SpaceExpander: Automated Drafting and Evaluation of Markush Claims for Chemical Space Expansion

Abstract Drafting Markush claims for chemical patents remains difficult because manual claim writing is slow, error prone, and often fails to capture related chemical space in a systematic manner. We developed SpaceExpander, a computational method that converts disclosed compounds into generalized Markush claims by extracting core scaffolds, defining variable positions, decomposing complex substituents, and expanding substituent space through fragment matching. We evaluated the method on 24 publicly available chemical patents and compared its performance with IntelliPatent. SpaceExpander achieved a mean atom level scaffold accuracy of 0.92 and exactly recovered the reference scaffold in 19 of 24 patents. By contrast, IntelliPatent could process only 2 patents from the same set, indicating more limited applicability to structurally diverse cases. We further examined practical claim coverage in a case study based on the Osimertinib patent. Using representative disclosed compounds as input, SpaceExpander drafted a Markush claim that covered 5 of 7 additional approved third-generation EGFR inhibitors beyond Osimertinib. These results show that SpaceExpander is a validated method for automated Markush claim drafting and chemical space expansion. Competing Interest Statement The authors have declared no competing interest.