Briana Sobecks

All Publications

• Mechanism of Gating and Isoform-Specific Inhibition in Renal CLC Chloride Channels. bioRxiv : the preprint server for biology Chien, C. T., Sobecks, B. L., Powers, A. S., Kreiter, J., Das, A., Barry, C. N., Chen, M., Hinman, A., Petrakian, C. F., Trifkovic, N., Williams, B., Wood, C. A., Xu, M., Dror, R. O., Chiu, W., Maduke, M. 2026

  Abstract

  Hyponatremia is a prevalent disorder marked by excess water retention and substantial morbidity, motivating interest in the CLC-Ka chloride channel as a therapeutic target. Selectively inhibiting CLC-Ka without affecting the closely related CLC-Kb is essential for preventing serious side effects. However, developing isoform-selective inhibitors has been challenging because most small molecules do not distinguish between CLC-Ka and CLC-Kb, and the basis for selectivity in the few known exceptions remains unclear. The small molecule BIM1 preferentially inhibits CLC-Ka over CLC-Kb, providing an opportunity to dissect isoform-specific pharmacology. To investigate this mechanism, we determined cryo-EM structures of BIM1 and BIM15, a related nonselective analog, bound to a CLC-K variant engineered to match the human CLC-Ka binding pocket. Structural and computational analyses reveal that inhibition and isoform selectivity are anchored by interactions with a conserved lysine, with surrounding binding-site residues subtly tuning the local electrostatic environment to promote or disfavor these contacts. These analyses further identify a dynamic extracellular loop that intermittently occludes the access pathway, indicating its role as a gate for ions and inhibitors. BIM15 engages this gating loop more extensively than BIM1, suggesting that differential loop engagement contributes to inhibitor selectivity. To probe how gating reshapes this region, we solved the structure in the presence of Ca2+, which favors channel opening, and found the gating loop ordered and withdrawn from the pathway. Together, these findings elucidate how CLC-K channels gate and how subtle binding-site differences and loop dynamics shape isoform-specific drug binding, providing a foundation for designing next-generation CLC-Ka inhibitors.

  View details for DOI 10.64898/2026.02.17.706469

  View details for PubMedID 41756880

  View details for PubMedCentralID PMC12934935

• Molecular mechanism of exchange coupling in CLC chloride/proton antiporters. Nature communications Aydin, D., Chien, C. T., Kreiter, J., Nava, A. R., Portasikova, J. M., Fojtik, L., Sobecks, B. L., Mosquera, C., Man, P., Dror, R. O., Chiu, W., Maduke, M. 2026

  Abstract

  The ubiquitous CLC membrane transporters are unique in their ability to exchange anions for cations. Despite extensive study, there is no mechanistic model that fully explains their 2:1 Cl‒/H+ stoichiometric exchange mechanism. Here, we provide such a model. Using differential hydrogen-deuterium exchange mass spectrometry, cryo-EM structure determination, and molecular dynamics simulations, we uncovered conformational dynamics in CLC-ec1, a bacterial CLC homolog that has served as a paradigm for this family of transporters. Simulations based on a cryo-EM structure at pH 3 revealed critical steps in the transport mechanism, including release of Cl‒ ions to the extracellular side, opening of the inner gate, and water wires that facilitate H+ transport. Surprisingly, these water wires occurred independently of Cl‒ binding, prompting us to reassess the relationship between Cl‒ binding and Cl‒/H+ coupling. Using isothermal titration calorimetry and quantitative flux assays on mutants with reduced Cl‒ binding affinity, we conclude that, while Cl‒ binding is necessary for coupling, even weak binding can support Cl‒/H+ coupling. By integrating our findings with existing literature, we establish a complete and efficient CLC 2:1 Cl‒/H+ exchange mechanism.

  View details for DOI 10.1038/s41467-025-68098-1

  View details for PubMedID 41507156

• Structure and mechanism of the mitochondrial calcium transporter NCLX. Nature Fan, M., Tsai, C. W., Zhang, J., Zhang, J., Krishnan, A. R., Liu, T. Y., Huang, Y. L., Aydin, D., Du, S., Sobecks, B. L., Rodriguez, M. X., Reiter, A. H., Bertozzi, C. R., Dror, R. O., Tsai, M. F., Feng, L. 2025

  Abstract

  As a key mitochondrial Ca2+ transporter, NCLX regulates intracellular Ca2+ signalling and vital mitochondrial processes1-3. The importance of NCLX in cardiac and nervous-system physiology is reflected by acute heart failure and neurodegenerative disorders caused by its malfunction4-9. Despite substantial advances in the field, the transport mechanisms of NCLX remain unclear. Here we report the cryo-electron microscopy structures of NCLX, revealing its architecture, assembly, major conformational states and a previously undescribed mechanism for alternating access. Functional analyses further reveal an unexpected transport function of NCLX as a H+/Ca2+ exchanger, rather than as a Na+/Ca2+ exchanger as widely believed1. These findings provide critical insights into mitochondrial Ca2+ homeostasis and signalling, offering clues for developing therapies to treat diseases related to abnormal mitochondrial Ca2+.

