1
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Schwartz AC, Stein RA, Gil-Iturbe E, Quick M, Mchaourab HS. Alternating access of a bacterial homolog of neurotransmitter: sodium symporters determined from AlphaFold2 ensembles and DEER spectroscopy. Proc Natl Acad Sci U S A 2024; 121:e2406063121. [PMID: 39302996 PMCID: PMC11459141 DOI: 10.1073/pnas.2406063121] [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: 03/25/2024] [Accepted: 08/16/2024] [Indexed: 09/22/2024] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) play critical roles in neural signaling by regulating neurotransmitter uptake into cells powered by sodium electrochemical gradients. Bacterial NSSs orthologs, including MhsT from Bacillus halodurans, have emerged as model systems to understand the structural motifs of alternating access in NSSs and the extent of conservation of these motifs across the family. Here, we apply a computational/experimental methodology to illuminate the conformational landscape of MhsT alternating access. Capitalizing on our recently developed method, Sampling Protein Ensembles and Conformational Heterogeneity with AlphaFold2 (SPEACH_AF), we derived clusters of MhsT models spanning the transition from inward-facing to outward-facing conformations. Systematic application of double electron-electron resonance (DEER) spectroscopy revealed ligand-dependent movements of multiple structural motifs that underpin MhsT's conformational cycle. Remarkably, comparative DEER analysis in detergent micelles and lipid nanodiscs highlights the profound effect of the environment on the energetics of conformational changes. Through experimentally derived selection of collective variables, we present a model of ion and substrate-powered transport by MhsT consistent with the conformational cycle derived from DEER. Our findings not only advance the understanding of MhsT's function but also uncover motifs of conformational dynamics conserved within the broader context of the NSS family and within the LeuT-fold class of transporters. Importantly, our methodological blueprint introduces an approach that can be applied across a diverse spectrum of transporters to describe their conformational landscapes.
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Affiliation(s)
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN37232
- Center for Applied AI in Protein Dynamics, Vanderbilt University, Nashville, TN37232
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY10032
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY10032
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY10032
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN37232
- Center for Applied AI in Protein Dynamics, Vanderbilt University, Nashville, TN37232
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2
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Dunn W, Bershad A, Krantz DE, Vermetten E. MDMA for treatment of PTSD and neurorehabilitation in military populations. NeuroRehabilitation 2024:NRE230270. [PMID: 39331116 DOI: 10.3233/nre-230270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
BACKGROUND Neurorehabilitation in military populations is complicated by higher rates of PTSD and unique characteristics of military institutions. These factors can adversely impact the patient-therapist therapeutic alliance and engagement with the rehabilitation process leading to poorer outcomes. MDMA is a non-classical psychedelic with pro-social and fear regulating properties. MDMA-assisted therapy is being explored as a novel treatment for PTSD that potentially offers rapid symptom improvement and enhances therapeutic alliance. OBJECTIVE A review of MDMA-assisted therapy for PTSD is provided in the context of neurorehabilitation in military populations. The molecular mechanism of MDMA is outlined and a novel application of MDMA for neurorehabilitation is proposed. METHODS This is an expert review and synthesis of the literature. RESULTS Results from late-stage clinical trials suggest MDMA-assisted therapy for PTSD would be of particular benefit for military populations with PTSD. The unique pro-social properties of MDMA could be leveraged to enhance the therapeutic alliance and patient engagement during neurorehabilitation. CONCLUSION The unique qualities and benefits of MDMA and MDMA-assisted therapy for PTSD suggest relevant application in military personnel undergoing neurorehabilitation. There are many similarities in patient-therapist dynamics in PTSD treatment and neurorehabilitation. The properties of MDMA which enhance therapeutic alliance, downregulate fear, and increase cognitive flexibility would potentially benefit both military personnel with and without PTSD undergoing neurorehabilitation.
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Affiliation(s)
- Walter Dunn
- Department of Veteran Affairs, VISN-22 Mental Illness Research Education Clinical Center, Los Angeles, CA, USA
- Semel Institute for Neuroscience and Human Behavior, University of California - Los Angeles, Los Angeles, CA, USA
| | - Anya Bershad
- Semel Institute for Neuroscience and Human Behavior, University of California - Los Angeles, Los Angeles, CA, USA
| | - David E Krantz
- Semel Institute for Neuroscience and Human Behavior, University of California - Los Angeles, Los Angeles, CA, USA
- Hatos Center for Neuropharmacology, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
| | - Eric Vermetten
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
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3
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. Structure 2024; 32:1528-1543.e3. [PMID: 39025067 PMCID: PMC11380583 DOI: 10.1016/j.str.2024.06.015] [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: 01/24/2024] [Revised: 05/30/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters, the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Samuel P Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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4
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Ji W, Miao A, Liang K, Liu J, Qi Y, Zhou Y, Duan X, Sun J, Lai L, Wu JX. Substrate binding and inhibition mechanism of norepinephrine transporter. Nature 2024; 633:473-479. [PMID: 39143211 DOI: 10.1038/s41586-024-07810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/10/2024] [Indexed: 08/16/2024]
Abstract
Norepinephrine transporter (NET; encoded by SLC6A2) reuptakes the majority of the released noradrenaline back to the presynaptic terminals, thereby affecting the synaptic noradrenaline level1. Genetic mutations and dysregulation of NET are associated with a spectrum of neurological conditions in humans, making NET an important therapeutic target1. However, the structure and mechanism of NET remain unclear. Here we provide cryogenic electron microscopy structures of the human NET (hNET) in three functional states-the apo state, and in states bound to the substrate meta-iodobenzylguanidine (MIBG) or the orthosteric inhibitor radafaxine. These structures were captured in an inward-facing conformation, with a tightly sealed extracellular gate and an open intracellular gate. The substrate MIBG binds at the centre of hNET. Radafaxine also occupies the substrate-binding site and might block the structural transition of hNET for inhibition. These structures provide insights into the mechanism of substrate recognition and orthosteric inhibition of hNET.
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Affiliation(s)
- Wenming Ji
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Anran Miao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Kai Liang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jiameng Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yuhan Qi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yue Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xinli Duan
- Beijing Jingtai Technology, Beijing, P. R. China
| | - Jixue Sun
- Beijing Jingtai Technology, Beijing, P. R. China
| | - Lipeng Lai
- Beijing Jingtai Technology, Beijing, P. R. China
| | - Jing-Xiang Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
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5
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Nielsen JC, Salomon K, Kalenderoglou IE, Bargmeyer S, Pape T, Shahsavar A, Loland CJ. Structure of the human dopamine transporter in complex with cocaine. Nature 2024; 632:678-685. [PMID: 39112703 DOI: 10.1038/s41586-024-07804-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/09/2024] [Indexed: 08/16/2024]
Abstract
The dopamine transporter (DAT) is crucial for regulating dopamine signalling and is the prime mediator for the rewarding and addictive effects of cocaine1. As part of the neurotransmitter sodium symporter family, DAT uses the Na+ gradient across cell membranes to transport dopamine against its chemical gradient2. The transport mechanism involves both intra- and extracellular gates that control substrate access to a central site. However, the molecular intricacies of this process and the inhibitory mechanism of cocaine have remained unclear. Here, we present the molecular structure of human DAT in complex with cocaine at a resolution of 2.66 Å. Our findings reveal that DAT adopts the expected LeuT-fold, posing in an outward-open conformation with cocaine bound at the central (S1) site. Notably, while an Na+ occupies the second Na+ site (Na2), the Na1 site seems to be vacant, with the side chain of Asn82 occupying the presumed Na+ space. This structural insight elucidates the mechanism for the cocaine inhibition of human DAT and deepens our understanding of neurotransmitter transport. By shedding light on the molecular underpinnings of how cocaine acts, our study lays a foundation for the development of targeted medications to combat addiction.
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Affiliation(s)
- Jeppe C Nielsen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Salomon
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris E Kalenderoglou
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Bargmeyer
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tillmann Pape
- Structural Molecular Biology Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Azadeh Shahsavar
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus J Loland
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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6
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Tan J, Xiao Y, Kong F, Zhang X, Xu H, Zhu A, Liu Y, Lei J, Tian B, Yuan Y, Yan C. Molecular basis of human noradrenaline transporter reuptake and inhibition. Nature 2024; 632:921-929. [PMID: 39048818 DOI: 10.1038/s41586-024-07719-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Noradrenaline, also known as norepinephrine, has a wide range of activities and effects on most brain cell types1. Its reuptake from the synaptic cleft heavily relies on the noradrenaline transporter (NET) located in the presynaptic membrane2. Here we report the cryo-electron microscopy (cryo-EM) structures of the human NET in both its apo state and when bound to substrates or antidepressant drugs, with resolutions ranging from 2.5 Å to 3.5 Å. The two substrates, noradrenaline and dopamine, display a similar binding mode within the central substrate binding site (S1) and within a newly identified extracellular allosteric site (S2). Four distinct antidepressants, namely, atomoxetine, desipramine, bupropion and escitalopram, occupy the S1 site to obstruct substrate transport in distinct conformations. Moreover, a potassium ion was observed within sodium-binding site 1 in the structure of the NET bound to desipramine under the KCl condition. Complemented by structural-guided biochemical analyses, our studies reveal the mechanism of substrate recognition, the alternating access of NET, and elucidate the mode of action of the four antidepressants.
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Affiliation(s)
- Jiaxin Tan
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuan Xiao
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Kong
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaochun Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Hanwen Xu
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Angqi Zhu
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiming Liu
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jianlin Lei
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Boxue Tian
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yafei Yuan
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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7
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Hu T, Yu Z, Zhao J, Meng Y, Salomon K, Bai Q, Wei Y, Zhang J, Xu S, Dai Q, Yu R, Yang B, Loland CJ, Zhao Y. Transport and inhibition mechanisms of the human noradrenaline transporter. Nature 2024; 632:930-937. [PMID: 39085602 DOI: 10.1038/s41586-024-07638-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/31/2024] [Indexed: 08/02/2024]
Abstract
The noradrenaline transporter (also known as norepinephrine transporter) (NET) has a critical role in terminating noradrenergic transmission by utilizing sodium and chloride gradients to drive the reuptake of noradrenaline (also known as norepinephrine) into presynaptic neurons1-3. It is a pharmacological target for various antidepressants and analgesic drugs4,5. Despite decades of research, its structure and the molecular mechanisms underpinning noradrenaline transport, coupling to ion gradients and non-competitive inhibition remain unknown. Here we present high-resolution complex structures of NET in two fundamental conformations: in the apo state, and bound to the substrate noradrenaline, an analogue of the χ-conotoxin MrlA (χ-MrlAEM), bupropion or ziprasidone. The noradrenaline-bound structure clearly demonstrates the binding modes of noradrenaline. The coordination of Na+ and Cl- undergoes notable alterations during conformational changes. Analysis of the structure of NET bound to χ-MrlAEM provides insight into how conotoxin binds allosterically and inhibits NET. Additionally, bupropion and ziprasidone stabilize NET in its inward-facing state, but they have distinct binding pockets. These structures define the mechanisms governing neurotransmitter transport and non-competitive inhibition in NET, providing a blueprint for future drug design.
