Expanding the scope of a catalogue search to bioisosteric fragment merges using a graph database approach

The efficiency of fragment-to-lead optimization could be improved by automated workflows for the design of follow-up compounds. Pipelines that are able to fully exploit the interaction opportunities identified from the crystal structures of bound fragments would greatly aid this goal. To do so, these pipelines need to require minimal intervention from the user and be computationally efficient. In this work, we describe an updated version of our fragment merging methodology, which provides several feature enhancements, primarily by expanding the chemical space searched, allowing the identification of more diverse follow-up compounds, thus maximizing the chances of finding successful hits. While the original method focused on finding ‘perfect merges’, meaning compounds that directly incorporate substructures from the original fragments, here we expand the search to what we term ‘bioisosteric merges’, involving the incorporation of substructures that replicate the pharmacophoric features of the original fragments but may not be exactly identical. Unlike existing pharmacophore and shape-based descriptors used for virtual screening, this approach combines the search for these properties with the incorporation of novelty, which is necessary when searching for ways to link together distinct substructures. Compared with ‘perfect merging’, our new approach is able to find compounds that are directly informed by structures within the original fragments but are more chemically diverse. We contrast our approach with the use of a pharmacophore-constrained docking pipeline, run in parallel for select fragment pairs, and show that our method requires between 1.1-45.9-fold less computational time for conformer generation per merging ‘hit’ identified, referring to compounds that show a favourable degree of shape and colour overlap and recapitulation of original fragment interactions. Overall, our results show that our method has potential to be used to generate designs inspired by all fragments within a given pocket.