The lysosomal ion channel TRPML1 plays a key role in autophagy, calcium signaling, and membrane trafficking, making it a compelling target for therapeutic development in lysosomal storage and neurodegenerative disorders.

A recent study from Astex Pharmaceuticals and collaborators showcases a robust high-throughput cryo-EM workflow developed for TRPML1, enabling detailed structural and functional analysis of this complex membrane protein.

To support functional interpretation, the compounds were also profiled using automated patch clamp electrophysiology (with the SyncroPatch 384) in a TRPML1V432P-expressing HEK293 cell line. The team observed clear structure-activity relationships (SAR), including:

• A shift from open to closed channel conformations depending on ligand class.

• Agonists consistently interacted with gating residues (such as F513 and Y507′), triggering conformational changes that open the ion channel. In contrast, antagonists bound in more diverse orientations and typically did not engage these gating residues, instead stabilizing the closed state.

• Interestingly, even closely related compounds (such as 4a and 5) adopted distinct binding modes. This highlights that small molecular changes can lead to entirely different orientations and interactions within the binding pocket, differences that may not be predictable from chemical structure alone. Without structural data, such divergent behavior could be missed, potentially misdirecting drug discovery efforts.

Notably, structures were obtained within one week of compound availability, enabling true design-structure-redesign cycles. These iterative cycles are the foundation of structure-based drug design (SBDD), an approach where medicinal chemists use high-resolution structural insights to design molecules, test their function, and refine designs based on new structures.

The study also highlights a key technical achievement: while membrane proteins are often difficult to study using X-ray crystallography (due to challenges in crystallization and their dynamic, flexible nature), cryo-EM overcomes these limitations. The authors demonstrate that cryo-EM can deliver the resolution, speed, and reliability needed to support real-time SBDD, even for traditionally challenging targets like TRPML1.

This study provides a powerful framework for the rational development of TRPML1 modulators and showcases how high-throughput cryo-EM can transform drug discovery for membrane proteins.

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Find the article here: High throughput cryo-EM provides structural understanding for modulators of the lysosomal ion channel TRPML1: Structure

Learn more about our Automated Patch Clamp platforms: Automated patch clamp – Nanion Technologies