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Zha J, He J, Wu C, Zhang M, Liu X, Zhang J. Designing drugs and chemical probes with the dualsteric approach. Chem Soc Rev 2023; 52:8651-8677. [PMID: 37990599 DOI: 10.1039/d3cs00650f] [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: 11/23/2023]
Abstract
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.
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Affiliation(s)
- Jinyin Zha
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jixiao He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengwei Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyang Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Liu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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2
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Qian M, Sun Z, Chen X, Van Calenbergh S. Study of G protein-coupled receptors dimerization: From bivalent ligands to drug-like small molecules. Bioorg Chem 2023; 140:106809. [PMID: 37651896 DOI: 10.1016/j.bioorg.2023.106809] [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: 04/12/2023] [Revised: 07/27/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
In the past decades an increasing number of studies revealed that G protein-coupled receptors (GPCRs) are capable of forming dimers or even higher-ordered oligomers, which may modulate receptor function and act as potential drug targets. In this review, we briefly summarized the design strategy of bivalent GPCR ligands and mainly focused on how to use them to study and/or detect GPCP dimerization in vitro and in vivo. Bivalent ligands show specific properties relative to their corresponding monomeric ligands because they are able to bind to GPCR homodimers or heterodimers simultaneously. For example, bivalent ligands with optimal length of spacers often exhibited higher binding affinities for dimers compared to that of monomers. Furthermore, bivalent ligands displayed specific signal transduction compared to monovalent ligands. Finally, we give our perspective on targeting GPCR dimers from traditional bivalent ligands to more drug-like small molecules.
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Affiliation(s)
- Mingcheng Qian
- School of Pharmacy, Changzhou University, Changzhou 213164, Jiangsu, China; Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium.
| | - Zhengyang Sun
- School of Pharmacy, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Xin Chen
- School of Pharmacy, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium.
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3
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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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4
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Aggarwal S, Mortensen OV. Discovery and Development of Monoamine Transporter Ligands. ADVANCES IN NEUROBIOLOGY 2023; 30:101-129. [PMID: 36928847 PMCID: PMC10074400 DOI: 10.1007/978-3-031-21054-9_4] [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] [Indexed: 03/18/2023]
Abstract
Monoamine transporters (MATs) are targets of a wide range of compounds that have been developed as therapeutic treatments for various neuropsychiatric and neurodegenerative disorders such as depression, ADHD, neuropathic pain, anxiety disorders, stimulant use disorders, epilepsy, and Parkinson's disease. The MAT family is comprised of three main members - the dopamine transporter (DAT), the norepinephrine transporter (NET), and the serotonin transporter (SERT). These transporters are through reuptake responsible for the clearance of their respective monoamine substrates from the extracellular space. The determination of X-ray crystal structures of MATs and their homologues bound with various substrates and ligands has resulted in a surge of structure-function-based studies of MATs to understand the molecular basis of transport function and the mechanism of various ligands that ultimately result in their behavioral effects. This review focusses on recent examples of ligand-based structure-activity relationship studies trying to overcome some of the challenges associated with previously developed MAT inhibitors. These studies have led to the discovery of unique and novel structurally diverse MAT ligands including allosteric modulators. These novel molecular scaffolds serve as leads for designing more effective therapeutic interventions by modulating the activities of MATs and ultimately their associated neurotransmission and behavioral effects.
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Affiliation(s)
- Shaili Aggarwal
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA.
| | - Ole Valente Mortensen
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA.