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Affiliation(s)
- Tuo Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhuoya Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Zhao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yufei Meng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kristine Salomon
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Qinru Bai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiqing Wei
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Shujing Xu
- Beijing Institute of Biotechnology, Beijing, China
| | - Qiuyun Dai
- Beijing Institute of Biotechnology, Beijing, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Bei Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yan Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.
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8
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Li Y, Wang X, Meng Y, Hu T, Zhao J, Li R, Bai Q, Yuan P, Han J, Hao K, Wei Y, Qiu Y, Li N, Zhao Y. Dopamine reuptake and inhibitory mechanisms in human dopamine transporter. Nature 2024; 632:686-694. [PMID: 39112701 DOI: 10.1038/s41586-024-07796-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/05/2024] [Indexed: 08/16/2024]
Abstract
The dopamine transporter has a crucial role in regulation of dopaminergic neurotransmission by uptake of dopamine into neurons and contributes to the abuse potential of psychomotor stimulants1-3. Despite decades of study, the structure, substrate binding, conformational transitions and drug-binding poses of human dopamine transporter remain unknown. Here we report structures of the human dopamine transporter in its apo state, and in complex with the substrate dopamine, the attention deficit hyperactivity disorder drug methylphenidate, and the dopamine-uptake inhibitors GBR12909 and benztropine. The dopamine-bound structure in the occluded state precisely illustrates the binding position of dopamine and associated ions. The structures bound to drugs are captured in outward-facing or inward-facing states, illuminating distinct binding modes and conformational transitions during substrate transport. Unlike the outward-facing state, which is stabilized by cocaine, GBR12909 and benztropine stabilize the dopamine transporter in the inward-facing state, revealing previously unseen drug-binding poses and providing insights into how they counteract the effects of cocaine. This study establishes a framework for understanding the functioning of the human dopamine transporter and developing therapeutic interventions for dopamine transporter-related disorders and cocaine addiction.
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Affiliation(s)
- Yue Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xianping Wang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yufei Meng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Tuo Hu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Zhao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Renjie Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qinru Bai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Pu Yuan
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Jun Han
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kun Hao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiqing Wei
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunlong Qiu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Na Li
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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9
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Zhao Z, Tajkhorshid E. GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. J Chem Inf Model 2024; 64:5680-5690. [PMID: 38990699 DOI: 10.1021/acs.jcim.4c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
A detailed understanding of ligand-protein interaction is essential for developing rational drug-design strategies. In recent years, technological advances in cryo-electron microscopy (cryo-EM) brought a new era to the structural determination of biological macromolecules and assemblies at high resolution, marking cryo-EM as a promising tool for studying ligand-protein interactions. However, even in high-resolution cryo-EM results, the densities for the bound small-molecule ligands are often of lower quality due to their relatively dynamic and flexible nature, frustrating their accurate coordinate assignment. To address the challenge of ligand modeling in cryo-EM maps, here we report the development of GOLEM (Genetic Optimization of Ligands in Experimental Maps), an automated and robust ligand docking method that predicts a ligand's pose and conformation in cryo-EM maps. GOLEM employs a Lamarckian genetic algorithm to perform a hybrid global/local search for exploring the ligand's conformational, orientational, and positional space. As an important feature, GOLEM explicitly considers water molecules and places them at optimal positions and orientations. GOLEM takes into account both molecular energetics and the correlation with the cryo-EM maps in its scoring function to optimally place the ligand. We have validated GOLEM against multiple cryo-EM structures with a wide range of map resolutions and ligand types, returning ligand poses in excellent agreement with the densities. As a VMD plugin, GOLEM is free of charge and accessible to the community. With these features, GOLEM will provide a valuable tool for ligand modeling in cryo-EM efforts toward drug discovery.
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Affiliation(s)
- Zhiyu Zhao
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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10
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Park H, Patel P, Haas R, Huerta EA. APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. Proc Natl Acad Sci U S A 2024; 121:e2311888121. [PMID: 38913887 PMCID: PMC11228474 DOI: 10.1073/pnas.2311888121] [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: 08/14/2023] [Accepted: 12/25/2023] [Indexed: 06/26/2024] Open
Abstract
The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.
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Affiliation(s)
- Hyun Park
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parth Patel
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Roland Haas
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - E A Huerta
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
- Department of Computer Science, The University of Chicago, Chicago, IL 60637
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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11
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Neumann J, Dhein S, Kirchhefer U, Hofmann B, Gergs U. Effects of congeners of amphetamine on the human heart. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:4615-4642. [PMID: 38340182 PMCID: PMC11166837 DOI: 10.1007/s00210-024-02983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
Central stimulatory and hallucinogenic drugs of abuse like amphetamine and most congeners of amphetamine can have cardiac harmful effects. These cardiac side effects can lead to morbidities and death. In this paper, we review current knowledge on the direct and indirect effects of these amphetamine congeners on the mammalian heart-more specifically, the isolated human heart muscle preparation. In detail, we address the question of whether and how these drugs affect cardiac contractility and their mechanisms of action. Based on this information, further research areas are defined, and further research efforts are proposed.
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Affiliation(s)
- Joachim Neumann
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Magdeburger Str. 4, 06112, D-06097, Halle, Germany.
| | - Stefan Dhein
- Rudolf-Boehm Institut für Pharmakologie und Toxikologie, Universität Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | | | - Britt Hofmann
- Cardiac Surgery, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, D-06097, Halle, Germany
| | - Ulrich Gergs
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Magdeburger Str. 4, 06112, D-06097, Halle, Germany
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12
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Zhang H, Yin YL, Dai A, Zhang T, Zhang C, Wu C, Hu W, He X, Pan B, Jin S, Yuan Q, Wang MW, Yang D, Xu HE, Jiang Y. Dimerization and antidepressant recognition at noradrenaline transporter. Nature 2024; 630:247-254. [PMID: 38750358 DOI: 10.1038/s41586-024-07437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/17/2024] [Indexed: 06/07/2024]
Abstract
The noradrenaline transporter has a pivotal role in regulating neurotransmitter balance and is crucial for normal physiology and neurobiology1. Dysfunction of noradrenaline transporter has been implicated in numerous neuropsychiatric diseases, including depression and attention deficit hyperactivity disorder2. Here we report cryo-electron microscopy structures of noradrenaline transporter in apo and substrate-bound forms, and as complexes with six antidepressants. The structures reveal a noradrenaline transporter dimer interface that is mediated predominantly by cholesterol and lipid molecules. The substrate noradrenaline binds deep in the central binding pocket, and its amine group interacts with a conserved aspartate residue. Our structures also provide insight into antidepressant recognition and monoamine transporter selectivity. Together, these findings advance our understanding of noradrenaline transporter regulation and inhibition, and provide templates for designing improved antidepressants to treat neuropsychiatric disorders.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Antao Dai
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Tianwei Zhang
- Lingang Laboratory, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chao Zhang
- National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Fudan University, Shanghai, China
| | - Canrong Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wen Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Qingning Yuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ming-Wei Wang
- Research Center for Deepsea Bioresources, Sanya, China
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Dehua Yang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Yi Jiang
- Lingang Laboratory, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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13
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Gou R, Yang J, Guo M, Chen Y, Xue W. CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design. J Chem Inf Model 2024; 64:4059-4070. [PMID: 38739718 DOI: 10.1021/acs.jcim.4c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Central nervous system (CNS) drugs have had a significant impact on treating a wide range of neurodegenerative and psychiatric disorders. In recent years, deep learning-based generative models have shown great potential for accelerating drug discovery and improving efficacy. However, specific applications of these techniques in CNS drug discovery have not been widely reported. In this study, we developed the CNSMolGen model, which uses a framework of bidirectional recurrent neural networks (Bi-RNNs) for de novo molecular design of CNS drugs. Results showed that the pretrained model was able to generate more than 90% of completely new molecular structures, which possessed the properties of CNS drug molecules and were synthesizable. In addition, transfer learning was performed on small data sets with specific biological activities to evaluate the potential application of the model for CNS drug optimization. Here, we used drugs against the classical CNS disease target serotonin transporter (SERT) as a fine-tuned data set and generated a focused database against the target protein. The potential biological activities of the generated molecules were verified by using the physics-based induced-fit docking study. The success of this model demonstrates its potential in CNS drug design and optimization, which provides a new impetus for future CNS drug development.
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Affiliation(s)
- Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jingyi Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Menghan Guo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yingjun Chen
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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14
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Hellsberg E, Boytsov D, Chen Q, Niello M, Freissmuth M, Rudnick G, Zhang YW, Sandtner W, Forrest LR. Identification of the potassium-binding site in serotonin transporter. Proc Natl Acad Sci U S A 2024; 121:e2319384121. [PMID: 38652746 PMCID: PMC11067047 DOI: 10.1073/pnas.2319384121] [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: 11/08/2023] [Accepted: 03/11/2024] [Indexed: 04/25/2024] Open
Abstract
Clearance of serotonin (5-hydroxytryptamine, 5-HT) from the synaptic cleft after neuronal signaling is mediated by serotonin transporter (SERT), which couples this process to the movement of a Na+ ion down its chemical gradient. After release of 5-HT and Na+ into the cytoplasm, the transporter faces a rate-limiting challenge of resetting its conformation to be primed again for 5-HT and Na+ binding. Early studies of vesicles containing native SERT revealed that K+ gradients can provide an additional driving force, via K+ antiport. Moreover, under appropriate conditions, a H+ ion can replace K+. Intracellular K+ accelerates the resetting step. Structural studies of SERT have identified two binding sites for Na+ ions, but the K+ site remains enigmatic. Here, we show that K+ antiport can drive substrate accumulation into vesicles containing SERT extracted from a heterologous expression system, allowing us to study the residues responsible for K+ binding. To identify candidate binding residues, we examine many cation binding configurations using molecular dynamics simulations, predicting that K+ binds to the so-called Na2 site. Site-directed mutagenesis of residues in this site can eliminate the ability of both K+ and H+ to drive 5-HT accumulation into vesicles and, in patch clamp recordings, prevent the acceleration of turnover rates and the formation of a channel-like state by K+ or H+. In conclusion, the Na2 site plays a pivotal role in orchestrating the sequential binding of Na+ and then K+ (or H+) ions to facilitate 5-HT uptake in SERT.
