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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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Shen Y, Duan H, Yuan L, Asikaer A, Liu Y, Zhang R, Liu Y, Wang Y, Lin Z. Computational biology-based study of the molecular mechanism of spermidine amelioration of acute pancreatitis. Mol Divers 2024; 28:2583-2601. [PMID: 37523101 DOI: 10.1007/s11030-023-10698-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Acute pancreatitis (AP) is an acute inflammatory gastrointestinal disease, the mortality and morbility of which has been on the increase in the past years. Spermidine, a natural polyamine, has a wide range of pharmacological effects including anti-inflammation, antioxidation, anti-aging, and anti-tumorigenic. This study aimed to investigate the reliable targets and molecular mechanisms of spermidine in treating AP. By employing computational biology methods including network pharmacology, molecular docking, and molecular dynamics (MD) simulations, we explored the potential targets of spermidine in improving AP with dietary supplementation. The computational biology results revealed that spermidine had high degrees (degree: 18, betweenness: 38.91; degree: 18, betweenness: 206.41) and stable binding free energy (ΔGbind: - 12.81 ± 0.55 kcal/mol, - 15.00 ± 1.00 kcal/mol) with acetylcholinesterase (AchE) and serotonin transporter (5-HTT). Experimental validation demonstrates that spermidine treatment could reduce the necrosis and AchE activity in pancreatic acinar cells. Cellular thermal shift assay (CETSA) results revealed that spermidine could bind to and stabilize the 5-HTT protein in acinar cells. Moreover, spermidine treatment impeded the rise of the expression of 5-HTT in pancreatic tissues of caerulein induced acute pancreatitis mice. In conclusion, serotonin transporter might be a reliable target of spermidine in treating AP. This study provides new idea for the exploration of potential targets of natural compounds.
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Affiliation(s)
- Yan Shen
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, People's Republic of China
| | - Hongtao Duan
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Lu Yuan
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Aiminuer Asikaer
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Yiyuan Liu
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Yang Liu
- Department of Hepatobiliary Surgery II, Guizhou Provincial People's Hospital, Guiyang, 550002, China
| | - Yuanqiang Wang
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, People's Republic of China
| | - Zhihua Lin
- Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Department of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, People's Republic of China.
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Karabulut S, Kaur H, Gauld JW. Applications and Potential of In Silico Approaches for Psychedelic Chemistry. Molecules 2023; 28:5966. [PMID: 37630218 PMCID: PMC10459288 DOI: 10.3390/molecules28165966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Molecular-level investigations of the Central Nervous System have been revolutionized by the development of computational methods, computing power, and capacity advances. These techniques have enabled researchers to analyze large amounts of data from various sources, including genomics, in vivo, and in vitro drug tests. In this review, we explore how computational methods and informatics have contributed to our understanding of mental health disorders and the development of novel drugs for neurological diseases, with a special focus on the emerging field of psychedelics. In addition, the use of state-of-the-art computational methods to predict the potential of drug compounds and bioinformatic tools to integrate disparate data sources to create predictive models is also discussed. Furthermore, the challenges associated with these methods, such as the need for large datasets and the diversity of in vitro data, are explored. Overall, this review highlights the immense potential of computational methods and informatics in Central Nervous System research and underscores the need for continued development and refinement of these techniques and more inclusion of Quantitative Structure-Activity Relationships (QSARs).
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Affiliation(s)
- Sedat Karabulut
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada;
| | - Harpreet Kaur
- Pharmala Biotech, 82 Richmond Street E, Toronto, ON M5C 1P1, Canada;
| | - James W. Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada;
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Akyuz E, Celik BR, Aslan FS, Sahin H, Angelopoulou E. Exploring the Role of Neurotransmitters in Multiple Sclerosis: An Expanded Review. ACS Chem Neurosci 2023; 14:527-553. [PMID: 36724132 DOI: 10.1021/acschemneuro.2c00589] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and neurodegenerative disease of the central nervous system (CNS). Although emerging evidence has shown that changes in neurotransmitter levels in the synaptic gap may contribute to the pathophysiology of MS, their specific role has not been elucidated yet. In this review, we aim to analyze preclinical and clinical evidence on the structural and functional changes in neurotransmitters in MS and critically discuss their potential role in MS pathophysiology. Preclinical studies have demonstrated that alterations in glutamate metabolism may contribute to MS pathophysiology, by causing excitotoxic neuronal damage. Dysregulated interaction between glutamate and GABA results in synaptic loss. The GABAergic system also plays an important role, by regulating the activity and plasticity of neural networks. Targeting GABAergic/glutamatergic transmission may be effective in fatigue and cognitive impairment in MS. Acetylcholine (ACh) and dopamine can also affect the T-mediated inflammatory responses, thereby being implicated in MS-related neuroinflammation. Also, melatonin might affect the frequency of relapses in MS, by regulating the sleep-wake cycle. Increased levels of nitric oxide in inflammatory lesions of MS patients may be also associated with axonal neuronal degeneration. Therefore, neurotransmitter imbalance may be critically implicated in MS pathophysiology, and future studies are needed for our deeper understanding of their role in MS.
