
==== Front
bioRxiv
BIORXIV
bioRxiv
Cold Spring Harbor Laboratory

10.1101/2024.03.05.583611
preprint
3
Article
Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1
De-la-Torre Pedro http://orcid.org/0000-0002-2434-3345

Martínez-García Claudia http://orcid.org/0009-0002-0266-3310

Gratias Paul http://orcid.org/0000-0002-5172-2316

Mun Matthew http://orcid.org/0000-0002-5471-4813

Santana Paula http://orcid.org/0000-0002-5742-4926

Akyuz Nurunisa http://orcid.org/0000-0002-6340-1915

González Wendy http://orcid.org/0000-0002-7535-6883

Indzhykulian Artur A. http://orcid.org/0000-0002-2076-6818

Ramírez David http://orcid.org/0000-0003-0002-1189

07 5 2024
2024.03.05.583611http://biorxiv.org/lookup/doi/10.1101/2024.03.05.583611
nihpp-2024.03.05.583611.pdf
Abstract

Our ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. Despite extensive research on otoprotective compounds targeting MET channels, our understanding of how small molecule modulators interact with these channels remains limited, hampering the discovery of novel compounds. Here, we propose a structure-based screening approach, integrating 3D-pharmacophore modeling, molecular simulations, and experimental validation. Our pipeline successfully identified several novel compounds and FDA-approved drugs that reduced dye uptake in cultured cochlear explants, indicating MET modulation activity. Molecular docking and free-energy estimations for binding allowed us to identify three potential drug binding sites within the channel pore, phospholipids, and key amino acids involved in modulator interactions. We also identified shared ligand-binding features between TMC and structurally related TMEM16 protein families, providing novel insights into their distinct inhibition, while potentially guiding the rational design of MET-channel-specific modulators. Our pipeline offers a broad application to discover small molecule modulators for a wide spectrum of mechanosensitive ion channels.
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pmc
