Pushing the boundaries of virtual screening scale of combinatorial spaces with the V-SYNTHES approach

Abstract

Computational screening of giga-scale chemical spaces opens a cost-effective path to high-quality hit identification, providing entry points for drug discovery. As these on-demand spaces grow and successful applications multiply, rigorous blind benchmarks like CACHE Challenges provide important performance metrics for computational tools. Here, we report the first application of the V-SYNTHES2 synthon-based screening approach to the 173-billion-compound Enamine xREAL Space, a 16-fold expansion beyond its previous benchmarks, demonstrating near-linear computational scaling with only a 10–15% increase in cost relative to the 11-billion-compound REAL Space. We applied this workflow in CACHE Challenge #2, targeting the RNA-binding site of NSP13 (SARS-CoV-2), and CACHE Challenge #4, targeting the tyrosine kinase-binding domain of CBLB, both pockets lacking established pharmacology and representing extreme hit-finding challenges. Under blinded, independently validated conditions, V-SYNTHES2 ranked among the top-performing submissions: the 8% hit rate for NSP13 exceeded the field average of 2.3% and placed the approach among the top three workflows, while for CBLB, one compound meeting predefined hit criteria was identified. These results demonstrate that V-SYNTHES2 maintains robust performance at giga-scale on ligand-depleted targets, precisely the conditions where data-driven approaches would face fundamental limitations, and establish a quantitative performance baseline for synthon-based screening of hundred-billion-compound chemical spaces.