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Affiliation(s)
- Eva Hellsberg
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
| | - Danila Boytsov
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna1090, Austria
| | - Qingyang Chen
- School of Life Sciences, Higher Education Mega Center, Guangzhou University, Guangzhou510006, China
| | - Marco Niello
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna1090, Austria
| | - Michael Freissmuth
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna1090, Austria
| | - Gary Rudnick
- Department of Pharmacology, Yale University, New Haven, CT06510
| | - Yuan-Wei Zhang
- School of Life Sciences, Higher Education Mega Center, Guangzhou University, Guangzhou510006, China
| | - Walter Sandtner
- Center of Physiology and Pharmacology, Department of Pharmacology, Medical University of Vienna, Vienna1090, Austria
| | - Lucy R. Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
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15
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Chen S, Huang X, Zhang X, Li C, Zhang YW. A Conserved Intramolecular Ion-Pair Plays a Critical but Divergent Role in Regulation of Dimerization and Transport Function among the Monoamine Transporters. Int J Mol Sci 2024; 25:4032. [PMID: 38612840 PMCID: PMC11011927 DOI: 10.3390/ijms25074032] [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: 01/30/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The monoamine transporters, including the serotonin transporter (SERT), dopamine transporter (DAT), and norepinephrine transporter (NET), are the therapeutic targets for the treatment of many neuropsychiatric disorders. Despite significant progress in characterizing the structures and transport mechanisms of these transporters, the regulation of their transport functions through dimerization or oligomerization remains to be understood. In the present study, we identified a conserved intramolecular ion-pair at the third extracellular loop (EL3) connecting TM5 and TM6 that plays a critical but divergent role in the modulation of dimerization and transport functions among the monoamine transporters. The disruption of the ion-pair interactions by mutations induced a significant spontaneous cross-linking of a cysteine mutant of SERT and an increase in cell surface expression but with an impaired specific transport activity. On the other hand, similar mutations of the corresponding ion-pair residues in both DAT and NET resulted in an opposite effect on their oxidation-induced dimerization, cell surface expression, and transport function. Reversible biotinylation experiments indicated that the ion-pair mutations slowed down the internalization of SERT but stimulated the internalization of DAT. In addition, cysteine accessibility measurements for monitoring SERT conformational changes indicated that substitution of the ion-pair residues resulted in profound effects on the rate constants for cysteine modification in both the extracellular and cytoplasmatic substrate permeation pathways. Furthermore, molecular dynamics simulations showed that the ion-pair mutations increased the interfacial interactions in a SERT dimer but decreased it in a DAT dimer. Taken together, we propose that the transport function is modulated by the equilibrium between monomers and dimers on the cell surface, which is regulated by a potential compensatory mechanism but with different molecular solutions among the monoamine transporters. The present study provided new insights into the structural elements regulating the transport function of the monoamine transporters through their dimerization.
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Affiliation(s)
| | | | | | | | - Yuan-Wei Zhang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (S.C.); (X.H.); (X.Z.); (C.L.)
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16
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Kalinichenko L, Kornhuber J, Sinning S, Haase J, Müller CP. Serotonin Signaling through Lipid Membranes. ACS Chem Neurosci 2024; 15:1298-1320. [PMID: 38499042 PMCID: PMC10995955 DOI: 10.1021/acschemneuro.3c00823] [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: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Serotonin (5-HT) is a vital modulatory neurotransmitter responsible for regulating most behaviors in the brain. An inefficient 5-HT synaptic function is often linked to various mental disorders. Primarily, membrane proteins controlling the expression and activity of 5-HT synthesis, storage, release, receptor activation, and inactivation are critical to 5-HT signaling in synaptic and extra-synaptic sites. Moreover, these signals represent information transmission across membranes. Although the lipid membrane environment is often viewed as fairly stable, emerging research suggests significant functional lipid-protein interactions with many synaptic 5-HT proteins. These protein-lipid interactions extend to almost all the primary lipid classes that form the plasma membrane. Collectively, these lipid classes and lipid-protein interactions affect 5-HT synaptic efficacy at the synapse. The highly dynamic lipid composition of synaptic membranes suggests that these lipids and their interactions with proteins may contribute to the plasticity of the 5-HT synapse. Therefore, this broader protein-lipid model of the 5-HT synapse necessitates a reconsideration of 5-HT's role in various associated mental disorders.
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Affiliation(s)
- Liubov
S. Kalinichenko
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Johannes Kornhuber
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
| | - Steffen Sinning
- Department
of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark
| | - Jana Haase
- School
of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Christian P. Müller
- Department
of Psychiatry and Psychotherapy, University
Clinic, Friedrich-Alexander-University of Erlangen-Nürnberg, Schwabachanlage 6, 91054, Erlangen, Germany
- Institute
of Psychopharmacology, Central Institute of Mental Health, Medical
Faculty Mannheim, Heidelberg University, 69047, Mannheim, Germany
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17
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Galetin A, Brouwer KLR, Tweedie D, Yoshida K, Sjöstedt N, Aleksunes L, Chu X, Evers R, Hafey MJ, Lai Y, Matsson P, Riselli A, Shen H, Sparreboom A, Varma MVS, Yang J, Yang X, Yee SW, Zamek-Gliszczynski MJ, Zhang L, Giacomini KM. Membrane transporters in drug development and as determinants of precision medicine. Nat Rev Drug Discov 2024; 23:255-280. [PMID: 38267543 PMCID: PMC11464068 DOI: 10.1038/s41573-023-00877-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/26/2024]
Abstract
The effect of membrane transporters on drug disposition, efficacy and safety is now well recognized. Since the initial publication from the International Transporter Consortium, significant progress has been made in understanding the roles and functions of transporters, as well as in the development of tools and models to assess and predict transporter-mediated activity, toxicity and drug-drug interactions (DDIs). Notable advances include an increased understanding of the effects of intrinsic and extrinsic factors on transporter activity, the application of physiologically based pharmacokinetic modelling in predicting transporter-mediated drug disposition, the identification of endogenous biomarkers to assess transporter-mediated DDIs and the determination of the cryogenic electron microscopy structures of SLC and ABC transporters. This article provides an overview of these key developments, highlighting unanswered questions, regulatory considerations and future directions.
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Affiliation(s)
- Aleksandra Galetin
- Centre for Applied Pharmacokinetic Research, School of Health Sciences, The University of Manchester, Manchester, UK.
| | - Kim L R Brouwer
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Kenta Yoshida
- Clinical Pharmacology, Genentech Research and Early Development, South San Francisco, CA, USA
| | - Noora Sjöstedt
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Lauren Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Xiaoyan Chu
- Department of Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, Merck & Co., Inc., Rahway, NJ, USA
| | - Raymond Evers
- Preclinical Sciences and Translational Safety, Johnson & Johnson, Janssen Pharmaceuticals, Spring House, PA, USA
| | - Michael J Hafey
- Department of Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, Merck & Co., Inc., Rahway, NJ, USA
| | - Yurong Lai
- Drug Metabolism, Gilead Sciences Inc., Foster City, CA, USA
| | - Pär Matsson
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Andrew Riselli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Hong Shen
- Department of Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb Research and Development, Princeton, NJ, USA
| | - Alex Sparreboom
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Manthena V S Varma
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design, Worldwide R&D, Pfizer Inc, Groton, CT, USA
| | - Jia Yang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Xinning Yang
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Lei Zhang
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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18
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Hou G, Hao M, Duan J, Han MH. The Formation and Function of the VTA Dopamine System. Int J Mol Sci 2024; 25:3875. [PMID: 38612683 PMCID: PMC11011984 DOI: 10.3390/ijms25073875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024] Open
Abstract
The midbrain dopamine system is a sophisticated hub that integrates diverse inputs to control multiple physiological functions, including locomotion, motivation, cognition, reward, as well as maternal and reproductive behaviors. Dopamine is a neurotransmitter that binds to G-protein-coupled receptors. Dopamine also works together with other neurotransmitters and various neuropeptides to maintain the balance of synaptic functions. The dysfunction of the dopamine system leads to several conditions, including Parkinson's disease, Huntington's disease, major depression, schizophrenia, and drug addiction. The ventral tegmental area (VTA) has been identified as an important relay nucleus that modulates homeostatic plasticity in the midbrain dopamine system. Due to the complexity of synaptic transmissions and input-output connections in the VTA, the structure and function of this crucial brain region are still not fully understood. In this review article, we mainly focus on the cell types, neurotransmitters, neuropeptides, ion channels, receptors, and neural circuits of the VTA dopamine system, with the hope of obtaining new insight into the formation and function of this vital brain region.
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Affiliation(s)
- Guoqiang Hou
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China (M.H.); (J.D.)
- Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mei Hao
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China (M.H.); (J.D.)
- Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiawen Duan
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China (M.H.); (J.D.)
- Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ming-Hu Han
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China (M.H.); (J.D.)
- Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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19
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Wei Y, Li R, Meng Y, Hu T, Zhao J, Gao Y, Bai Q, Li N, Zhao Y. Transport mechanism and pharmacology of the human GlyT1. Cell 2024; 187:1719-1732.e14. [PMID: 38513663 DOI: 10.1016/j.cell.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/09/2023] [Accepted: 02/21/2024] [Indexed: 03/23/2024]
Abstract
The glycine transporter 1 (GlyT1) plays a crucial role in the regulation of both inhibitory and excitatory neurotransmission by removing glycine from the synaptic cleft. Given its close association with glutamate/glycine co-activated NMDA receptors (NMDARs), GlyT1 has emerged as a central target for the treatment of schizophrenia, which is often linked to hypofunctional NMDARs. Here, we report the cryo-EM structures of GlyT1 bound with substrate glycine and drugs ALX-5407, SSR504734, and PF-03463275. These structures, captured at three fundamental states of the transport cycle-outward-facing, occluded, and inward-facing-enable us to illustrate a comprehensive blueprint of the conformational change associated with glycine reuptake. Additionally, we identified three specific pockets accommodating drugs, providing clear insights into the structural basis of their inhibitory mechanism and selectivity. Collectively, these structures offer significant insights into the transport mechanism and recognition of substrate and anti-schizophrenia drugs, thus providing a platform to design small molecules to treat schizophrenia.
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Affiliation(s)
- Yiqing Wei
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renjie Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yufei Meng
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tuo Hu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yiwei Gao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinru Bai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Li
- Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Yan Zhao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.
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20
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Nguyen H, Cheng MH, Lee JY, Aggarwal S, Mortensen OV, Bahar I. Allosteric modulation of serotonin and dopamine transporters: New insights from computations and experiments. Curr Res Physiol 2024; 7:100125. [PMID: 38836245 PMCID: PMC11148570 DOI: 10.1016/j.crphys.2024.100125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 06/06/2024] Open
Abstract
Human monoamine transporters (MATs) are critical to regulating monoaminergic neurotransmission by translocating their substrates from the synaptic space back into the presynaptic neurons. As such, their primary substrate binding site S1 has been targeted by a wide range of compounds for treating neuropsychiatric and neurodegenerative disorders including depression, ADHD, neuropathic pain, and anxiety disorders. We present here a comparative study of the structural dynamics and ligand-binding properties of two MATs, dopamine transporter (DAT) and serotonin transporter (SERT), with focus on the allosteric modulation of their transport function by drugs or substrates that consistently bind a secondary site S2, proposed to serve as an allosteric site. Our systematic analysis of the conformational space and dynamics of a dataset of 50 structures resolved for DAT and SERT in the presence of one or more ligands/drugs reveals the specific residues playing a consistent role in coordinating the small molecules bound to subsites S2-I and S2-II within S2, such as R476 and Y481 in dDAT and E494, P561, and F556 in hSERT. Further analysis reveals how DAT and SERT differ in their two principal modes of structural changes, PC1 and PC2. Notably, PC1 underlies the transition between outward- and inward-facing states of the transporters as well as their gating; whereas PC2 supports the rearrangements of TM helices near the S2 site. Finally, the examination of cross-correlations between structural elements lining the respective sites S1 and S2 point to the crucial role of coupled motions between TM6a and TM10. In particular, we note the involvement of hSERT residues F335 and G338, and E493-E494-T497 belonging to these two respective helices, in establishing the allosteric communication between S1 and S2. These results help understand the molecular basis of the action of drugs that bind to the S2 site of DAT or SERT. They also provide a basis for designing allosteric modulators that may provide better control of specific interactions and cellular pathways, rather than indiscriminately inhibiting the transporter by targeting its orthosteric site.
