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Guo Y, Yang G, Liu H, Chai J, Chen J, Shanklin J, Liu Q, Liu B, Lu M. Structure and mechanism of human vesicular polyamine transporter. Nat Commun 2025; 16:4142. [PMID: 40319071 PMCID: PMC12049414 DOI: 10.1038/s41467-025-59549-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Accepted: 04/25/2025] [Indexed: 05/07/2025] Open
Abstract
Polyamines play essential roles in gene expression and modulate neuronal transmission in mammals. Vesicular polyamine transporters (VPAT) from the SLC18 family exploit the transmembrane H+ gradient to translocate polyamines into secretory vesicles, enabling the quantal release of polyamine neuromodulators and underpinning learning and memory formation. Here, we report the cryo-electron microscopy structures of human VPAT in complex with spermine, spermidine, H+, or tetrabenazine, elucidating discrete lumen-facing states of the antiporter and pivotal interactions between VPAT and its substrate or inhibitor. Leveraging structure-inspired mutagenesis studies and protein structure prediction, we deduce an unforeseen mechanism whereby the polyamine and H+ compete for multiple acidic protein residues both directly and indirectly, and rationalize how the antidopaminergic therapeutic tetrabenazine impedes vesicular transport of polyamines. This study unravels the mechanism of an H+-coupled polyamine antiporter, reveals mechanistic diversity between VPAT and other SLC18 antiporters, and raises new prospects for combating human disorders of polyamine homeostasis.
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Affiliation(s)
- Yi Guo
- Center for Proteomics & Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, 3333 Green Bay Road, North Chicago, IL, 60064, USA
| | - Ge Yang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55921, USA
| | - Haijiao Liu
- Biology Department, Brookhaven National Laboratory, Bldg. 463, Upton, NY, 11973, USA
- Department of Materials Sciences & Chemical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jin Chai
- Biology Department, Brookhaven National Laboratory, Bldg. 463, Upton, NY, 11973, USA
| | - Jie Chen
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55921, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Bldg. 463, Upton, NY, 11973, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Bldg. 463, Upton, NY, 11973, USA.
| | - Bin Liu
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55921, USA.
| | - Min Lu
- Center for Proteomics & Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, 3333 Green Bay Road, North Chicago, IL, 60064, USA.
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Fan J, Xie W, Ke H, Zhang J, Wang J, Wang H, Guo N, Bai Y, Lei X. Structural Basis for Inhibition of Urate Reabsorption in URAT1. JACS AU 2025; 5:1308-1319. [PMID: 40151250 PMCID: PMC11937972 DOI: 10.1021/jacsau.4c01188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 02/11/2025] [Accepted: 02/12/2025] [Indexed: 03/29/2025]
Abstract
The urate transporter 1 (URAT1) is the primary urate transporter in the kidney responsible for urate reabsorption and, therefore, is crucial for urate homeostasis. Hyperuricemia causes the common human disease gout and other pathological consequences. Inhibition of urate reabsorption through URAT1 has been shown as a promising strategy in alleviating hyperuricemia, and clinical and preclinical drug candidates targeting URAT1 are emerging. However, how small molecules inhibit URAT1 remains undefined, and the lack of accurate URAT1 complex structures hinders the development of better therapeutics. Here, we present cryoelectron microscopy structures of a humanized rat URAT1 bound with benzbromarone, lingdolinurad, and verinurad, elucidating the structural basis for drug recognition and inhibition. The three small molecules reside in the URAT1 central cavity with different binding modes, locking URAT1 in an inward-facing conformation. This study provides mechanistic insights into the drug modulation of URAT1 and sheds light on the rational design of potential URAT1-specific therapeutics for treating hyperuricemia.
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Affiliation(s)
- Junping Fan
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenjun Xie
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Han Ke
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jing Zhang
- Jiangsu
JITRI Molecular Engineering Inst. Co., Ltd., Jiangsu 215500, China
| | - Jin Wang
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haijun Wang
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Nianxin Guo
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yingjie Bai
- Institute
for Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Xiaoguang Lei
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Institute of Organic
Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
- Institute
for Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China
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Elbahnsi A, Dudas B, Callebaut I, Hinzpeter A, Miteva MA. ATP-Binding Cassette and Solute Carrier Transporters: Understanding Their Mechanisms and Drug Modulation Through Structural and Modeling Approaches. Pharmaceuticals (Basel) 2024; 17:1602. [PMID: 39770445 PMCID: PMC11676857 DOI: 10.3390/ph17121602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 11/25/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025] Open
Abstract
The ATP-binding cassette (ABC) and solute carrier (SLC) transporters play pivotal roles in cellular transport mechanisms, influencing a wide range of physiological processes and impacting various medical conditions. Recent advancements in structural biology and computational modeling have provided significant insights into their function and regulation. This review provides an overview of the current knowledge of human ABC and SLC transporters, emphasizing their structural and functional relationships, transport mechanisms, and the contribution of computational approaches to their understanding. Current challenges and promising future research and methodological directions are also discussed.
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Affiliation(s)
- Ahmad Elbahnsi
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS, Université Paris Cité, 75006 Paris, France
| | - Balint Dudas
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS, Université Paris Cité, 75006 Paris, France
| | - Isabelle Callebaut
- Muséum National d’Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie—IMPMC, Sorbonne Université, 75005 Paris, France
| | - Alexandre Hinzpeter
- CNRS, INSERM, Institut Necker Enfants Malades—INEM, Université Paris Cité, 75015 Paris, France
| | - Maria A. Miteva
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS, Université Paris Cité, 75006 Paris, France
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4
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Yadav R, Gati C. Packaging monoamine neurotransmitters. Cell Res 2024; 34:185-186. [PMID: 38242944 PMCID: PMC10907750 DOI: 10.1038/s41422-023-00922-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024] Open
Affiliation(s)
- Ravi Yadav
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- The Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Cornelius Gati
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
- The Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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