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Affiliation(s)
- Enes Akyuz
- Department of Biophysics, International School of Medicine, University of Health Sciences, Istanbul, Turkey, 34668
| | - Betul Rana Celik
- Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey, 34668
| | - Feyza Sule Aslan
- Hamidiye International School of Medicine, University of Health Sciences, Istanbul, Turkey, 34668
| | - Humeyra Sahin
- School of Medicine, Bezmialem Vakif University, Istanbul, Turkey, 34093
| | - Efthalia Angelopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece, 115 27
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Evaluation of Neurotropic Activity and Molecular Docking Study of New Derivatives of pyrano[4″,3″:4',5']pyrido[3',2':4,5]thieno[3,2- d]pyrimidines on the Basis of pyrano[3,4- c]pyridines. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113380. [PMID: 35684318 PMCID: PMC9182472 DOI: 10.3390/molecules27113380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
Abstract
Background: Heterocyclic compounds and their fused analogs, which contain pharmacophore fragments such as pyridine, thiophene and pyrimidine rings, are of great interest due to their broad spectrum of biological activity. Chemical compounds containing two or more pharmacophore groups due to additional interactions with active receptor centers usually enhance biological activity and can even lead to a new type of activity. The search for new effective neurotropic drugs in the series of derivatives of heterocycles containing pharmacophore groups in organic, bioorganic and medical chemistry is a serious problem. Methods: Modern methodology of drugs involves synthesis, physicochemical study, molecular modeling and selection of active compounds through virtual screening and experimental evaluation of the biological activity of new chimeric compounds with pharmacophore fragments. For the synthesis of new compounds, classical organic methods were used and developed. For the evaluation of neurotropic activity of new synthesized compounds, some biological methods were used according to indicators characterizing anticonvulsant, sedative and antianxiety activity as well as side effects. For docking analysis, various soft ware packages and methods were used. Results: As a result of multistep reactions, 11 new, tri- and tetracyclic heterocyclic systems were obtained. The studied compounds exhibit protection against pentylenetetrazole (PTZ) seizures as well as some psychotropic effects. The biological assays evidenced that nine of the eleven studied compounds showed a high anticonvulsant activity by antagonism with pentylenetetrazole. The toxicity of the compounds is low, and they do not induce muscle relaxation in the studied doses. According to the study of psychotropic activity, it was found that the selected compounds have an activating behavior and anxiolytic effects on the “open field” and “elevated plus maze” (EPM) models. The data obtained indicate the anxiolytic (antianxiety) activity of the derivatives of tricyclic thieno[2,3-b]pyridines and tetracyclic pyridothieno[3,2-d]pyrimidin-8-ones, especially pronounced in compounds 3b–f and 4e. The studied compounds increase the latent time of first immobilization on the “forced swimming” (FS) model and exhibit antidepressant effects; compounds 3e and 3f especially exhibit these effects, similarly to diazepam. Docking studies revealed that compounds 3c and 4b bound tightly in the active site of γ-aminobutyric acid type A (GABAA) receptors with a value of the scoring function that estimates free energy of binding (∆G) at −10.0 ± 5 kcal/mol. Compound 4e showed the best affinity ((∆G) at −11.0 ± 0.54 kcal/mol) and seems to be an inhibitor of serotonin (SERT) transporter. Compounds 3c–f and 4e practically bound with the groove of T4L of 5HT_1A and blocked it completely, while the best affinity observed was in compound 3f ((∆G) at −9.3 ± 0.46 kcal/mol). Conclusions: The selected compounds have an anticonvulsant, activating behavior and anxiolytic effects and at the same time exhibit antidepressant effects.