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Affiliation(s)
- Hoang Nguyen
- Laufer Center for Physical and Quantitative Biology and, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Ji Young Lee
- Laufer Center for Physical and Quantitative Biology and, USA
| | - Shaili Aggarwal
- Department of Pharmacology and Physiology, Drexel University School of Medicine, Philadelphia, PA, 19102, USA
| | - Ole Valente Mortensen
- Department of Pharmacology and Physiology, Drexel University School of Medicine, Philadelphia, PA, 19102, USA
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology and, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
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21
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Tu G, Fu T, Zheng G, Xu B, Gou R, Luo D, Wang P, Xue W. Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. J Chem Inf Model 2024; 64:1433-1455. [PMID: 38294194 DOI: 10.1021/acs.jcim.3c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are involved in the transportation of diverse solute ions and small molecules into cells. There are approximately 450 SLCs within the human body, and more than a quarter of them are emerging as attractive therapeutic targets for multiple complex diseases, e.g., depression, cancer, and diabetes. However, only 44 unique transporters (∼9.8% of the SLC superfamily) with 3D structures and specific binding sites have been reported. To design innovative and effective drugs targeting diverse SLCs, there are a number of obstacles that need to be overcome. However, computational chemistry, including physics-based molecular modeling and machine learning- and deep learning-based artificial intelligence (AI), provides an alternative and complementary way to the classical drug discovery approach. Here, we present a comprehensive overview on recent advances and existing challenges of the computational techniques in structure-based drug design of SLCs from three main aspects: (i) characterizing multiple conformations of the proteins during the functional process of transportation, (ii) identifying druggability sites especially the cryptic allosteric ones on the transporters for substrates and drugs binding, and (iii) discovering diverse small molecules or synthetic protein binders targeting the binding sites. This work is expected to provide guidelines for a deep understanding of the structure and function of the SLC superfamily to facilitate rational design of novel modulators of the transporters with the aid of state-of-the-art computational chemistry technologies including artificial intelligence.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Binbin Xu
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610200, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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22
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Vaughan RA, Henry LK, Foster JD, Brown CR. Post-translational mechanisms in psychostimulant-induced neurotransmitter efflux. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2024; 99:1-33. [PMID: 38467478 DOI: 10.1016/bs.apha.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The availability of monoamine neurotransmitters in the brain is under the control of dopamine, norepinephrine, and serotonin transporters expressed on the plasma membrane of monoaminergic neurons. By regulating transmitter levels these proteins mediate crucial functions including cognition, attention, and reward, and dysregulation of their activity is linked to mood and psychiatric disorders of these systems. Amphetamine-based transporter substrates stimulate non-exocytotic transmitter efflux that induces psychomotor stimulation, addiction, altered mood, hallucinations, and psychosis, thus constituting a major component of drug neurochemical and behavioral outcomes. Efflux is under the control of transporter post-translational modifications that synergize with other regulatory events, and this review will summarize our knowledge of these processes and their role in drug mechanisms.
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Affiliation(s)
- Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - James D Foster
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
| | - Christopher R Brown
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
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23
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577062. [PMID: 38352416 PMCID: PMC10862720 DOI: 10.1101/2024.01.24.577062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A. Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Samuel P. Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael A. Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Present address: Novartis Biomedical Research, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Lead contact
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24
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Biosca-Brull J, Ona G, Alarcón-Franco L, Colomina MT. A transcriptomic analysis in mice following a single dose of ibogaine identifies new potential therapeutic targets. Transl Psychiatry 2024; 14:41. [PMID: 38242896 PMCID: PMC10798990 DOI: 10.1038/s41398-024-02773-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/21/2024] Open
Abstract
Ibogaine (IBO) is an atypical psychedelic with a complex mechanism of action. To date, the mechanisms that may underlie its anti-addictive effects are still not defined. This study aims to identify changes in gene expression induced by a single oral dose of IBO in the cortex of mice by means of a transcriptomic analysis for the first time. Our results showed significant alterations in gene expression in mouse frontal cortex samples 4 h after a single oral dose of IBO. Specifically, genes involved in hormonal pathways and synaptogenesis exhibited upregulation, while genes associated with apoptotic processes and endosomal transports showed downregulation. The findings were further corroborated through quantitative polymerase chain reaction (qPCR) analysis. However, the validation of gene expression related to hormonal pathways did not entirely align with the transcriptomic analysis results, possibly due to the brain region from which tissue was collected. Sex differences were observed, with female mice displaying more pronounced alterations in gene expression after IBO treatment. High variability was observed across individual animals. However, this study represents a significant advancement in comprehending IBO's molecular actions. The findings highlight the influence of IBO on gene expression, particularly on hormonal pathways, synaptogenesis, apoptotic processes, and endosomal transports. The identification of sex differences underscores the importance of considering sex as a potential factor influencing IBO's effects. Further research to assess different time points after IBO exposure is warranted.
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Affiliation(s)
- Judit Biosca-Brull
- Universitat Rovira i Virgili, Research Group in Neurobehavior and Health (NEUROLAB), Tarragona, Spain
- Universitat Rovira i Virgili, Department of Psychology and Research Center for Behavior Assessment (CRAMC), Tarragona, Spain
- Universitat Rovira i Virgili, Center of Environmental, Food and Toxicological Technology (TECNATOX), Reus, Spain
| | - Genis Ona
- ICEERS-International Center for Ethnobotanical Education, Research, and Services, Barcelona, Spain
- Universitat Rovira i Virgili, Department of Anthropology, Philosophy and Social Work, Tarragona, Spain
| | - Lineth Alarcón-Franco
- Universitat Rovira i Virgili, Research Group in Neurobehavior and Health (NEUROLAB), Tarragona, Spain
- Grupo de Investigación Infetarre, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Maria Teresa Colomina
- Universitat Rovira i Virgili, Research Group in Neurobehavior and Health (NEUROLAB), Tarragona, Spain.
- Universitat Rovira i Virgili, Department of Psychology and Research Center for Behavior Assessment (CRAMC), Tarragona, Spain.
- Universitat Rovira i Virgili, Center of Environmental, Food and Toxicological Technology (TECNATOX), Reus, Spain.
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25
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Ferrada E, Wiedmer T, Wang WA, Frommelt F, Steurer B, Klimek C, Lindinger S, Osthushenrich T, Garofoli A, Brocchetti S, Bradberry S, Huang J, MacNamara A, Scarabottolo L, Ecker GF, Malarstig A, Superti-Furga G. Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8. J Mol Biol 2024; 436:168383. [PMID: 38070861 DOI: 10.1016/j.jmb.2023.168383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
Creatine is an essential metabolite for the storage and rapid supply of energy in muscle and nerve cells. In humans, impaired metabolism, transport, and distribution of creatine throughout tissues can cause varying forms of mental disability, also known as creatine deficiency syndrome (CDS). So far, 80 mutations in the creatine transporter (SLC6A8) have been associated to CDS. To better understand the effect of human genetic variants on the physiology of SLC6A8 and their possible impact on CDS, we studied 30 missense variants including 15 variants of unknown significance, two of which are reported here for the first time. We expressed these variants in HEK293 cells and explored their subcellular localization and transport activity. We also applied computational methods to predict variant effect and estimate site-specific changes in thermodynamic stability. To explore variants that might have a differential effect on the transporter's conformers along the transport cycle, we constructed homology models of the inward facing, and outward facing conformations. In addition, we used mass-spectrometry to study proteins that interact with wild type SLC6A8 and five selected variants in HEK293 cells. In silico models of the protein complexes revealed how two variants impact the interaction interface of SLC6A8 with other proteins and how pathogenic variants lead to an enrichment of ER protein partners. Overall, our integrated analysis disambiguates the pathogenicity of 15 variants of unknown significance revealing diverse mechanisms of pathogenicity, including two previously unreported variants obtained from patients suffering from the creatine deficiency syndrome.
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Affiliation(s)
- Evandro Ferrada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Wen-An Wang
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Barbara Steurer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Klimek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Andrea Garofoli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Jiahui Huang
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | | | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Anders Malarstig
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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26
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Duan W, Cao D, Wang S, Cheng J. Serotonin 2A Receptor (5-HT 2AR) Agonists: Psychedelics and Non-Hallucinogenic Analogues as Emerging Antidepressants. Chem Rev 2024; 124:124-163. [PMID: 38033123 DOI: 10.1021/acs.chemrev.3c00375] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Psychedelics make up a group of psychoactive compounds that induce hallucinogenic effects by activating the serotonin 2A receptor (5-HT2AR). Clinical trials have demonstrated the traditional psychedelic substances like psilocybin as a class of rapid-acting and long-lasting antidepressants. However, there is a pressing need for rationally designed 5-HT2AR agonists that possess optimal pharmacological profiles in order to fully reveal the therapeutic potential of these agonists and identify safer drug candidates devoid of hallucinogenic effects. This Perspective provides an overview of the structure-activity relationships of existing 5-HT2AR agonists based on their chemical classifications and discusses recent advancements in understanding their molecular pharmacology at a structural level. The encouraging clinical outcomes of psychedelics in depression treatment have sparked drug discovery endeavors aimed at developing novel 5-HT2AR agonists with improved subtype selectivity and signaling bias properties, which could serve as safer and potentially nonhallucinogenic antidepressants. These efforts can be significantly expedited through the utilization of structure-based methods and functional selectivity-directed screening.
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Affiliation(s)
- Wenwen Duan
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Dongmei Cao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Sheng Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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27
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Gradisch R, Schlögl K, Lazzarin E, Niello M, Maier J, Mayer FP, Alves da Silva L, Skopec SMC, Blakely RD, Sitte HH, Mihovilovic MD, Stockner T. Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors. Nat Commun 2024; 15:417. [PMID: 38195746 PMCID: PMC10776687 DOI: 10.1038/s41467-023-44637-6] [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: 07/17/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
The presynaptic serotonin transporter (SERT) clears extracellular serotonin following vesicular release to ensure temporal and spatial regulation of serotonergic signalling and neurotransmitter homeostasis. Prescription drugs used to treat neurobehavioral disorders, including depression, anxiety, and obsessive-compulsive disorder, trap SERT by blocking the transport cycle. In contrast, illicit drugs of abuse like amphetamines reverse SERT directionality, causing serotonin efflux. Both processes result in increased extracellular serotonin levels. By combining molecular dynamics simulations with biochemical experiments and using a homologous series of serotonin analogues, we uncovered the coupling mechanism between the substrate and the transporter, which triggers the uptake of serotonin. Free energy analysis showed that only scaffold-bound substrates could initiate SERT occlusion through attractive long-range electrostatic interactions acting on the bundle domain. The associated spatial requirements define substrate and inhibitor properties, enabling additional possibilities for rational drug design approaches.