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5
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Nepal B, Das S, Reith ME, Kortagere S. Overview of the structure and function of the dopamine transporter and its protein interactions. Front Physiol 2023; 14:1150355. [PMID: 36935752 PMCID: PMC10020207 DOI: 10.3389/fphys.2023.1150355] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
The dopamine transporter (DAT) plays an integral role in dopamine neurotransmission through the clearance of dopamine from the extracellular space. Dysregulation of DAT is central to the pathophysiology of numerous neuropsychiatric disorders and as such is an attractive therapeutic target. DAT belongs to the solute carrier family 6 (SLC6) class of Na+/Cl- dependent transporters that move various cargo into neurons against their concentration gradient. This review focuses on DAT (SCL6A3 protein) while extending the narrative to the closely related transporters for serotonin and norepinephrine where needed for comparison or functional relevance. Cloning and site-directed mutagenesis experiments provided early structural knowledge of DAT but our contemporary understanding was achieved through a combination of crystallization of the related bacterial transporter LeuT, homology modeling, and subsequently the crystallization of drosophila DAT. These seminal findings enabled a better understanding of the conformational states involved in the transport of substrate, subsequently aiding state-specific drug design. Post-translational modifications to DAT such as phosphorylation, palmitoylation, ubiquitination also influence the plasma membrane localization and kinetics. Substrates and drugs can interact with multiple sites within DAT including the primary S1 and S2 sites involved in dopamine binding and novel allosteric sites. Major research has centered around the question what determines the substrate and inhibitor selectivity of DAT in comparison to serotonin and norepinephrine transporters. DAT has been implicated in many neurological disorders and may play a role in the pathology of HIV and Parkinson's disease via direct physical interaction with HIV-1 Tat and α-synuclein proteins respectively.
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Affiliation(s)
- Binod Nepal
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Sanjay Das
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Maarten E. Reith
- Department of Psychiatry, New York University School of Medicine, New York City, NY, United States
| | - Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- *Correspondence: Sandhya Kortagere,
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6
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Ruchala I, Battisti UM, Nguyen VT, Chen RYT, Glennon RA, Eltit JM. Functional characterization of N-octyl 4-methylamphetamine variants and related bivalent compounds at the dopamine and serotonin transporters using Ca 2+ channels as sensors. Toxicol Appl Pharmacol 2021; 419:115513. [PMID: 33785354 PMCID: PMC8148225 DOI: 10.1016/j.taap.2021.115513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/21/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
The early characterization of ligands at the dopamine and serotonin transporters, DAT and SERT, respectively, is important for drug discovery, forensic sciences, and drug abuse research. 4-Methyl amphetamine (4-MA) is a good example of an abused drug whose overdose can be fatal. It is a potent substrate at DAT and SERT where its simplest secondary amine (N-methyl 4-MA) retains substrate activity at them. In contrast, N-n-butyl 4-MA is very weak, therefore it was categorized as inactive at these transporters. Here, N-octyl 4-MA and other related compounds were synthesized, and their activities were evaluated at DAT and SERT. To expedite this endeavor, cells expressing DAT or SERT were co-transfected with a voltage-gated Ca2+ channel and, the genetically-encoded Ca2+ sensor, GCaMP6s. Control compounds and the newly synthesized molecules were tested on these cells using an automated multi-well fluorescence plate reader; substrates and inhibitors were identified successfully at DAT and SERT. N-Octyl 4-MA and three bivalent compounds were inhibitors at these transporters. These findings were validated by measuring Ca2+-mobilization using quantitative fluorescence microscopy. The bivalent molecules were the most potent of the series and were further characterized in an uptake-inhibition assay. Compared to cocaine, they showed comparable potency inhibiting uptake at DAT and higher potency at SERT. These observations support a previous hypothesis that amphetamine-related (and, here, N-extended alkyl and) bivalent arylalkylamine molecules are active at monoamine transporters, showing potent activity as reuptake inhibitors, and implicate the involvement of a distant auxiliary binding feature to account for their actions at DAT and SERT.
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Affiliation(s)
- Iwona Ruchala
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, United States of America
| | - Umberto M Battisti
- Deparment of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, United States of America
| | - Vy T Nguyen
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, United States of America
| | - Rita Yu-Tzu Chen
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, United States of America
| | - Richard A Glennon
- Deparment of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, United States of America
| | - Jose M Eltit
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, United States of America.
