Predictive Minisci late stage functionalization with transfer learning

Emma King-Smith, Felix A. Faber, Usa Reilly, Anton V. Sinitskiy, Qingyi Yang, Bo Liu, Dennis Hyek and Alpha A. Lee ()
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Emma King-Smith: University of Cambridge
Felix A. Faber: University of Cambridge
Usa Reilly: Pfizer Worldwide Research
Anton V. Sinitskiy: Pfizer Worldwide Research
Qingyi Yang: Pfizer Worldwide Research
Bo Liu: Spectrix Analytic Services, LLC.
Dennis Hyek: Spectrix Analytic Services, LLC.
Alpha A. Lee: University of Cambridge

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Structural diversification of lead molecules is a key component of drug discovery to explore chemical space. Late-stage functionalizations (LSFs) are versatile methodologies capable of installing functional handles on richly decorated intermediates to deliver numerous diverse products in a single reaction. Predicting the regioselectivity of LSF is still an open challenge in the field. Numerous efforts from chemoinformatics and machine learning (ML) groups have made strides in this area. However, it is arduous to isolate and characterize the multitude of LSF products generated, limiting available data and hindering pure ML approaches. We report the development of an approach that combines a message passing neural network and 13C NMR-based transfer learning to predict the atom-wise probabilities of functionalization for Minisci and P450-based functionalizations. We validated our model both retrospectively and with a series of prospective experiments, showing that it accurately predicts the outcomes of Minisci-type and P450 transformations and outperforms the well-established Fukui-based reactivity indices and other machine learning reactivity-based algorithms.

Date: 2024
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DOI: 10.1038/s41467-023-42145-1

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