Harnessing AlphaFold to reveal hERG channel conformational state secrets
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been the resolution of discrete conformational states of transmembrane ion channel proteins. An example is KV11...
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eLife Sciences Publications Ltd
2025-07-01
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| Online Access: | https://elifesciences.org/articles/104901 |
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| author | Khoa Ngo Pei-Chi Yang Vladimir Yarov-Yarovoy Colleen E Clancy Igor Vorobyov |
| author_facet | Khoa Ngo Pei-Chi Yang Vladimir Yarov-Yarovoy Colleen E Clancy Igor Vorobyov |
| author_sort | Khoa Ngo |
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| description | To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been the resolution of discrete conformational states of transmembrane ion channel proteins. An example is KV11.1 (hERG), comprising the primary cardiac repolarizing current, Ikr. hERG is a notorious drug anti-target against which all promising drugs are screened to determine potential for arrhythmia. Drug interactions with the hERG inactivated state are linked to elevated arrhythmia risk, and drugs may become trapped during channel closure. While prior studies have applied AlphaFold to predict alternative protein conformations, we show that the inclusion of carefully chosen structural templates can guide these predictions toward distinct functional states. This targeted modeling approach is validated through comparisons with experimental data, including proposed state-dependent structural features, drug interactions from molecular docking, and ion conduction properties from molecular dynamics simulations. Remarkably, AlphaFold not only predicts inactivation mechanisms of the hERG channel that prevent ion conduction but also uncovers novel molecular features explaining enhanced drug binding observed during inactivation, offering a deeper understanding of hERG channel function and pharmacology. Furthermore, leveraging AlphaFold-derived states enhances computational screening by significantly improving agreement with experimental drug affinities, an important advance for hERG as a key drug safety target where traditional single-state models miss critical state-dependent effects. By mapping protein residue interaction networks across closed, open, and inactivated states, we identified critical residues driving state transitions validated by prior mutagenesis studies. This innovative methodology sets a new benchmark for integrating deep learning-based protein structure prediction with experimental validation. It also offers a broadly applicable approach using AlphaFold to predict discrete protein conformations, reconcile disparate data, and uncover novel structure–function relationships, ultimately advancing drug safety screening and enabling the design of safer therapeutics. |
| format | Article |
| id | doaj-art-d2c933e8a1cc4dbf9d4a963ee6eaf225 |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | eLife Sciences Publications Ltd |
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| series | eLife |
| spelling | doaj-art-d2c933e8a1cc4dbf9d4a963ee6eaf2252025-08-20T03:25:12ZengeLife Sciences Publications LtdeLife2050-084X2025-07-011310.7554/eLife.104901Harnessing AlphaFold to reveal hERG channel conformational state secretsKhoa Ngo0https://orcid.org/0000-0002-7454-2924Pei-Chi Yang1https://orcid.org/0000-0002-5753-1131Vladimir Yarov-Yarovoy2https://orcid.org/0000-0002-2325-4834Colleen E Clancy3https://orcid.org/0000-0001-6849-4885Igor Vorobyov4https://orcid.org/0000-0002-4767-5297Center for Precision Medicine and Data Science, University of California, Davis, Davis, United States; Department of Physiology and Membrane Biology, University of California, Davis, Davis, United StatesCenter for Precision Medicine and Data Science, University of California, Davis, Davis, United States; Department of Physiology and Membrane Biology, University of California, Davis, Davis, United StatesCenter for Precision Medicine and Data Science, University of California, Davis, Davis, United States; Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States; Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, United StatesCenter for Precision Medicine and Data Science, University of California, Davis, Davis, United States; Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States; Department of Pharmacology, University of California, Davis, Davis, United StatesDepartment of Physiology and Membrane Biology, University of California, Davis, Davis, United States; Department of Pharmacology, University of California, Davis, Davis, United StatesTo design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been the resolution of discrete conformational states of transmembrane ion channel proteins. An example is KV11.1 (hERG), comprising the primary cardiac repolarizing current, Ikr. hERG is a notorious drug anti-target against which all promising drugs are screened to determine potential for arrhythmia. Drug interactions with the hERG inactivated state are linked to elevated arrhythmia risk, and drugs may become trapped during channel closure. While prior studies have applied AlphaFold to predict alternative protein conformations, we show that the inclusion of carefully chosen structural templates can guide these predictions toward distinct functional states. This targeted modeling approach is validated through comparisons with experimental data, including proposed state-dependent structural features, drug interactions from molecular docking, and ion conduction properties from molecular dynamics simulations. Remarkably, AlphaFold not only predicts inactivation mechanisms of the hERG channel that prevent ion conduction but also uncovers novel molecular features explaining enhanced drug binding observed during inactivation, offering a deeper understanding of hERG channel function and pharmacology. Furthermore, leveraging AlphaFold-derived states enhances computational screening by significantly improving agreement with experimental drug affinities, an important advance for hERG as a key drug safety target where traditional single-state models miss critical state-dependent effects. By mapping protein residue interaction networks across closed, open, and inactivated states, we identified critical residues driving state transitions validated by prior mutagenesis studies. This innovative methodology sets a new benchmark for integrating deep learning-based protein structure prediction with experimental validation. It also offers a broadly applicable approach using AlphaFold to predict discrete protein conformations, reconcile disparate data, and uncover novel structure–function relationships, ultimately advancing drug safety screening and enabling the design of safer therapeutics.https://elifesciences.org/articles/104901voltage-gated potassium channelhERGAlphaFoldmolecular dockingmolecular dynamics simulationarrhythmia |
| spellingShingle | Khoa Ngo Pei-Chi Yang Vladimir Yarov-Yarovoy Colleen E Clancy Igor Vorobyov Harnessing AlphaFold to reveal hERG channel conformational state secrets eLife voltage-gated potassium channel hERG AlphaFold molecular docking molecular dynamics simulation arrhythmia |
| title | Harnessing AlphaFold to reveal hERG channel conformational state secrets |
| title_full | Harnessing AlphaFold to reveal hERG channel conformational state secrets |
| title_fullStr | Harnessing AlphaFold to reveal hERG channel conformational state secrets |
| title_full_unstemmed | Harnessing AlphaFold to reveal hERG channel conformational state secrets |
| title_short | Harnessing AlphaFold to reveal hERG channel conformational state secrets |
| title_sort | harnessing alphafold to reveal herg channel conformational state secrets |
| topic | voltage-gated potassium channel hERG AlphaFold molecular docking molecular dynamics simulation arrhythmia |
| url | https://elifesciences.org/articles/104901 |
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