CRUSH—Cleavage Rules Using SMIRKS Heuristics: an enhanced molecular fragmentation algorithm

Abstract Molecular fragmentation methods are central to fragment-based discovery, virtual screening, and de novo molecular design, yet most existing approaches remain constrained by classical retrosynthetic rules that limit the scope and chemical space exploration beyond medicinal chemistry applications. Here we introduce CRUSH (Cleavage Rules Using SMIRKS Heuristics), an enhanced, chemistry-aware fragmentation algorithm that extends traditional retrosynthetic bond disconnection and building-block generation strategies to enable fine-grained and chemically meaningful molecular deconstruction. CRUSH adopts a flexible bond cleavage strategy in which a curated set of SMIRKS-based heuristics is applied exhaustively across all eligible bonds at each fragmentation step, enabling systematic exploration of multiple alternative disconnection pathways rather than committing to the first applicable retrosynthetic rule. Using a unified benchmarking framework across five chemically diverse datasets, including drug-like molecules, natural products, peptides, macrocycles, and alimentary compounds, we demonstrate that CRUSH consistently increases fragment yield and substantially expands chemical space coverage compared with the well-established methods. Notably, CRUSH-derived fragments access exclusive regions of chemical space that remain unexplored by existing approaches, a result that is consistent across both low- and high-resolution molecular fingerprint representations. Structurally, CRUSH generates smaller and less complex fragments, a profile particularly advantageous for fragment-based and diversity-driven workflows. Collectively, these results establish CRUSH as a robust and versatile molecular fragmentation framework that complements, and in exploratory contexts surpasses, current methods, providing a strong foundation for fragment-based chemoinformatics applications across multiple chemistry domains. As part of this work, implementation of the CRUSH fragmentation algorithm is made freely available at https://github.com/EdgL2/CRUSH . Scientific contribution This study introduces CRUSH, a chemistry-aware molecular fragmentation method that extends beyond traditional medicinal chemistry retrosynthetic rules to enable fine-grained and chemically meaningful bond disconnections. CRUSH consistently increases fragment yield and uniquely expands chemical space coverage across diverse datasets and molecular representations, generating smaller and less complex fragments well suited for fragment-based, exploratory, and de novo design workflows.