FragmentRetro: A Quadratic Retrosynthetic Method Based on Fragmentation Algorithms

Retrosynthesis, the process of deconstructing a target molecule into simpler precursors, is crucial for computer-aided synthesis planning (CASP). Widely adopted tree-search methods often suffer from exponential computational complexity. In this work, we introduce FragmentRetro, a novel retrosynthetic method that leverages fragmentation algorithms, specifically BRICS and r-BRICS, combined with stock-aware exploration and pattern fingerprint screening to achieve quadratic complexity. FragmentRetro recursively combines molecular fragments and verifies their presence in a building block set, providing sets of fragment combinations as retrosynthetic solutions. We present the first formal computational analysis of retrosynthetic methods, showing that tree search exhibits exponential complexity <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>O</mml:mi><mml:mrow><mml:mo>(</mml:mo><mml:msup><mml:mi>b</mml:mi><mml:mi>h</mml:mi></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math>, DirectMultiStep scales as <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>O</mml:mi><mml:mrow><mml:mo>(</mml:mo><mml:msup><mml:mi>h</mml:mi><mml:mn>6</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math>, and FragmentRetro achieves <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>O</mml:mi><mml:mrow><mml:mo>(</mml:mo><mml:msup><mml:mi>h</mml:mi><mml:mn>2</mml:mn></mml:msup><mml:mo>)</mml:mo></mml:mrow></mml:math>, where <i>h</i> represents the number of heavy atoms in the target molecule and <i>b</i> is the branching factor for tree search. Evaluations on PaRoutes, USPTO-190, and natural products demonstrate that FragmentRetro achieves high solved rates with competitive runtime, including cases where tree search fails. The method benefits from fingerprint screening, which significantly reduces substructure matching complexity. While FragmentRetro focuses on efficiently identifying fragment-based solutions rather than full reaction pathways, its computational advantages and ability to generate strategic starting candidates establish it as a powerful foundational component for scalable and automated synthesis planning.