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Huang B, Liu H, Wu Y, Li C, Tang Q, Zhang YW. Two Lignan Glycosides from Albizia julibrissin Durazz. Noncompetitively Inhibit Serotonin Transporter. Pharmaceuticals (Basel) 2022; 15:ph15030344. [PMID: 35337141 PMCID: PMC8954383 DOI: 10.3390/ph15030344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 12/11/2022] Open
Abstract
Albizia julibrissin Durazz. is one of the most common herbs used for depression and anxiety treatment, but its molecular basis and mechanism of action as an antidepressant or anxiolytic drug are not understood. In this study, we separated and identified two lignan glycosides that inhibit serotonin transporter (SERT) noncompetitively by decreasing Vmax with little change in Km for its fluorescence substrate. In addition, treatment with lignan glycosides did not alter total and cell surface expression levels of the transporter protein. The two compounds decreased the accessibility of a cysteine residue placed in the extracellular substrate permeation pathway by inducing a conformational shift toward an outward-closed state of SERT. These results are consistent with molecular docking for the association of the lignan glycosides to the allosteric site in SERT. The present work supports the proposal that these compounds act on SERT by a novel underlying mechanism of action different from that of conventional antidepressant drugs.
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Affiliation(s)
- Bishan Huang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (B.H.); (H.L.); (Y.W.); (C.L.)
| | - Hanhe Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (B.H.); (H.L.); (Y.W.); (C.L.)
| | - Yingyao Wu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (B.H.); (H.L.); (Y.W.); (C.L.)
| | - Chan Li
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (B.H.); (H.L.); (Y.W.); (C.L.)
| | - Qingfa Tang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China;
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou 510515, China
| | - Yuan-Wei Zhang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (B.H.); (H.L.); (Y.W.); (C.L.)
- Correspondence:
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Jarończyk M, Walory J. Novel Molecular Targets of Antidepressants. Molecules 2022; 27:533. [PMID: 35056845 PMCID: PMC8778443 DOI: 10.3390/molecules27020533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
Antidepressants target a variety of proteins in the central nervous system (CNS), the most important belonging to the family of G-protein coupled receptors and the family of neurotransmitter transporters. The increasing number of crystallographic structures of these proteins have significantly contributed to the knowledge of their mechanism of action, as well as to the design of new drugs. Several computational approaches such as molecular docking, molecular dynamics, and virtual screening are useful for elucidating the mechanism of drug action and are important for drug design. This review is a survey of molecular targets for antidepressants in the CNS and computer based strategies to discover novel compounds with antidepressant activity.
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Overlap and Specificity in the Substrate Spectra of Human Monoamine Transporters and Organic Cation Transporters 1, 2, and 3. Int J Mol Sci 2021; 22:ijms222312816. [PMID: 34884618 PMCID: PMC8657982 DOI: 10.3390/ijms222312816] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/23/2022] Open
Abstract
Human monoamine transporters (MATs) are cation transporters critically involved in neuronal signal transmission. While inhibitors of MATs have been intensively studied, their substrate spectra have received far less attention. Polyspecific organic cation transporters (OCTs), predominantly known for their role in hepatic and renal drug elimination, are also expressed in the central nervous system and might modulate monoaminergic signaling. Using HEK293 cells overexpressing MATs or OCTs, we compared uptake of 48 compounds, mainly phenethylamine and tryptamine derivatives including matched molecular pairs, across noradrenaline, dopamine and serotonin transporters and OCTs (1, 2, and 3). Generally, MATs showed surprisingly high transport activities for numerous analogs of neurotransmitters, but their substrate spectra were limited by molar mass. Human OCT2 showed the broadest substrate spectrum, and also the highest overlap with MATs substrates. Comparative kinetic analyses revealed that the radiotracer meta-iodobenzylguanidine had the most balanced uptake across all six transporters. Matched molecular pair analyses comparing MAT and OCT uptake using the same methodology could provide a better understanding of structural determinants for high cell uptake by MATs or OCTs. The data may result in a better understanding of pharmacokinetics and toxicokinetics of small molecular organic cations and, possibly, in the development of more specific radiotracers for MATs.
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