Syndirella: synthesis-directed fragment elaboration enables extensive and cost-effective binding site exploration beyond catalog compounds

Abstract

(Synthesis Directed Elaborations), which presents a candidate elaboration space around input fragment-derived scaffolds, constrained to HT-compatible reactions and catalog reactants, for cost-effective sampling of many scaffolds' elaborations in a single experimental cycle. Applied to three viral protein targets, Syndirella designs demonstrated pharmacophore diversity, recapitulating known fragment interactions, identifying novel functionally relevant ones, and accessing chemical space absent from commercial catalogs. A companion paper details validation on a calcium-binding protein, yielding crystallographic structures and measurable binding, with in-house synthesis achieving a 71% cost reduction over catalog purchasing, labor and consumables included. Reactant rather than product procurement gives potentially 2.5 times as many accessible compounds and higher interaction productivity for the same budget. Syndirella is most impactful for structure-enabled campaigns with fragment-bound crystal structures, robust HT chemistry, and assays compatible with crude reaction mixtures, and is available at https://github.com/oxpig/syndirella.