Protein-directed dynamic combinatorial chemistry
Bhat, Venugopal T.
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Dynamic combinatorial chemistry (DCC) is a novel approach to medicinal chemistry which integrates the synthesis and screening of small molecule libraries into a single step. The concept uses reversible chemical reactions to present a dynamic library of candidate structures to a template which selects and removes the best binder from equilibrium. Using this evolutionary process with a biopolymer template, such as a protein, leads to the protein directing the synthesis of its own best ligand. Biological DCC applications are extremely challenging since the thermodynamic criterion of reversibility has to be met under physiological conditions to ensure stability of the biomolecular template. The list of reversible reactions satisfying these stringent criteria is limited and is a major constraint on achieving both reaction and structural diversity in adaptive dynamic libraries. This thesis reports the development of a catalysed version of acylhydrazone dynamic libraries which are truly adaptive under protein-friendly conditions. In the presence of aniline as a trans-imination catalyst, acylhydrazone dynamic combinatorial libraries equilibrate rapidly at pH 6.2 and are switched off by an increase in pH. We designed acylhydrazone libraries targeting the enzyme superfamily Glutathione-S-Transferase (GST) using a scaffold aldehyde, 4-chloro-3-nitrobenzaldehyde, which is structurally related to a known GST substrate chlorodinitrobenzene. On interfacing these dynamic libraries with two different GST enzymes (SjGST from the helminth worm Schistosoma japonicum and hGSTP1-1, a human isoform and an important oncology drug target) we observed isoformselective amplification effects with two different acylhydrazones selected by the proteins. To explore the potential of anchoring in our DCC methodology we conjugated the endogenous GST ligand, glutathione (GSH) onto the scaffold chloronitrobenzaldehyde. The GSH recognition motif acts as an anchor and allows us to explore the hydrophobic binding site of the enzyme in a fragment-based approach. The presence of the glutathione moiety led to increased solubility of the library members and a DCC experiment with the enzymes led to the selection of conjugate hydrazones with significant binding ability. Multi-level dynamic libraries use multiple exchange processes in the same system to increase their accessible structural diversity. These exchange reactions may be orthogonal, where the different chemistries can be activated or deactivated independently of each other, or simultaneous, where all the processes are dynamic and crossover under the same conditions. Together, these interacting molecular networks provide an exciting experimental approach to the emerging field of systems chemistry. We demonstrate that two reversible reactions, conjugate addition of thiols to enones and hydrazone formation, are fully compatible and orthogonal to one another in a single dynamic library. Hydrazone exchange takes place at acidic pH, while conjugate addition operates at basic pH. Simple pH change can be used to switch between each process and establish two channels of reactivity.