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Affiliation(s)
- Ralph Gradisch
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Katharina Schlögl
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060, Vienna, Austria
| | - Erika Lazzarin
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Marco Niello
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
- Genetics of Cognition Laboratory, Neuroscience area, Istituto Italiano di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Julian Maier
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Felix P Mayer
- Florida Atlantic University, Department of Biomedical Science, Jupiter, FL, 33458, USA
- Stiles-Nicholson Brain Institute, Jupiter, FL, 33458, USA
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Leticia Alves da Silva
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Sophie M C Skopec
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Randy D Blakely
- Florida Atlantic University, Department of Biomedical Science, Jupiter, FL, 33458, USA
- Stiles-Nicholson Brain Institute, Jupiter, FL, 33458, USA
| | - Harald H Sitte
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
- Al-Ahliyya Amman University, Hourani Center for Applied Scientific Research, Amman, Jordan
- Medical University of Vienna, Center for Addiction Research and Science, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Marko D Mihovilovic
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria.
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28
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Ivan VE, Tomàs-Cuesta DP, Esteves IM, Curic D, Mohajerani M, McNaughton BL, Davidsen J, Gruber AJ. The Nonclassic Psychedelic Ibogaine Disrupts Cognitive Maps. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:275-283. [PMID: 38298796 PMCID: PMC10829624 DOI: 10.1016/j.bpsgos.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 02/02/2024] Open
Abstract
Background The ability of psychedelic compounds to profoundly alter mental function has been long known, but the underlying changes in cellular-level information encoding remain poorly understood. Methods We used two-photon microscopy to record from the retrosplenial cortex in head-fixed mice running on a treadmill before and after injection of the nonclassic psychedelic ibogaine (40 mg/kg intraperitoneally). Results We found that the cognitive map, formed by the representation of position encoded by ensembles of individual neurons in the retrosplenial cortex, was destabilized by ibogaine when mice had to infer position between tactile landmarks. This corresponded with increased neural activity rates, loss of correlation structure, and increased responses to cues. Ibogaine had surprisingly little effect on the size-frequency distribution of network activity events, suggesting that signal propagation within the retrosplenial cortex was largely unaffected. Conclusions Taken together, these data support proposals that compounds with psychedelic properties disrupt representations that are important for constraining neocortical activity, thereby increasing the entropy of neural signaling. Furthermore, the loss of expected position encoding between landmarks recapitulated effects of hippocampal impairment, suggesting that disruption of cognitive maps or other hippocampal processing may be a contributing mechanism of discoordinated neocortical activity in psychedelic states.
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Affiliation(s)
- Victorita E. Ivan
- Canadian Center for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - David P. Tomàs-Cuesta
- Canadian Center for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Ingrid M. Esteves
- Canadian Center for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Davor Curic
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - Majid Mohajerani
- Canadian Center for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Bruce L. McNaughton
- Canadian Center for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
- Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California
| | - Joern Davidsen
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - Aaron J. Gruber
- Canadian Center for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
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29
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Clarke A, Farr CV, El-Kasaby A, Szöllősi D, Freissmuth M, Sucic S, Stockner T. Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis. Protein Sci 2024; 33:e4842. [PMID: 38032325 PMCID: PMC10751730 DOI: 10.1002/pro.4842] [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: 07/24/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023]
Abstract
In chordates, energy buffering is achieved in part through phosphocreatine, which requires cellular uptake of creatine by the membrane-embedded creatine transporter (CRT1/SLC6A8). Mutations in human slc6a8 lead to creatine transporter deficiency syndrome, for which there is only limited treatment. Here, we used a combined homology modeling, molecular dynamics, and experimental approach to generate a structural model of CRT1. Our observations support the following conclusions: contrary to previous proposals, C144, a key residue in the substrate binding site, is not present in a charged state. Similarly, the side chain D458 must be present in a protonated form to maintain the structural integrity of CRT1. Finally, we identified that the interaction chain Y148-creatine-Na+ is essential to the process of occlusion, which occurs via a "hold-and-pull" mechanism. The model should be useful to study the impact of disease-associated point mutations on the folding of CRT1 and identify approaches which correct folding-deficient mutants.
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Affiliation(s)
- Amy Clarke
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Clemens V Farr
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ali El-Kasaby
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Daniel Szöllősi
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Freissmuth
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Sonja Sucic
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology and the Gaston H. Glock Research Laboratories for Exploratory Drug Development, Center of Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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30
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Kim J, He MJ, Widmann AK, Lee FS. The role of neurotrophic factors in novel, rapid psychiatric treatments. Neuropsychopharmacology 2024; 49:227-245. [PMID: 37673965 PMCID: PMC10700398 DOI: 10.1038/s41386-023-01717-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023]
Abstract
Neurotrophic factors are a family of growth factors that modulate cellular growth, survival, and differentiation. For many decades, it has been generally believed that a lack of neurotrophic support led to the decreased neuronal synaptic plasticity, death, and loss of non-neuronal supportive cells seen in neuropsychiatric disorders. Traditional psychiatric medications that lead to immediate increases in neurotransmitter levels at the synapse have been shown also to elevate synaptic neurotrophic levels over weeks, correlating with the time course of the therapeutic effects of these drugs. Recent advances in psychiatric treatments, such as ketamine and psychedelics, have shown a much faster onset of therapeutic effects (within minutes to hours). They have also been shown to lead to a rapid release of neurotrophins into the synapse. This has spurred a significant shift in understanding the role of neurotrophins and how the receptor tyrosine kinases that bind neurotrophins may work in concert with other signaling systems. In this review, this renewed understanding of synaptic receptor signaling interactions and the clinical implications of this mechanistic insight will be discussed within the larger context of the well-established roles of neurotrophic factors in psychiatric disorders and treatments.
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Affiliation(s)
- Jihye Kim
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Michelle J He
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Alina K Widmann
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Francis S Lee
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA.
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Madrid-Gambin F, Fabregat-Safont D, Gomez-Gomez A, Olesti E, Mason NL, Ramaekers JG, Pozo OJ. Present and future of metabolic and metabolomics studies focused on classical psychedelics in humans. Biomed Pharmacother 2023; 169:115775. [PMID: 37944438 DOI: 10.1016/j.biopha.2023.115775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Psychedelics are classical hallucinogen drugs that induce a marked altered state of consciousness. In recent years, there has been renewed attention to the possible use of classical psychedelics for the treatment of certain mental health disorders. However, further investigation to better understand their biological effects in humans, their mechanism of action, and their metabolism in humans is needed when considering the development of future novel therapeutic approaches. Both metabolic and metabolomics studies may help for these purposes. On one hand, metabolic studies aim to determine the main metabolites of the drug. On the other hand, the application of metabolomics in human psychedelics studies can help to further understand the biological processes underlying the psychedelic state and the mechanisms of action underlying their therapeutic potential. This review presents the state of the art of metabolic and metabolomic studies after lysergic acid diethylamide (LSD), mescaline, N,N-dimethyltryptamine (DMT) and β-carboline alkaloids (ayahuasca brew), 5-methoxy-DMT and psilocybin administrations in humans. We first describe the characteristics of the published research. Afterward, we reviewed the main results obtained by both metabolic and metabolomics (if available) studies in classical psychedelics and we found out that metabolic and metabolomics studies in psychedelics progress at two different speeds. Thus, whereas the main metabolites for classical psychedelics have been robustly established, the main metabolic alterations induced by psychedelics need to be explored. The integration of metabolomics and pharmacokinetics for investigating the molecular interaction between psychedelics and multiple targets may open new avenues in understanding the therapeutic role of psychedelics.
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Affiliation(s)
- Francisco Madrid-Gambin
- Applied Metabolomics Research Group, Hospital del Mar Research Institute, 08003 Barcelona, Spain.
| | - David Fabregat-Safont
- Applied Metabolomics Research Group, Hospital del Mar Research Institute, 08003 Barcelona, Spain; Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water, University Jaume I, 12071 Castelló, Spain
| | - Alex Gomez-Gomez
- Applied Metabolomics Research Group, Hospital del Mar Research Institute, 08003 Barcelona, Spain; CERBA Internacional, Chromatography Department, 08203 Sabadell, Spain
| | - Eulàlia Olesti
- Department of Clinical Pharmacology, Area Medicament, Hospital Clinic of Barcelona, 08036 Barcelona, Spain; Clinical Pharmacology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Natasha L Mason
- Department of Neuropsychology and Psychopharmacology, Faculty of Psychology and Neuroscience, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Johannes G Ramaekers
- Department of Neuropsychology and Psychopharmacology, Faculty of Psychology and Neuroscience, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Oscar J Pozo
- Applied Metabolomics Research Group, Hospital del Mar Research Institute, 08003 Barcelona, Spain.
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Li M, Zhang X, Chen S, Liu H, Zhang YW. Unique Substrate Recognition and Sodium-Substrate Binding Stoichiometry in a Bacterial Serotonin Transporter, TuriSERT. Int J Mol Sci 2023; 24:17112. [PMID: 38069433 PMCID: PMC10707687 DOI: 10.3390/ijms242317112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
All resolved high-resolution structures of the transporters in the neurotransmitter sodium symporter (NSS) family revealed that the NSS members share common structural and mechanistic features for substrate and ion binding and transport. However, a recently reported bacterial orthologue of the human serotonin transporter (hSERT), TuriSERT, possesses a structural characteristic specific for amino acid substrate binding but does transport a biogenic amine. The unique structural feature of TuriSERT requires a novel configuration for coordinating its substrate and ions. In the present study, we characterized TuriSERT expressed in Escherichia coli cells with a fluorescent substrate by biochemical, structural, and pharmacological approaches. Substrate transport by TuriSERT requires Na+ but not Cl-. Replacement of Asp262 by asparagine renders TuriSERT Cl--dependent. Substitutions of the corresponding Na1 residues did not alter Na+ dependence on substrate transport, whereas the mutation of a Na2 site residue led to a loss of transport activity, suggesting that Na+ binds only to the Na2 site in TuriSERT. In addition, substitutions of several residues essential for recognizing 5-hydroxytryptamine (5-HT) in hSERT had little effect on 5-HT displacement potency in transport assay for TuriSERT. In contrast, mutations of the residues that are proposed to coordinate with 5-HT in our docking model dramatically reduced 5-HT displacement. Furthermore, our results indicated that all tested antidepressants showed a weak inhibitory effect on TuriSERT. The present study demonstrated the existence of a unique substrate binding site and 1:1 stoichiometry of sodium-substrate binding in TuriSERT, a novel structural finding for the NSS transporters.
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Affiliation(s)
| | | | | | | | - Yuan-Wei Zhang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (M.L.); (X.Z.); (S.C.); (H.L.)
