Design in the dark – REFiL sheds light on fragment-based drug discovery

The ARC CFBD aims to advance the techniques and workflows of fragment-based drug design to establish new avenues for drug discovery. Our team have used our novel workflow called REFiL (Rapid Elaboration of Fragments into Leads) to demonstrate accelerated development of leads for drug discovery. This new method has the potential to produce a drastic reduction in cost for R&D, as well as expedite identification of potential drug leads.

Fragment-Based Drug Discovery (FBDD) is an established field of study where small drug building blocks of less than 20 non-hydrogen atoms (i.e. fragments) form the basis for lead-like compounds. Fragment-based leads are superior candidates for progressing through to drug development because they offer opportunities to incorporate better physical properties and, therefore, tackles the issue of late stage attrition that can occur in traditional drug discovery pipelines.

Despite these advantages, FBDD is not without its drawbacks. Elaboration of fragments into potent leads typically relies on structural data, usually in the form of X-ray crystallography, which is a costly bottleneck and limits the type of protein targets to those that readily crystallise. Generation of various elaborated compounds to test for potency is also inherently expensive and time-consuming – rendered more laborious by the need for compound purification. Unfortunately, it is often the case that these elaborated compounds achieve meagre affinity gains that fail to justify the cost of consumables for synthesis or purification.

Our REFiL workflow aimed to address these hurdles. First, our program of analogue design leverages chemical diversity in lieu of structural data to guide compound generation. Second, this chemistry is performed in parallel, on microscale and in a plate-based format using curated reagent libraries, making this highly cost- and time-efficient. These elaborated libraries can then be assessed unpurified using Off-Rate Screening by SPR. This ability to generate huge amounts of chemical matter which could be assessed unpurified drastically expedited this traditionally laborious process. The workflow boasts an impressive 100-fold affinity improvement in the space of under a year to achieve lead-like compounds.

Published on ChemRxiv, the team applied the REFiL workflow to develop lead-like compounds for the extra terminal domain of bromodomain-3 (BRD3-ET), a target for cancer therapeutics. Bromodomain containing proteins are key regulators of transcription in the cell cycle, and the oncological potential of these proteins is well established.

The application of REFiL to BRD-3ET led to three promising analogues for further development into lead-like compounds. On a target specific level, this represents a huge step in the fields of oncology and epigenetics as the role of the extra terminal domain is poorly elucidated. Designing lead-like compounds for BRD-3ET will help illuminate the holistic function of this protein in transcriptional activity.

The impact of this workflow has widespread application potential throughout the pharmaceutical industry. It could see a reduction in R&D costs from failed early stage candidates. More topically, the cheap and expedited nature of lead generation by REFiL is sorely needed in tackling COVID-19 and other poorly understood diseases. We stand to greatly fine-tune our understanding of disease with the generalised application of this workflow.

Rapid elaboration of fragments into leads applied to Bromodomain-3 extra terminal domain
Adams, L. A.; Wilkinson-White, L. E.; Gunzburg, M. J.; Headey, S. J.; Scanlon, M. J.; Capuano, B.; Mackay, J. P.; Doak, B. C.

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ARC Centre for Fragment-Based Design