Advancing Biochemical Molecule Registration, Representation and Search for New Drug Modalities
Kevin Pinto-Gil, Leonardo De Maria, Anaïs F. M. Noisier, Susan Leung, Arthur Garon, Andrey I. Frolov, Sunay V. Chankeshwara, Mattias Bood, Lars Brive, Nicholas P. Tomkinson, Daniel Álvarez-García, Johan Broddefalk, K. Phin Chooi, Abdul Ingar, Hannah L. Bolt, Gian Marco Ghiandoni · Journal of Chemical Information and Modeling · 2026
The pharmaceutical industry's shift toward new drug modalities, including therapeutic peptides, modified oligonucleotides, and antibody-drug conjugates, has exposed fundamental gaps in cheminformatics infrastructure. Unlike small molecules, which benefit from mature representation standards and reliable data exchange, new modalities lack robust and interoperable systems capable of capturing their structural and chemical complexity. Drawing on our experience at AstraZeneca, we examine these challenges across peptides, oligonucleotides, and ADCs, focusing on the limitations of current approaches, particularly HELM. We show that these limitations arise from both technical constraints, as new modalities exceed the scope of purely atomistic or sequence-based representations, and organizational gaps, including unresolved standardization and governance. We argue that local solutions exacerbate fragmentation, and that vendor- and community-driven standards, open implementations, and stronger governance are required to enable standardized and interoperable chemical information systems for next-generation therapeutics.