Designing Soluble PROTACs: Strategies and Preliminary Guidelines

• Published in: Journal of medicinal chemistry 2022-10, Vol.65 (19), p.12639-12649
• Main Authors: García Jiménez, Diego, Rossi Sebastiano, Matteo, Vallaro, Maura, Mileo, Valentina, Pizzirani, Daniela, Moretti, Elisa, Ermondi, Giuseppe, Caron, Giulia
• Format: Article
• Language: English
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.2c00201

Solubility optimization is a crucial step to obtaining oral PROTACs. Here we measured the thermodynamic solubilities (log S) of 21 commercial PROTACs. Next, we measured BRlogD and log k w IAM (lipophilicity), EPSA, and Δ log k w IAM (polarity) and showed that lipophilicity plays a major role in governing log S, but a contribution of polarity cannot be neglected. Two-/three-dimensional descriptors calculated on conformers arising from conformational sampling and steered molecular dynamics failed in modeling solubility. Infographic tools were used to identify a privileged region of soluble PROTACs in a chemical space defined by BRlogD, log k w IAM and topological polar surface area, while machine learning provided a log S classification model. Finally, for three pairs of PROTACs we measured the solubility, lipophilicity, and polarity of the building blocks and identified the limits of estimating PROTAC solubility from the synthetic components. Overall, this paper provides promising guidelines for optimizing PROTAC solubility in early drug discovery programs.