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7
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Qian M, Ricarte A, Wouters E, Dalton JAR, Risseeuw MDP, Giraldo J, Van Calenbergh S. Discovery of a true bivalent dopamine D 2 receptor agonist. Eur J Med Chem 2021; 212:113151. [PMID: 33450620 DOI: 10.1016/j.ejmech.2020.113151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/06/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
Employing two different alkyne-modified dopamine agonists to construct bivalent compounds via click chemistry resulted in the identification of a bivalent ligand (11c) for dopamine D2 receptor homodimer, which, compared to its parent monomeric alkyne, showed a 16-fold higher binding affinity for the dopamine D2 receptor and a 5-fold higher potency in a cAMP assay in HEK 293T cells stably expressing D2R. Molecular modeling revealed that 11c can indeed bridge the orthosteric binding sites of a D2R homodimer in a relaxed conformation via the TM5-TM6 interface and allows to largely rationalize the results of the receptor assays.
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Affiliation(s)
- Mingcheng Qian
- Department of Medicinal Chemistry, School of Pharmacy, Changzhou University, Changzhou, 213164, Jiangsu, China; Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Adrián Ricarte
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigaciói InnovacióParc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Elise Wouters
- Laboratory of Toxicology, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigaciói InnovacióParc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística, Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigaciói InnovacióParc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000, Ghent, Belgium.
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8
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Pharmacological Characterization of 4-Methylthioamphetamine Derivatives. Molecules 2020; 25:molecules25225310. [PMID: 33203055 PMCID: PMC7696343 DOI: 10.3390/molecules25225310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/30/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022] Open
Abstract
Amphetamine derivatives have been used in a wide variety of pathologies because of their pharmacological properties as psychostimulants, entactogens, anorectics, and antidepressants. However, adverse cardiovascular effects (sympathomimetics) and substance abuse problems (psychotropic and hallucinogenic effects) have limited their use. 4-Methylthioamphetamine (MTA) is an amphetamine derivative that has shown to inhibit monoamine uptake and monoamine oxidase. However, the pharmacological characterization (neurochemical, behavioral, and safety) of its derivatives 4-ethylthioamphetamine (ETA) and 4-methylthio-phenil-2-butanamine (MT-But) have not been studied. In the current experiments, we show that ETA and MT-But do not increase locomotor activity and conditioned place preference with respect to MTA. At the neurochemical level, ETA and MT-But do not increase in vivo DA release in striatum, but ETA and MT-But affect the nucleus accumbens bioaccumulation of DA and DOPAC. Regarding cardiovascular effects, the administration of MTA and ETA increased the mean arterial pressure and only ETA significantly increases the heart rate. Our results show that the pharmacological and safety profiles of MTA are modulated by changing the methyl-thio group or the methyl group of the aminoethyl chain.
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9
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Xue W, Fu T, Zheng G, Tu G, Zhang Y, Yang F, Tao L, Yao L, Zhu F. Recent Advances and Challenges of the Drugs Acting on Monoamine Transporters. Curr Med Chem 2020; 27:3830-3876. [DOI: 10.2174/0929867325666181009123218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 01/06/2023]
Abstract
Background:
The human Monoamine Transporters (hMATs), primarily including hSERT,
hNET and hDAT, are important targets for the treatment of depression and other behavioral disorders
with more than the availability of 30 approved drugs.
Objective:
This paper is to review the recent progress in the binding mode and inhibitory mechanism of
hMATs inhibitors with the central or allosteric binding sites, for the benefit of future hMATs inhibitor
design and discovery. The Structure-Activity Relationship (SAR) and the selectivity for hit/lead compounds
to hMATs that are evaluated by in vitro and in vivo experiments will be highlighted.
Methods:
PubMed and Web of Science databases were searched for protein-ligand interaction, novel
inhibitors design and synthesis studies related to hMATs.