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Mayer FP, Niello M, Bulling S, Zhang YW, Li Y, Kudlacek O, Holy M, Kooti F, Sandtner W, Rudnick G, Schmid D, Sitte HH. Mephedrone induces partial release at human dopamine transporters but full release at human serotonin transporters. Neuropharmacology 2023; 240:109704. [PMID: 37703919 DOI: 10.1016/j.neuropharm.2023.109704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/07/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023]
Abstract
Mephedrone (4-methylmethcathinone) is a cathinone derivative that is recreationally consumed for its energizing and empathogenic effects. The stimulating properties are believed to arise from the ability of mephedrone to interact with the high-affinity transporters for dopamine (DA) (DAT) and norepinephrine (NET), whereas the entactogenic effect presumably relies on its activity at the serotonin (5-HT) transporter (SERT). Early studies found that mephedrone acts as a releaser at NET, DAT and SERT, and thus promotes efflux of the respective monoamines. Evidence linked drug-induced reverse transport of 5-HT via SERT to prosocial effects, whereas activity at DAT is strongly correlated with abuse liability. Consequently, we sought to evaluate the pharmacology of mephedrone at human (h) DAT and SERT, heterologously expressed in human embryonic kidney 293 cells, in further detail. In line with previous studies, we report that mephedrone evokes carrier-mediated release via hDAT and hSERT. We found this effect to be sensitive to the protein kinase C inhibitor GF109203X. Electrophysiological recordings revealed that mephedrone is actively transported by hDAT and hSERT. However, mephedrone acts as a full substrate of hSERT but as a partial substrate of hDAT. Furthermore, when compared to fully efficacious releasing agents at hDAT and hSERT (i.e. S(+)-amphetamine and para-chloroamphetamine, respectively) mephedrone displays greater efficacy as a releaser at hSERT than at hDAT. In summary, this study provides additional insights into the molecular mechanism of action of mephedrone at hDAT and hSERT.
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Affiliation(s)
- Felix P Mayer
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Marco Niello
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Simon Bulling
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Yuan-Wei Zhang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8066, USA
| | - Yang Li
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Oliver Kudlacek
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Marion Holy
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Fatemeh Kooti
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Gary Rudnick
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8066, USA
| | - Diethart Schmid
- Institute for Physiology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria
| | - Harald H Sitte
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria; Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, Amman, Jordan; Center for Addiction Research and Science - AddRess, Medical University of Vienna, Waehringer Strasse 13a, A-1090, Vienna, Austria.
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Ona G, Reverte I, Rossi GN, Dos Santos RG, Hallak JE, Colomina MT, Bouso JC. Main targets of ibogaine and noribogaine associated with its putative anti-addictive effects: A mechanistic overview. J Psychopharmacol 2023; 37:1190-1200. [PMID: 37937505 DOI: 10.1177/02698811231200882] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
BACKGROUND There is a growing interest in studying ibogaine (IBO) as a potential treatment for substance use disorders (SUDs). However, its clinical use has been hindered for mainly two reasons: First, the lack of randomized, controlled studies informing about its safety and efficacy. And second, IBO's mechanisms of action remain obscure. It has been challenging to elucidate a predominant mechanism of action responsible for its anti-addictive effects. OBJECTIVE To describe the main targets of IBO and its main metabolite, noribogaine (NOR), in relation to their putative anti-addictive effects, reviewing the updated literature available. METHODS A comprehensive search involving MEDLINE and Google Scholar was undertaken, selecting papers published until July 2022. The inclusion criteria were both theoretical and experimental studies about the pharmacology of IBO. Additional publications were identified in the references of the initial papers. RESULTS IBO and its main metabolite, NOR, can modulate several targets associated with SUDs. Instead of identifying key targets, the action of IBO should be understood as a complex modulation of multiple receptor systems, leading to potential synergies. The elucidation of IBO's pharmacology could be enhanced through the application of methodologies rooted in the polypharmacology paradigm. Such approaches possess the capability to describe multifaceted patterns within multi-target drugs. CONCLUSION IBO displays complex effects through multiple targets. The information detailed here should guide future research on both mechanistic and therapeutic studies.
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Affiliation(s)
- Genís Ona
- International Center for Ethnobotanical Education, Research, and Service (ICEERS), Barcelona, Spain
- Department of Psychology and Research Center for Behavior Assessment (CRAMC), Universitat Rovira i Virgili, Tarragona, Spain
- Medical Anthropology Research Center (MARC), Universitat Rovira i Virgili, Tarragona, Spain
| | - Ingrid Reverte
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
- Santa Lucia Foundation (IRCCS Fondazione Santa Lucia), Rome, Italy
| | - Giordano N Rossi
- Department of Neurosciences and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rafael G Dos Santos
- Department of Neurosciences and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National Institute for Translational Medicine (INCT-TM), CNPq, Ribeirão Preto (SP), Brazil
| | - Jaime Ec Hallak
- Department of Neurosciences and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- National Institute for Translational Medicine (INCT-TM), CNPq, Ribeirão Preto (SP), Brazil
| | - Maria Teresa Colomina
- Department of Psychology and Research Center for Behavior Assessment (CRAMC), Universitat Rovira i Virgili, Tarragona, Spain
| | - José Carlos Bouso
- International Center for Ethnobotanical Education, Research, and Service (ICEERS), Barcelona, Spain
- Medical Anthropology Research Center (MARC), Universitat Rovira i Virgili, Tarragona, Spain
- Department of Neurosciences and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Stefanski A, Pérez-Palma E, Brünger T, Montanucci L, Gati C, Klöckner C, Johannesen KM, Goodspeed K, Macnee M, Deng AT, Aledo-Serrano Á, Borovikov A, Kava M, Bouman AM, Hajianpour MJ, Pal DK, Engelen M, Hagebeuk EEO, Shinawi M, Heidlebaugh AR, Oetjens K, Hoffman TL, Striano P, Freed AS, Futtrup L, Balslev T, Abulí A, Danvoye L, Lederer D, Balci T, Nouri MN, Butler E, Drewes S, van Engelen K, Howell KB, Khoury J, May P, Trinidad M, Froelich S, Lemke JR, Tiller J, Freed AN, Kang JQ, Wuster A, Møller RS, Lal D. SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis. Brain 2023; 146:5198-5208. [PMID: 37647852 PMCID: PMC10689929 DOI: 10.1093/brain/awad292] [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: 12/16/2022] [Revised: 06/05/2023] [Accepted: 07/08/2023] [Indexed: 09/01/2023] Open
Abstract
Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6 and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease versus non-severe disease (P = 2.9 × 10-3, 95% confidence interval: 1.5-15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 portal (https://slc6a1-portal.broadinstitute.org/).
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Affiliation(s)
- Arthur Stefanski
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Eduardo Pérez-Palma
- Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago de Chile 7610658, Chile
| | - Tobias Brünger
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, Cologne 50931, Germany
| | - Ludovica Montanucci
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cornelius Gati
- Department of Biological Sciences, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Genetics, University Hospital of Copenhagen, Rigshispitalet, Copenhagen 2100, Denmark
| | - Kimberly Goodspeed
- Children’s Health, Medical Center, Dallas, TX 75235, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marie Macnee
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, Cologne 50931, Germany
| | - Alexander T Deng
- Clinical Genetics, Guys and St Thomas NHS Trust, London SE19RT, UK
| | - Ángel Aledo-Serrano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid 28034, Spain
| | - Artem Borovikov
- Research and Counseling Department, Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Maina Kava
- Department of Neurology and Metabolic Medicine, Perth Children’s Hospital, Perth 6009, Australia
- School of Paediatrics and Child Health, UWA Medical School, University of Western Australia, Perth 6009, Australia
| | - Arjan M Bouman
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam 3015GD, The Netherlands
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics and Genomics, Albany Medical College, Albany Med Health System, Albany, NY 12208, USA
| | - Deb K Pal
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College, London SE58AF, UK
- Department of Basic and Clinical Neurosciences, King’s College Hospital, London SE59RS, UK
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam Public Health, Amsterdam University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Eveline E O Hagebeuk
- Department of Pediatric Neurology, Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede and Zwolle 2103SW, The Netherlands
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St.Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kathryn Oetjens
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA
| | - Trevor L Hoffman
- Department of Regional Genetics, Anaheim, Southern California Kaiser Permanente Medical Group, CA 92806, USA
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa 16147, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa 16132, Italy
| | - Amanda S Freed
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA 91101, USA
| | - Line Futtrup
- Department of Paediatrics, Regional Hospital of Central Jutland, Viborg 8800, Denmark
| | - Thomas Balslev
- Department of Paediatrics, Regional Hospital of Central Jutland, Viborg 8800, Denmark
- Centre for Educational Development, Aarhus University, Aarhus 8200, Denmark
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, University Hospital Vall d’Hebron, Barcelona 08035, Spain
| | - Leslie Danvoye
- Department of Neurology, Université catholique de Louvain, Cliniques universitaires Saint-Luc, Brussels 1200, Belgium
| | - Damien Lederer
- Centre for Human Genetics, Institute for Pathology and Genetics, Gosselies 6041, Belgium
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A3K7, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5A5, Canada
| | - Maryam Nabavi Nouri
- Department of Paediatrics, Division of Pediatric Neurology, London Health Sciences Centre, London, ON N6A5W9, Canada
| | | | - Sarah Drewes
- Department of Medical Genetics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Kalene van Engelen
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Katherine B Howell
- Department of Neurology, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Jean Khoury
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Marena Trinidad
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Steven Froelich
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig 04103, Germany
| | | | | | - Jing-Qiong Kang
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA
- Neuroscience Graduate Program, Vanderbilt University, Nashville, TN 37235, USA
- Department of Neurology, Vanderbilt Brain Institute, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Kennedy Center of Human Development, Nashville, TN 37203, USA
| | - Arthur Wuster
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark
| | - Dennis Lal
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
- Stanley Center of Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Neurology, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
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Wang X, Che F, Zhang X, Li P, Zhang W, Tang B. Tracing Superoxide Anion in Serotonergic Neurons of Living Mouse Brains with Depression by Small-Molecule Fluorescence Probes. Anal Chem 2023; 95:15614-15620. [PMID: 37830753 DOI: 10.1021/acs.analchem.3c02701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
In brains, the serotonergic neurons are the unique resource of the neurotransmitter serotonin, which plays a pivotal role in the physiology of the brain. The dysfunction of serotonergic neurons caused by oxidative stress in the brain is closely related to the occurrence and development of various mental diseases, such as depression. As the biomarker of oxidative stress, the superoxide anion radical (O2•-) can cause oxidative damage to proteins, nucleic acids and lipids, disturbing the function of neurons and brains. A serotonin transporter (SERT) specifically expresses in serotonergic neurons, which is the biomarker of serotonergic neurons. Thus, we created two novel small molecular fluorescent probes (PA-CA and HT-CA) for imaging O2•- in serotonergic neurons of living brains of mice based on specific targeting groups of SERT. Both PA-CA and HT-CA exert excellent SERT-targetable and glorious selectivity for O2•-. Those two probes could monitor the boost of O2•- in living hsert-HEK293 cells that specifically express SERT under oxidative stress. With two-photon fluorescence imaging, we revealed for the first time that O2•- is significantly increased in serotonergic neurons in living brains of mice with depression. More importantly, proteomic analyses suggested that O2•- could oxidize cysteine and histidine in the active site of SERT, which is involved in the development of depression. This work provides new materials for living brain imaging and offers new strategy for unraveling the pathophysiology of depression.
