation. To broaden explorable chemical space, prioritised chemistries lie outside the reaction toolkit that currently dominates discovery. Furthermore, to complement existing cysteine-directed RF sets, we will deliberately exploit electrophilic "warheads" with distinctive (particularly lysine-directed) reactivity. Having established this capability, we will: (a) investigate extension of direct-to-biology experimentation beyond amide coupling chemistry; and (b) execute biological mapping of the distinctive RFs using chemical proteomics and machine learning. We will thus demonstrate that diverse RF sets, accessible via the new chemistries, can enable liganding of the "dark" proteome.