Results:
Literature data indicate that since the first crystal structure determinations of the homologous
bacterial Leucine Transporter (LeuT) complexed with clomipramine, a sizable database of over 100 experimental
structures or computational models has been accumulated that now defines a substantial degree
of structural variability hMATs-ligands recognition. In the meanwhile, a number of novel hMATs
inhibitors have been discovered by medicinal chemistry with significant help from computational models.
Conclusion:
The reported new compounds act on hMATs as well as the structures of the transporters
complexed with diverse ligands by either experiment or computational modeling have shed light on the
poly-pharmacology, multimodal and allosteric regulation of the drugs to transporters. All of the studies
will greatly promote the Structure-Based Drug Design (SBDD) of structurally novel scaffolds with high
activity and selectivity for hMATs.
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Affiliation(s)
- Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Guoxun Zheng
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Gao Tu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Yang Zhang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Lixia Yao
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, United States
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug Research, Chongqing University, Chongqing 401331, China
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10
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Zhu R, Sandtner W, Ahiable JEA, Newman AH, Freissmuth M, Sitte HH, Hinterdorfer P. Allosterically Linked Binding Sites in Serotonin Transporter Revealed by Single Molecule Force Spectroscopy. Front Mol Biosci 2020; 7:99. [PMID: 32656227 PMCID: PMC7325972 DOI: 10.3389/fmolb.2020.00099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/01/2020] [Indexed: 01/24/2023] Open
Abstract
Crystal structures and experiments relying on the tools of molecular pharmacology reported conflicting results on ligand binding sites in neurotransmitter/sodium symporters (NSS). We explored the number and functionality of ligand binding sites of NSS in a physiological setting by designing novel tools for atomic force microscopy (AFM). These allow for directly measuring the interaction forces between the serotonin transporter (SERT) and the antidepressant S-citalopram (S-CIT) on the single molecule level: the AFM cantilever tips were functionalized with S-CIT via a flexible polyethylene glycol (PEG) linker. The tip chemistry was validated by specific force measurements and recognition imaging on CHO cells. Two distinct populations of characteristic binding strengths of S-CIT binding to SERT were revealed in Na+-containing buffer. In contrast, in Li+-containing buffer, SERT showed only low force interactions. Conversely, the vestibular mutant SERT-G402H merely displayed the high force population. These observations provide physical evidence for the existence of two binding sites in SERT. The dissociation rate constant of both binding sites was extracted by varying the dynamics of the force-probing experiments. Competition experiments revealed that the two sites are allosterically coupled and exert reciprocal modulation.
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Affiliation(s)
- Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Walter Sandtner
- 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
| | - Joan E A Ahiable
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, Baltimore, MD, United States
| | - 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
| | - Harald H Sitte
- 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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11
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A functionalized hydroxydopamine quinone links thiol modification to neuronal cell death. Redox Biol 2019; 28:101377. [PMID: 31760358 PMCID: PMC6880099 DOI: 10.1016/j.redox.2019.101377] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/09/2019] [Accepted: 11/07/2019] [Indexed: 01/22/2023] Open
Abstract
Recent findings suggest that dopamine oxidation contributes to the development of Parkinson's disease (PD); however, the mechanistic details remain elusive. Here, we compare 6-hydroxydopamine (6-OHDA), a product of dopamine oxidation that commonly induces dopaminergic neurodegeneration in laboratory animals, with a synthetic alkyne-functionalized 6-OHDA variant. This synthetic molecule provides insights into the reactivity of quinone and neuromelanin formation. Employing Huisgen cycloaddition chemistry (or “click chemistry”) and fluorescence imaging, we found that reactive 6-OHDA p-quinones cause widespread protein modification in isolated proteins, lysates and cells. We identified cysteine thiols as the target site and investigated the impact of proteome modification by quinones on cell viability. Mass spectrometry following cycloaddition chemistry produced a large number of 6-OHDA modified targets including proteins involved in redox regulation. Functional in vitro assays demonstrated that 6-OHDA inactivates protein disulfide isomerase (PDI), which is a central player in protein folding and redox homeostasis. Our study links dopamine oxidation to protein modification and protein folding in dopaminergic neurons and the PD model. Chemical modification of 6-OHDA increases stability of 6-OHDA p-quinone by preventing neuromelanin formation. Modified 6-OHDA enables visualization of thiol-dependent protein modification by p-quinone. Wide-spread proteome modification by 6-OHDA p-quinone impairs neuroblastoma viability. 6-OHDA p-quinone inactivates PDI linking dopamine oxidation to protein unfolding.