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Affiliation(s)
- Xin Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, Shandong People's Republic of China
| | - Feida Che
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, Shandong People's Republic of China
| | - Xin Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, Shandong People's Republic of China
| | - Ping Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, Shandong People's Republic of China
| | - Wen Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, Shandong People's Republic of China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institutes of Biomedical Sciences, Shandong Normal University, Jinan 250014, Shandong People's Republic of China
- Laoshan Laboratory, Qingdao 266237, ShandongPeople's Republic of China
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Chen JY, Wu K, Guo MM, Song W, Huang ST, Zhang YM. The PrL Glu→avBNST GABA circuit rapidly modulates depression-like behaviors in male mice. iScience 2023; 26:107878. [PMID: 37810240 PMCID: PMC10551841 DOI: 10.1016/j.isci.2023.107878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/20/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
Depression is a global disease with a high prevalence. Here, we examine the role of the circuit from prelimbic mPFC (PrL) to the anterior ventral bed nucleus of the stria terminalis (avBNST) in depression-like mice through behavioral tests, immunofluorescence, chemogenetics, optogenetics, pharmacology, and fiber photometry. Mice exposed to chronic restraint stress with individual housing displayed depression-like behaviors. Optogenetic or chemogenetic activation of the avBNST-projecting glutamatergic neurons in the PrL had an antidepressant effect. Moreover, we found that α-amino-3-hydroxy-5-methyl-4-isoxazole-propionicacid receptors (AMPARs) play a dominant role in this circuit. Systemic administration of ketamine profoundly alleviated depression-like behaviors in the mice and rapidly rescued the decreased activity in the PrLGlu→avBNSTGABA circuit. Furthermore, the fast-acting effect of ketamine on depressive behaviors was diminished when the circuit was inhibited. To summarize, activating the PrLGlu→avBNSTGABA circuit quickly ameliorated depression-like behaviors. Thus, we propose the PrLGlu→avBNSTGABA circuit as a target for fast regulation of depression.
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Affiliation(s)
- Jie-ying Chen
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou, Jiangsu 221002, China
| | - Ke Wu
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou, Jiangsu 221002, China
| | - Miao-miao Guo
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou, Jiangsu 221002, China
| | - Wei Song
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou, Jiangsu 221002, China
| | - Si-ting Huang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou, Jiangsu 221002, China
| | - Yong-mei Zhang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China
- NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou, Jiangsu 221002, China
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Salomon K, Abramyan AM, Plenge P, Wang L, Bundgaard C, Bang-Andersen B, Loland CJ, Shi L. Dynamic extracellular vestibule of human SERT: Unveiling druggable potential with high-affinity allosteric inhibitors. Proc Natl Acad Sci U S A 2023; 120:e2304089120. [PMID: 37792512 PMCID: PMC10576121 DOI: 10.1073/pnas.2304089120] [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: 03/13/2023] [Accepted: 08/15/2023] [Indexed: 10/06/2023] Open
Abstract
The serotonin transporter (SERT) tightly regulates synaptic serotonin levels and has been the primary target of antidepressants. Binding of inhibitors to the allosteric site of human SERT (hSERT) impedes the dissociation of antidepressants bound at the central site and may enhance the efficacy of such antidepressants to potentially reduce their dosage and side effects. Here, we report the identification of a series of high-affinity allosteric inhibitors of hSERT in a unique scaffold, with the lead compound, Lu AF88273 (3-(1-(2-(1H-indol-3-yl)ethyl)piperidin-4-yl)-6-chloro-1H-indole), having 2.1 nM allosteric potency in inhibiting imipramine dissociation. In addition, we find that Lu AF88273 also inhibits serotonin transport in a noncompetitive manner. The binding pose of Lu AF88273 in the allosteric site of hSERT is determined with extensive molecular dynamics simulations and rigorous absolute binding free energy perturbation (FEP) calculations, which show that a part of the compound occupies a dynamically formed small cavity. The predicted binding location and pose are validated by site-directed mutagenesis and can explain much of the structure-activity relationship of these inhibitors using the relative binding FEP calculations. Together, our findings provide a promising lead compound and the structural basis for the development of allosteric drugs targeting hSERT. Further, they demonstrate that the divergent allosteric sites of neurotransmitter transporters can be selectively targeted.
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Affiliation(s)
- Kristine Salomon
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200Copenhagen N, Denmark
| | - Ara M. Abramyan
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, NIH, Baltimore, MD21224
- Schrödinger, Inc., San Diego, CA92121
| | - Per Plenge
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200Copenhagen N, Denmark
| | | | - Christoffer Bundgaard
- Medicinal Chemistry and Translational DMPK, H. Lundbeck A/S, DK-2500Copenhagen-Valby, Denmark
| | - Benny Bang-Andersen
- Medicinal Chemistry and Translational DMPK, H. Lundbeck A/S, DK-2500Copenhagen-Valby, Denmark
| | - Claus J. Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200Copenhagen N, Denmark
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, NIH, Baltimore, MD21224
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Fu T, Zeng S, Zheng Q, Zhu F. The Important Role of Transporter Structures in Drug Disposition, Efficacy, and Toxicity. Drug Metab Dispos 2023; 51:1316-1323. [PMID: 37295948 DOI: 10.1124/dmd.123.001275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
The ATP-binding cassette (ABC) and solute carrier (SLC) transporters are critical determinants of drug disposition, clinical efficacy, and toxicity as they specifically mediate the influx and efflux of various substrates and drugs. ABC transporters can modulate the pharmacokinetics of many drugs via mediating the translocation of drugs across biologic membranes. SLC transporters are important drug targets involved in the uptake of a broad range of compounds across the membrane. However, high-resolution experimental structures have been reported for a very limited number of transporters, which limits the study of their physiologic functions. In this review, we collected structural information on ABC and SLC transporters and described the application of computational methods in structure prediction. Taking P-glycoprotein (ABCB1) and serotonin transporter (SLC6A4) as examples, we assessed the pivotal role of structure in transport mechanisms, details of ligand-receptor interactions, drug selectivity, the molecular mechanisms of drug-drug interactions, and differences caused by genetic polymorphisms. The data collected contributes toward safer and more effective pharmacological treatments. SIGNIFICANCE STATEMENT: The experimental structure of ATP-binding cassette and solute carrier transporters was collected, and the application of computational methods in structure prediction was described. P-glycoprotein and serotonin transporter were used as examples to reveal the pivotal role of structure in transport mechanisms, drug selectivity, the molecular mechanisms of drug-drug interactions, and differences caused by genetic polymorphisms.
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Affiliation(s)
- Tingting Fu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
| | - Su Zeng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
| | - Qingchuan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China (F.Z.); School of Pharmaceutical Sciences, Jilin University, Changchun, China (T.F., Q.Z.); College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China (S.Z., F.Z.); and Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China (F.Z.)
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Jahanabadi S, Amiri S, Karkeh-Abadi M, Razmi A. Natural psychedelics in the treatment of depression; a review focusing on neurotransmitters. Fitoterapia 2023; 169:105620. [PMID: 37490982 DOI: 10.1016/j.fitote.2023.105620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023]
Abstract
Natural psychedelic compounds are emerging as potential novel therapeutics in psychiatry. This review will discuss how natural psychedelics exert their neurobiological therapeutic effects, and how different neurotransmission systems mediate the effects of these compounds. Further, current therapeutic strategies for depression, and novel mechanism of action of natural psychedelics in the treatment of depression will be discussed. In this review, our focus will be on N, N-dimethyltryptamine (DMT), reversible type A monoamine oxidase inhibitors, mescaline-containing cacti, psilocybin/psilocin-containing mushrooms, ibogaine, muscimol extracted from Amanita spp. mushrooms and ibotenic acid.
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Affiliation(s)
- Samane Jahanabadi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran; Pharmaceutical Science Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Shayan Amiri
- Division of Neurodegenerative Disorders, St Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada; Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada.
| | - Mehdi Karkeh-Abadi
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran
| | - Ali Razmi
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran.
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41
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Schlessinger A, Zatorski N, Hutchinson K, Colas C. Targeting SLC transporters: small molecules as modulators and therapeutic opportunities. Trends Biochem Sci 2023; 48:801-814. [PMID: 37355450 PMCID: PMC10525040 DOI: 10.1016/j.tibs.2023.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023]
Abstract
Solute carrier (SLCs) transporters mediate the transport of a broad range of solutes across biological membranes. Dysregulation of SLCs has been associated with various pathologies, including metabolic and neurological disorders, as well as cancer and rare diseases. SLCs are therefore emerging as key targets for therapeutic intervention with several recently approved drugs targeting these proteins. Unlocking this large and complex group of proteins is essential to identifying unknown SLC targets and developing next-generation SLC therapeutics. Recent progress in experimental and computational techniques has significantly advanced SLC research, including drug discovery. Here, we review emerging topics in therapeutic discovery of SLCs, focusing on state-of-the-art approaches in structural, chemical, and computational biology, and discuss current challenges in transporter drug discovery.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Nicole Zatorski
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Colas
- University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria.
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42
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Yang D, Zhao Z, Tajkhorshid E, Gouaux E. Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Proc Natl Acad Sci U S A 2023; 120:e2304602120. [PMID: 37436958 PMCID: PMC10629533 DOI: 10.1073/pnas.2304602120] [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: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 07/14/2023] Open
Abstract
The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here, we develop methods to isolate SERT from porcine brain (pSERT) using a mild, nonionic detergent, utilize fluorescence-detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to the central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to the pSERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules.
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Affiliation(s)
- Dongxue Yang
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
- HHMI, Oregon Health and Science University, Portland, OR97239
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43
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Deng S, Zhang H, Gou R, Luo D, Liu Z, Zhu F, Xue W. Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. J Chem Inf Model 2023. [PMID: 37410882 DOI: 10.1021/acs.jcim.3c00477] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Human dopamine transporter (hDAT) regulates the reuptake of extracellular dopamine (DA) and is an essential therapeutic target for central nervous system (CNS) diseases. The allosteric modulation of hDAT has been identified for decades. However, the molecular mechanism underlying the transportation is still elusive, which hinders the rational design of allosteric modulators against hDAT. Here, a systematic structure-based method was performed to explore allosteric sites on hDAT in inward-open (IO) conformation and to screen compounds with allosteric affinity. First, the model of the hDAT structure was constructed based on the recently reported Cryo-EM structure of the human serotonin transporter (hSERT) and Gaussian-accelerated molecular dynamics (GaMD) simulation was further utilized for the identification of intermediate energetic stable states of the transporter. Then, with the potential druggable allosteric site on hDAT in IO conformation, virtual screening of seven enamine chemical libraries (∼440,000 compounds) was processed, resulting in 10 compounds being purchased for in vitro assay and with Z1078601926 discovered to allosterically inhibit hDAT (IC50 = 0.527 [0.284; 0.988] μM) when nomifensine was introduced as an orthosteric ligand. Finally, the synergistic effect underlying the allosteric inhibition of hDAT by Z1078601926 and nomifensine was explored using additional GaMD simulation and postbinding free energy analysis. The hit compound discovered in this work not only provides a good starting point for lead optimization but also demonstrates the usability of the method for the structure-based discovery of novel allosteric modulators of other therapeutic targets.