  View details for DOI 10.1038/s41586-025-09491-0

  View details for PubMedID 40931067

  View details for PubMedCentralID 5731245

• A cryptic pocket in CB1 drives peripheral and functional selectivity NATURE Rangari, V., O'Brien, E. S., Powers, A. S., Slivicki, R. A., Bertels, Z., Appourchaux, K., Aydin, D., Ramos-Gonzalez, N., Mwirigi, J., Lin, L., Mangutov, E., Sobecks, B. L., Awad-Agbaria, Y., Uphade, M. B., Aguilar, J., Peddada, T., Shiimura, Y., Huang, X., Folarin-Hines, J., Payne, M., Kalathil, A., Varga, B. R., Kobilka, B. K., Pradhan, A. A., Cameron, M. D., Kumar, K., Dror, R. O., Gereau, R. W., Majumdar, S. 2025

  Abstract

  The current opioid overdose epidemic highlights the urgent need to develop safer and more effective treatments for chronic pain1. Cannabinoid receptor type 1 (CB1) is a promising non-opioid target for pain relief, but its clinical use has been limited by centrally mediated psychoactivity and tolerance. We overcame both issues by designing peripherally restricted CB1 agonists that minimize arrestin recruitment. We achieved these goals by computationally designing positively charged derivatives of the potent CB1 agonist MDMB-Fubinaca2. We designed these ligands to occupy a cryptic pocket identified through molecular dynamics simulations-an extended binding pocket that opens rarely and leads to the conserved signalling residue D2.50 (ref. 3). We used structure determination, pharmacological assays and molecular dynamics simulations to verify the binding modes of these ligands and to determine the molecular mechanism by which they achieve this dampening of arrestin recruitment. Our lead ligand, VIP36, is highly peripherally restricted and demonstrates notable efficacy in three mouse pain models, with 100-fold dose separation between analgesic efficacy and centrally mediated side effects. VIP36 exerts analgesic efficacy through peripheral CB1 receptors and shows limited analgesic tolerance. These results show how targeting a cryptic pocket in a G-protein-coupled receptor can lead to enhanced peripheral selectivity, biased signalling, desired in vivo pharmacology and reduced adverse effects. This has substantial implications for chronic pain treatment but could also revolutionize the design of drugs targeting other G-protein-coupled receptors.

  View details for DOI 10.1038/s41586-025-08618-7

  View details for Web of Science ID 001437495800001

  View details for PubMedID 40044849

  View details for PubMedCentralID 8154745

• Signaling Modulation Mediated by Ligand Water Interactions with the Sodium Site at μOR. ACS central science Ople, R. S., Ramos-Gonzalez, N., Li, Q., Sobecks, B. L., Aydin, D., Powers, A. S., Faouzi, A., Polacco, B. J., Bernhard, S. M., Appourchaux, K., Sribhashyam, S., Eans, S. O., Tsai, B. A., Dror, R. O., Varga, B. R., Wang, H., Hüttenhain, R., McLaughlin, J. P., Majumdar, S. 2024; 10 (8): 1490-1503

  Abstract

  The mu opioid receptor (μOR) is a target for clinically used analgesics. However, adverse effects, such as respiratory depression and physical dependence, necessitate the development of alternative treatments. Recently we reported a novel strategy to design functionally selective opioids by targeting the sodium binding allosteric site in μOR with a supraspinally active analgesic named C6guano. Presently, to improve systemic activity of this ligand, we used structure-based design, identifying a new ligand named RO76 where the flexible alkyl linker and polar guanidine guano group is swapped with a benzyl alcohol, and the sodium site is targeted indirectly through waters. A cryoEM structure of RO76 bound to the μOR-Gi complex confirmed that RO76 interacts with the sodium site residues through a water molecule, unlike C6guano which engages the sodium site directly. Signaling assays coupled with APEX based proximity labeling show binding in the sodium pocket modulates receptor efficacy and trafficking. In mice, RO76 was systemically active in tail withdrawal assays and showed reduced liabilities compared to those of morphine. In summary, we show that targeting water molecules in the sodium binding pocket may be an avenue to modulate signaling properties of opioids, and which may potentially be extended to other G-protein coupled receptors where this site is conserved.

  View details for DOI 10.1021/acscentsci.4c00525

  View details for PubMedID 39220695

  View details for PubMedCentralID PMC11363324

• Dual Role of Strigolactone Signaling Partner in Decreasing Substrate Hydrolysis Journal of Physical Chemistry B Sobecks, B. L., Chen, J., Shukla, D. 2022

  View details for DOI 10.1021/acs.jpcb.1c10663