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Joseph D, Pidathala S, Mallela AK, Penmatsa A. Structure and Gating Dynamics of Na +/Cl - Coupled Neurotransmitter Transporters. Front Mol Biosci 2019; 6:80. [PMID: 31555663 PMCID: PMC6742698 DOI: 10.3389/fmolb.2019.00080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022] Open
Abstract
Neurotransmitters released at the neural synapse through vesicle exocytosis are spatiotemporally controlled by the action of neurotransmitter transporters. Integral membrane proteins of the solute carrier 6 (SLC6) family are involved in the sodium and chloride coupled uptake of biogenic amine neurotransmitters including dopamine, serotonin, noradrenaline and inhibitory neurotransmitters including glycine and γ-amino butyric acid. This ion-coupled symport works through a well-orchestrated gating of substrate through alternating-access, which is mediated through movements of helices that resemble a rocking-bundle. A large array of commercially prescribed drugs and psychostimulants selectively target neurotransmitter transporters thereby modulating their levels in the synaptic space. Drug-induced changes in the synaptic neurotransmitter levels can be used to treat depression or neuropathic pain whereas in some instances prolonged usage can lead to habituation. Earlier structural studies of bacterial neurotransmitter transporter homolog LeuT and recent structure elucidation of the Drosophila dopamine transporter (dDAT) and human serotonin transporter (hSERT) have yielded a wealth of information in understanding the transport and inhibition mechanism of neurotransmitter transporters. Computational studies based on the structures of dDAT and hSERT have shed light on the dynamics of varied components of these molecular gates in affecting the uphill transport of neurotransmitters. This review seeks to address structural dynamics of neurotransmitter transporters at the extracellular and intracellular gates and the effect of inhibitors on the ligand-binding pocket. We also delve into the effect of additional factors including lipids and cytosolic domains that influence the translocation of neurotransmitters across the membrane.
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Affiliation(s)
- Deepthi Joseph
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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13
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Hellsberg E, Ecker GF, Stary-Weinzinger A, Forrest LR. A structural model of the human serotonin transporter in an outward-occluded state. PLoS One 2019; 14:e0217377. [PMID: 31251747 PMCID: PMC6599148 DOI: 10.1371/journal.pone.0217377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
The human serotonin transporter hSERT facilitates the reuptake of its endogenous substrate serotonin from the synaptic cleft into presynaptic neurons after signaling. Reuptake regulates the availability of this neurotransmitter and therefore hSERT plays an important role in balancing human mood conditions. In 2016, the first 3D structures of this membrane transporter were reported in an inhibitor-bound, outward-open conformation. These structures revealed valuable information about interactions of hSERT with antidepressant drugs. Nevertheless, the question remains how serotonin facilitates the specific conformational changes that open and close pathways from the synapse and to the cytoplasm as required for transport. Here, we present a serotonin-bound homology model of hSERT in an outward-occluded state, a key intermediate in the physiological cycle, in which the interactions with the substrate are likely to be optimal. Our approach uses two template structures and includes careful refinement and comprehensive computational validation. According to microsecond-long molecular dynamics simulations, this model exhibits interactions between the gating residues in the extracellular pathway, and these interactions differ from those in an outward-open conformation of hSERT bound to serotonin. Moreover, we predict several features of this state by monitoring the intracellular gating residues, the extent of hydration, and, most importantly, protein-ligand interactions in the central binding site. The results illustrate common and distinct characteristics of these two transporter states and provide a starting point for future investigations of the transport mechanism in hSERT.
