Fragment expansion with NUDELs - poised DNA-encoded libraries

Abstract

Optimisation of the affinity of lead compounds is a critical challenge in the identification of drug candidates and chemical probes. Fragment-based drug discovery has become established as one of the methods of choice for drug discovery starting with small, low affinity compounds. Due to their low affinity, evolution of fragments to desirable levels of affinity is often a key challenge. The accepted best method for increasing the potency of fragments is by iterative fragment growing, which can be very time consuming. Here, we introduce a paradigm for fragment optimisation using poised DNA-encoded chemical libraries (DELs). The synthesis of a poised DEL allows the coupling of any active fragment for a target protein, allowing rapid discovery of potent ligands. This is illustrated for bromodomain-containing protein 4 (BRD4), in which a weakly binding fragment was coupled to a 42-member poised DEL via Suzuki-Miyaura cross coupling resulting in the identification of an inhibitor with nanomolar affinity in a single step. The potency of the compound was shown to arise from the synergistic combination of substructures, which would have been very difficult to discover by any other method and was rationalised by X-ray crystallography. The compound showed attractive lead-like properties suitable for further optimisation and demonstrated BRD4-dependent cellular pharmacology. This work demonstrates the power of poised DELs to rapidly optimise fragments, representing an attractive generic approach to drug discovery.

Fragment-based drug discovery campaigns guided by native mass spectrometry

“…123 Furthermore, recent nMS experiment are extending beyond recombinant purified samples towards biomolecules extracted from their native, cellular settings and we envision that this will be extended towards analysis in situ in the native cellular setting including on a global proteome scale, allowing the identification of endogenous ligands/cofactors and/or the deorphanisation of drug targets. [124][125][126][127][128][129][130][131][132] FBDD has also integrated with new methodologies such as DNA-encoded libraries, [133][134][135] fluorine observed NMR screening methods 136,137 and mini-frag libraries screened by X-ray crystallography. 138,139 It will be interesting to see if nMS can be applied in parallel with these emerging FBDD-related technologies.…”