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bioRxiv · 10.1101/2025.05.13.653789

TRPM8 protein dynamics correlates with ligand structure and cellular function

Mebrat, M. D.·Luu, D. D.·Hilton, J. K.·Kim, M.·Parrott, K.·Cherry, B. R.·Levitus, M.·Journigan, V. B.·Van Horn, W. D.
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Abstract

Protein dynamics have emerged as a key feature associated with function in various systems. Here, NMR-based studies coupled with computational cheminformatics and cellular function are leveraged to identify a relationship between the human cold and menthol receptor TRPM8 dynamics, chemical structure, and cellular potency. TRPM8 is a validated target for a variety of pain indications but generally has been clinically limited by on-target side effects impacting thermosensing and thermoregulation. This study shows that cheminformatic analysis of a TRPM8 regulating small molecule ligand library correlates with cellular function. Electrophysiology studies further validate the relationship and show a correlation between chemical structure and functional features such as compound potency. Solution NMR studies of the TRPM8 voltage sensing-like domain, which houses the canonical menthol ligand binding site, show that ligand binding conformationally selects NMR-detected TRPM8 dynamics in a manner that quantitatively correlates with chemical structure. The relationship between chemical structure and protein dynamics can be used predictively, where a chemical structure is predictive of dynamics in a latent reduced dimensionality space. Moreover, the robustness of the conformational selection of the dynamic ensemble is evaluated by varying related and divergent chemotypes, signal-to-noise sensitivity, and sample bias. Taken together, this study identifies that protein dynamics can serve as a quantifiable bridge between chemical structure and cellular function, which has implications for drug discovery in difficult systems.

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Mebrat, M. D., Luu, D. D., Hilton, J. K., Kim, M., Parrott, K., Cherry, B. R., Levitus, M., Journigan, V. B., Van Horn, W. D.. 2025-05-15. TRPM8 protein dynamics correlates with ligand structure and cellular function. https://doi.org/10.1101/2025.05.13.653789

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