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Affiliation(s)
- Eva Hellsberg
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | | | - Lucy R. Forrest
- Computational Structural Biology Unit, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD, United States of America
- * E-mail:
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14
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Ladefoged LK, Zeppelin T, Schiøtt B. Molecular modeling of neurological membrane proteins − from binding sites to synapses. Neurosci Lett 2019; 700:38-49. [DOI: 10.1016/j.neulet.2018.05.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 01/07/2023]
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15
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Núñez-Vivanco G, Fierro A, Moya P, Iturriaga-Vásquez P, Reyes-Parada M. 3D similarities between the binding sites of monoaminergic target proteins. PLoS One 2018; 13:e0200637. [PMID: 30028869 PMCID: PMC6054423 DOI: 10.1371/journal.pone.0200637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/30/2018] [Indexed: 02/06/2023] Open
Abstract
The study of binding site similarities can be relevant to understand the interaction of different drugs at several molecular targets. The increasing availability of protein crystal structures and the development of novel algorithms designed to evaluate three-dimensional similarities, represent a great opportunity to explore the existence of electronic and shape features shared by clinically relevant proteins, which could assist drug design and discovery. Proteins involved in the recognition of monoaminergic neurotransmitters, such as monoamine transporters or monoamine oxidases (MAO) have been related to several psychiatric and neurological disorders such as depression or Parkinson’s disease. In this work, we evaluated the possible existence of similarities among the binding sites of the serotonin transporter (SERT), the dopamine transporter (DAT), MAO-A and MAO-B. This study was carried out using molecular simulation methodologies linked to the statistical algorithm PocketMatch, which was modified in order to obtain similarities profiles. Our results show that DAT and SERT exhibit a high degree of 3-D similarities all along the pathway that is presumably involved in the substrate transport process. Distinct differences, on the other hand, were found both at the extracellular and the intracellular ends of the transporters, which might be involved in the selective initial recognition of the corresponding substrate. Similarities were also found between the active (catalytic) site of MAO-A and the extracellular vestibule of SERT (the S2 binding site). These results suggest some degree of structural convergence for these proteins, which have different functions, tissue distribution and genetic origin, but which share the same endogenous ligand (serotonin). Beyond the functional implications, these findings are valuable for the design of both selective and non-selective ligands.
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Affiliation(s)
- Gabriel Núñez-Vivanco
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Escuela de Ingeniería Civil en Bioinformática, Universidad de Talca, Talca, Chile
| | | | - Pablo Moya
- Instituto de Fisiología, Universidad de Valparaíso, Valparaíso, Chile.,Centro Interdisciplinario de Neurociencia de Valparaíso CINV, Universidad de Valparaíso, Valparaíso, Chile
| | | | - Miguel Reyes-Parada
- School of Medicine, Faculty of Medical Sciences, University of Santiago de Chile, Santiago, Chile.,Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Talca, Chile
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16
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Abstract
The dopamine (DAT), serotonin (SERT), and norepinephrine (NET) transporters, which are collectively referred to as monoamine transporters (MATs), play significant roles in regulating the neuronal response to these neurotransmitters. MATs terminate the action of these neurotransmitters by translocating them from the synaptic space into the presynaptic neurons. These three transmitters are responsible for controlling a number of physiological, emotional, and behavioral functions, with their transporters being the site of action of drugs employed for the treatment of a variety of conditions, including depression, anxiety, ADHD, schizophrenia, and psychostimulant abuse. Provided in this unit is information on the localization and regulation of MATs and the structural components of these proteins most responsible for the translocation process. Also included is a brief description of the evolution of ligands that interact with these transporters, as well as current theories concerning the pharmacological effects of substances that interact with these sites, including the molecular mechanisms of action of uptake inhibitors and allosteric modulators. Data relating to the presence, structure, and functions of allosteric modulators are included as well. The aim of this review is to provide background information on MATs to those who are new to this field, with a focus on the therapeutic potential of compounds that interact with these substrate transport sites. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shaili Aggarwal
