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Emigh Cortez AM, DeMarco KR, Furutani K, Bekker S, Sack JT, Wulff H, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural modeling of hERG channel-drug interactions using Rosetta. Front Pharmacol 2023; 14:1244166. [PMID: 38035013 PMCID: PMC10682396 DOI: 10.3389/fphar.2023.1244166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
The human ether-a-go-go-related gene (hERG) not only encodes a potassium-selective voltage-gated ion channel essential for normal electrical activity in the heart but is also a major drug anti-target. Genetic hERG mutations and blockage of the channel pore by drugs can cause long QT syndrome, which predisposes individuals to potentially deadly arrhythmias. However, not all hERG-blocking drugs are proarrhythmic, and their differential affinities to discrete channel conformational states have been suggested to contribute to arrhythmogenicity. We used Rosetta electron density refinement and homology modeling to build structural models of open-state hERG channel wild-type and mutant variants (Y652A, F656A, and Y652A/F656 A) and a closed-state wild-type channel based on cryo-electron microscopy structures of hERG and EAG1 channels. These models were used as protein targets for molecular docking of charged and neutral forms of amiodarone, nifekalant, dofetilide, d/l-sotalol, flecainide, and moxifloxacin. We selected these drugs based on their different arrhythmogenic potentials and abilities to facilitate hERG current. Our docking studies and clustering provided atomistic structural insights into state-dependent drug-channel interactions that play a key role in differentiating safe and harmful hERG blockers and can explain hERG channel facilitation through drug interactions with its open-state hydrophobic pockets.
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Affiliation(s)
- Aiyana M. Emigh Cortez
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kevin R. DeMarco
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kazuharu Furutani
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, Tokushima Bunri University, Tokushima, Japan
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- American River College, Sacramento, CA, United States
| | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
- Center for Precision Medicine and Data Sciences, University of California, Davis, Davis, CA, United States
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
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Ngo K, Rouen K, Dawson JRD, DeMarco K, Emigh Cortez AM, Maly J, Lopez Mateos D, Yarov-Yarovoy V, Clancy CE, Vorobyov IV. Computational assessment of molecular mechanisms underlying hERG K + channel conduction and affinity for drug binding. Biophys J 2023; 122:179a. [PMID: 36782843 DOI: 10.1016/j.bpj.2022.11.1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Khoa Ngo
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Kyle Rouen
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - John R D Dawson
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Kevin DeMarco
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Aiyana M Emigh Cortez
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Jan Maly
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Diego Lopez Mateos
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA; Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Igor V Vorobyov
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA; Department of Pharmacology, University of California Davis, Davis, CA, USA
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Ngo K, Rouen KC, Dawson JR, Emigh Cortez AM, Lopez Mateos D, Maly J, DeMarco K, Yarov-Yarovoy V, Vorobyov I, Clancy CE. Multi-Scale modeling of state-dependent drug binding to the hERG channel. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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