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Affiliation(s)
- Shengzhe Deng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Haiwei Zhang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Department of Pathology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical Co., Ltd., Luzhou 646000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Zhu A, Huang J, Kong F, Tan J, Lei J, Yuan Y, Yan C. Molecular basis for substrate recognition and transport of human GABA transporter GAT1. Nat Struct Mol Biol 2023:10.1038/s41594-023-00983-z. [PMID: 37400655 DOI: 10.1038/s41594-023-00983-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 03/31/2023] [Indexed: 07/05/2023]
Abstract
γ-Aminobutyric acid (GABA), an important inhibitory neurotransmitter in the central nervous system, is recycled through specific GABA transporters (GATs). GAT1, which is mainly expressed in the presynaptic terminals of axons, is a potential drug target of neurological disorders due to its essential role in GABA transport. Here we report four cryogenic electron microscopy structures of human GAT1, at resolutions of 2.2-3.2 Å. GAT1 in substrate-free form or in complex with the antiepileptic drug tiagabine exhibits an inward-open conformation. In the presence of GABA or nipecotic acid, inward-occluded structures are captured. The GABA-bound structure reveals an interaction network bridged by hydrogen bonds and ion coordination for GABA recognition. The substrate-free structure unwinds the last helical turn of transmembrane helix TM1a to release sodium ions and substrate. Complemented by structure-guided biochemical analyses, our studies reveal detailed mechanism of GABA recognition and transport, and elucidate mode of action of the inhibitors, nipecotic acid and tiagabine.
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Affiliation(s)
- Angqi Zhu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junhao Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Kong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaxin Tan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jianlin Lei
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yafei Yuan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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45
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Shahsavar A, Wellendorph P. GABA transport cycle: beyond a GAT feeling. Nat Struct Mol Biol 2023:10.1038/s41594-023-01032-5. [PMID: 37400656 DOI: 10.1038/s41594-023-01032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Affiliation(s)
- Azadeh Shahsavar
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Petrine Wellendorph
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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46
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Nayak SR, Joseph D, Höfner G, Dakua A, Athreya A, Wanner KT, Kanner BI, Penmatsa A. Cryo-EM structure of GABA transporter 1 reveals substrate recognition and transport mechanism. Nat Struct Mol Biol 2023; 30:1023-1032. [PMID: 37400654 PMCID: PMC10352132 DOI: 10.1038/s41594-023-01011-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/04/2023] [Indexed: 07/05/2023]
Abstract
The inhibitory neurotransmitter γ-aminobutyric acid (GABA) is cleared from the synaptic cleft by the sodium- and chloride-coupled GABA transporter GAT1. Inhibition of GAT1 prolongs the GABAergic signaling at the synapse and is a strategy to treat certain forms of epilepsy. In this study, we present the cryo-electron microscopy structure of Rattus norvegicus GABA transporter 1 (rGAT1) at a resolution of 3.1 Å. The structure elucidation was facilitated by epitope transfer of a fragment-antigen binding (Fab) interaction site from the Drosophila dopamine transporter (dDAT) to rGAT1. The structure reveals rGAT1 in a cytosol-facing conformation, with a linear density in the primary binding site that accommodates a molecule of GABA, a displaced ion density proximal to Na site 1 and a bound chloride ion. A unique insertion in TM10 aids the formation of a compact, closed extracellular gate. Besides yielding mechanistic insights into ion and substrate recognition, our study will enable the rational design of specific antiepileptics.
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Affiliation(s)
| | - Deepthi Joseph
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Georg Höfner
- Department of Pharmacy, Center for Drug Research, Ludwig Maximilians University of Munich, Munich, Germany
| | - Archishman Dakua
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Biophysics Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Arunabh Athreya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Klaus T Wanner
- Department of Pharmacy, Center for Drug Research, Ludwig Maximilians University of Munich, Munich, Germany
| | - Baruch I Kanner
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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Dvorak V, Superti-Furga G. Structural and functional annotation of solute carrier transporters: implication for drug discovery. Expert Opin Drug Discov 2023; 18:1099-1115. [PMID: 37563933 DOI: 10.1080/17460441.2023.2244760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
INTRODUCTION Solute carriers (SLCs) represent the largest group of membrane transporters in the human genome. They play a central role in controlling the compartmentalization of metabolism and most of this superfamily is linked to human disease. Despite being in general considered druggable and attractive therapeutic targets, many SLCs remain poorly annotated, both functionally and structurally. AREAS COVERED The aim of this review is to provide an overview of functional and structural parameters of SLCs that play important roles in their druggability. To do this, the authors provide an overview of experimentally solved structures of human SLCs, with emphasis on structures solved in complex with chemical modulators. From the functional annotations, the authors focus on SLC localization and SLC substrate annotations. EXPERT OPINION Recent progress in the structural and functional annotations allows to refine the SLC druggability index. Particularly the increasing number of experimentally solved structures of SLCs provides insights into mode-of-action of a significant number of chemical modulators of SLCs.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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48
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Singh I, Seth A, Billesbølle CB, Braz J, Rodriguiz RM, Roy K, Bekele B, Craik V, Huang XP, Boytsov D, Pogorelov VM, Lak P, O'Donnell H, Sandtner W, Irwin JJ, Roth BL, Basbaum AI, Wetsel WC, Manglik A, Shoichet BK, Rudnick G. Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Cell 2023; 186:2160-2175.e17. [PMID: 37137306 PMCID: PMC10306110 DOI: 10.1016/j.cell.2023.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/05/2023] [Accepted: 04/06/2023] [Indexed: 05/05/2023]
Abstract
The serotonin transporter (SERT) removes synaptic serotonin and is the target of anti-depressant drugs. SERT adopts three conformations: outward-open, occluded, and inward-open. All known inhibitors target the outward-open state except ibogaine, which has unusual anti-depressant and substance-withdrawal effects, and stabilizes the inward-open conformation. Unfortunately, ibogaine's promiscuity and cardiotoxicity limit the understanding of inward-open state ligands. We docked over 200 million small molecules against the inward-open state of the SERT. Thirty-six top-ranking compounds were synthesized, and thirteen inhibited; further structure-based optimization led to the selection of two potent (low nanomolar) inhibitors. These stabilized an outward-closed state of the SERT with little activity against common off-targets. A cryo-EM structure of one of these bound to the SERT confirmed the predicted geometry. In mouse behavioral assays, both compounds had anxiolytic- and anti-depressant-like activity, with potencies up to 200-fold better than fluoxetine (Prozac), and one substantially reversed morphine withdrawal effects.
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Affiliation(s)
- Isha Singh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Anubha Seth
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Christian B Billesbølle
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Joao Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ramona M Rodriguiz
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Kasturi Roy
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Bethlehem Bekele
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xi-Ping Huang
- Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Danila Boytsov
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Vladimir M Pogorelov
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Walter Sandtner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA
| | - Bryan L Roth
- Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - William C Wetsel
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC 27710, USA; Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA.
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall Suite 508D, San Francisco, CA 94143, USA.
| | - Gary Rudnick
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8066, USA.
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49
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Tu G, Xu B, Luo D, Liu J, Liu Z, Chen G, Xue W. Multi-state Model-Based Identification of Cryptic Allosteric Sites on Human Serotonin Transporter. ACS Chem Neurosci 2023; 14:1686-1694. [PMID: 37067527 DOI: 10.1021/acschemneuro.3c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Serotonin transporter (SERT) plays a fundamental role in taking the synaptic cleft serotonin back to the presynaptic neuron. The discovery of allosteric SERT modulators represents the next-generation medication for psychiatric disorders such as depression. Here, based on the cryo-EM structures of ibogaine in complex with SERT in distinct conformations, the multiple functional structures of the transporter bound to serotonin, including outward-open (OOholo), outward-occluded (OCholo), and inward-open (IOholo and IOholo'), were carefully characterized by induced-fit docking Gaussian-accelerated molecular dynamics (IFD-GaMD) simulation and the free-energy landscape analysis. Further MM/GBSA binding free energy, per-residue contribution, and molecular interaction fingerprint calculations revealed the interaction variations of serotonin with SERT in functional structures, which confirmed the allostery of SERT during serotonin reuptake. Moreover, five unique cryptic allosteric sites, which are druggable and capable of targeting by small molecules, were identified on the characterized multistate structures. These results provide structural and energetic information for the molecular mechanism of serotonin reuptake and will provide opportunities for the development of novel therapeutics based on the identified new allosteric sites on SERT.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Binbin Xu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jin Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou 646000, China
| | - Gang Chen
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou 646000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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50
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Wang XN, Zhang JC, Zhang HY, Wang XF, You CX. Ectopic expression of MmSERT, a mouse serotonin transporter gene, regulates salt tolerance and ABA sensitivity in apple and Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107627. [PMID: 36940523 DOI: 10.1016/j.plaphy.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
5-hydroxytryptamine (5-HT) is ubiquitously present in animals and plants, playing a vital regulatory role. SERT, a conserved serotonin reuptake transporter in animals, regulates intracellular and extracellular concentrations of 5-HT. Few studies have reported 5-HT transporters in plants. Hence, we cloned MmSERT, a serotonin reuptake transporter, from Mus musculus. Ectopic expression of MmSERT into apple calli, apple roots and Arabidopsis. Because 5-HT plays a momentous role in plant stress tolerance, we used MmSERT transgenic materials for stress treatment. We found that MmSERT transgenic materials, including apple calli, apple roots and Arabidopsis, exhibited a stronger salt tolerance phenotype. The reactive oxygen species (ROS) produced were significantly lower in MmSERT transgenic materials compared with controls under salt stress. Meanwhile, MmSERT induced the expression of SOS1, SOS3, NHX1, LEA5 and LTP1 in response to salt stress. 5-HT is the precursor of melatonin, which regulates plant growth under adversity and effectively scavenges ROS. Detection of MmSERT transgenic apple calli and Arabidopsis revealed higher melatonin levels than controls. Besides, MmSERT decreased the sensitivity of apple calli and Arabidopsis to abscisic acid (ABA). In summary, these results demonstrated that MmSERT plays a vital role in plant stress resistances, which perhaps serves as a reference for the application of transgenic technology to improve crops in the future.
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Affiliation(s)
- Xiao-Na Wang
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Jiu-Cheng Zhang
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Hai-Yuan Zhang
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xiao-Fei Wang
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, MOA Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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