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Pennsylvania
| | - Ole V Mortensen
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Pennsylvania
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17
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Foreman KW. A general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands. PLoS One 2017; 12:e0188134. [PMID: 29166663 PMCID: PMC5699851 DOI: 10.1371/journal.pone.0188134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/01/2017] [Indexed: 01/13/2023] Open
Abstract
Empirical data has shown that bivalent inhibitors can bind a given target protein significantly better than their monomeric counterparts. However, predicting the corresponding theoretical fold improvements has been challenging. The current work builds off the reacted-site probability approach to provide a straightforward baseline reference model for predicting fold-improvements in effective affinity of dimerized ligands over their monomeric counterparts. For the more familiar irreversibly linked bivalents, the model predicts a weak dependence on tether length and a scaling of the effective affinity with the 3/2 power of the monomer’s affinity. For the previously untreated case of the emerging technology of reversibly linking dimers, the effective affinity is also significantly improved over the affinity of the non-dimerizing monomers. The model is related back to experimental quantities, such as EC50s, and the approaches to fully characterize the system given the assumptions of the model. Because of the predicted significant potency gains, both irreversibly and reversibly linked bivalent ligands offer the potential to be a disruptive technology in pharmaceutical research.
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Grouleff J, Koldsø H, Miao Y, Schiøtt B. Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT. ACS Chem Neurosci 2017; 8:619-628. [PMID: 27966884 DOI: 10.1021/acschemneuro.6b00359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The human monoamine transporters (MATs) facilitate the reuptake of monoamine neurotransmitters from the synaptic cleft. MATs are linked to a number of neurological diseases and are the targets of both therapeutic and illicit drugs. Until recently, no high-resolution structures of the human MATs existed, and therefore, studies of this transporter family have relied on investigations of the homologues bacterial transporters such as the leucine transporter LeuT, which has been crystallized in several conformational states. A two-substrate transport mechanism has been suggested for this transporter family, which entails that high-affinity binding of a second substrate in an extracellular site is necessary for the substrate in the central binding site to be transported. Compelling evidence for this mechanism has been presented, however, a number of equally compelling accounts suggest that the transporters function through a mechanism involving only a single substrate and a single high-affinity site. To shed light on this apparent contradiction, we have performed extensive molecular dynamics simulations of LeuT in the outward-occluded conformation with either one or two substrates bound to the transporter. We have also calculated the substrate binding affinity in each of the two proposed binding sites through rigorous free energy simulations. Results show that substrate binding is unstable in the extracellular vestibule and the substrate binding affinity within the suggested extracellular site is very low (0.2 and 3.3 M for the two dominant binding modes) compared to the central substrate binding site (14 nM). This suggests that for LeuT in the outward-occluded conformation only a single high-affinity substrate binding site exists.
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Affiliation(s)
- Julie Grouleff
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
| | - Heidi Koldsø
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
| | - Yinglong Miao
- Howard
Hughes Medical Institute and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
| | - Birgit Schiøtt
- Center
for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience
Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, 8000 Aarhus
C, Denmark
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19
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Topiol S, Bang-Andersen B, Sanchez C, Plenge P, Loland CJ, Juhl K, Larsen K, Bregnedal P, Bøgesø KP. X-ray structure based evaluation of analogs of citalopram: Compounds with increased affinity and selectivity compared with R-citalopram for the allosteric site (S2) on hSERT. Bioorg Med Chem Lett 2017; 27:470-478. [DOI: 10.1016/j.bmcl.2016.12.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 01/25/2023]
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