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Ma T, Wang L, Chai A, Liu C, Cui W, Yuan S, Wing Ngor Au S, Sun L, Zhang X, Zhang Z, Lu J, Gao Y, Wang P, Li Z, Liang Y, Vogel H, Wang YT, Wang D, Yan K, Zhang H. Cryo-EM structures of ClC-2 chloride channel reveal the blocking mechanism of its specific inhibitor AK-42. Nat Commun 2023; 14:3424. [PMID: 37296152 PMCID: PMC10256776 DOI: 10.1038/s41467-023-39218-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
ClC-2 transports chloride ions across plasma membranes and plays critical roles in cellular homeostasis. Its dysfunction is involved in diseases including leukodystrophy and primary aldosteronism. AK-42 was recently reported as a specific inhibitor of ClC-2. However, experimental structures are still missing to decipher its inhibition mechanism. Here, we present cryo-EM structures of apo ClC-2 and its complex with AK-42, both at 3.5 Å resolution. Residues S162, E205 and Y553 are involved in chloride binding and contribute to the ion selectivity. The side-chain of the gating glutamate E205 occupies the putative central chloride-binding site, indicating that our structure represents a closed state. Structural analysis, molecular dynamics and electrophysiological recordings identify key residues to interact with AK-42. Several AK-42 interacting residues are present in ClC-2 but not in other ClCs, providing a possible explanation for AK-42 specificity. Taken together, our results experimentally reveal the potential inhibition mechanism of ClC-2 inhibitor AK-42.
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Grants
- National Natural Science Foundation of China (National Science Foundation of China)
- National Science and Technology Innovation 2030 Major Program (No. 2022ZD0211900)
- the Science and Technology Innovation Committee of Shenzhen(No. JCYJ20200109150700942), the Key-Area Research and Development Program of Guangdong Province (2019B030335001), the Shenzhen Fund for Guangdong Provincial High Level Clinical Key Specialties (No. SZGSP013), and the Shenzhen Key Medical Discipline Construction Fund (No. SZXK042)
- The Shenzhen Key Laboratory of Computer Aided Drug Discovery, Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China, Funding number: ZDSYS20201230165400001. The Chinese Academy of Science President’s International Fellowship Initiative (PIFI) (No. 2020FSB0003), Guangdong Retired Expert (granted by Guangdong Province), National Overseas High Level Talent Introduction Plan-Foreign Expert from Organization Department of the CPC Central Committee (1000 talent project), Shenzhen Pengcheng Scientist, NSFC-SNSF Funding (No. 32161133022), AlphaMol & SIAT Joint Laboratory, Shenzhen Government Top-talent Working Funding and Guangdong Province Academician Work Funding.
- NSFC-Guangdong Joint Fund-U20A6005, Shenzhen Key Laboratory of Translational Research for Brain Diseases (ZDSYS20200828154800001)
- Shenzhen Science and Technology Program (No. JCYJ20220530115214033 and No. KQTD20210811090115021)
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Affiliation(s)
- Tao Ma
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Lei Wang
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Anping Chai
- Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, 518055, Shenzhen, Guangdong, China
| | - Chao Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Wenqiang Cui
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuguang Yuan
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Shannon Wing Ngor Au
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Liang Sun
- Shenzhen Shuli Tech Co., Ltd, 518126, Shenzhen, Guangdong, China
| | - Xiaokang Zhang
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, 518055, Shenzhen, Guangdong, China
- Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China
| | - Zhenzhen Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Jianping Lu
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020, China
| | - Yuanzhu Gao
- Cryo-EM Facility Center, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Peiyi Wang
- Cryo-EM Facility Center, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Zhifang Li
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yujie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518020, China
| | - Horst Vogel
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Yu Tian Wang
- Shenzhen Key Laboratory of Translational Research for Brain Diseases, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, Guangdong, China.
| | - Daping Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, 518000, Shenzhen, China.
| | - Kaige Yan
- School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Huawei Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
- Department of Biomedical Engineering, Southern University of Science and Technology, 518055, Shenzhen, China.
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