1
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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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2
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Sinha P, Yadav AK. Repurposing integrase inhibitors against human T-lymphotropic virus type-1: a computational approach. J Biomol Struct Dyn 2024:1-12. [PMID: 38234060 DOI: 10.1080/07391102.2024.2304681] [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: 08/10/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
Adult T-cell Lymphoma (ATL) is caused by the delta retrovirus family member known as Human T-cell Leukaemia Type I (HTLV-1). Due to the unavailability of any cure, the study gained motivation to identify some repurposed drugs against the virus. A quick and accurate method of screening licensed medications for finding a treatment for HTLV-1 is by cheminformatics drug repurposing in order to analyze a dataset of FDA approved integrase antivirals against HTLV-1 infection. To determine how the antiviral medications interacted with the important residues in the HTLV-1 integrase active regions, molecular docking modeling was used. The steady behavior of the ligands inside the active region was then confirmed by molecular dynamics for the probable receptor-drug complexes. Cabotegravir, Raltegravir and Elvitegravir had the best docking scores with the target, indicating that they can tightly bind to the HTLV-1 integrase. Moreover, MD simulation revealed that the Cabotegravir-HTLV-1, Raltegravir-HTLV-1 and Elvitegravir-HTLV-1 interactions were stable. It is obvious that more testing of these medicines in both clinical trials and experimental tests is necessary to demonstrate their efficacy against HTLV-1 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prashasti Sinha
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Anil Kumar Yadav
- Department of Physics, School of Physical & Decision Science, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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3
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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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4
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Wang P, Yan F, Dong J, Wang S, Shi Y, Zhu M, Zuo Y, Ma H, Xue R, Zhai D, Song X. A multiple-step screening protocol to identify norepinephrine and dopamine reuptake inhibitors for depression. Phys Chem Chem Phys 2023; 25:8341-8354. [PMID: 36880666 DOI: 10.1039/d2cp05676c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Depression severely impairs the health of people all over the world. Cognitive dysfunction due to depression has resulted in a severe economic burden to family and society induced by the reduction of social functioning of patients. Norepinephrine-dopamine reuptake inhibitors (NDRIs) targeted with the human norepinephrine transporter (hNET) and distributed with the human dopamine transporter (hDAT) simultaneously treat depression and improve cognitive function, and they effectively prevent sexual dysfunction and other side effects. Because many patients continue to poorly respond to NDRIs, it is urgent to discover novel NDRI antidepressants that do not interfere with cognitive function. The aim of this work was to selectively identify novel NDRI candidates acting against hNET and hDAT from large compound libraries by a comprehensive strategy integrating support vector machine (SVM) models, ADMET, molecular docking, in vitro binding assays, molecular dynamics simulation, and binding energy calculation. First, 6522 compounds that do not inhibit the human serotonin transporter (hSERT) were obtained by SVM models of hNET, hDAT, and non-target hSERT with similarity analyses from compound libraries. ADMET and molecular docking were then used to identify compounds that could potently bind to the hNET and hDAT with satisfactory ADMET, and 4 compounds were successfully identified. According to their docking scores and ADMET information, 3719810 was advanced for profiling by in vitro assays as a novel NDRI lead compound due to its strongest druggability and balancing activities. Encouragingly, 3719810 performed comparative activities on two targets, with Ki values of 7.32 μM for hNET and 5.23 μM for hDAT. To obtain candidates with additional activities and balance the activities of 2 targets, 5 analogs were optimized, and 2 novel scaffold compounds were successively designed. By assessment of molecular docking, molecular dynamics simulations, and binding energy calculations, 5 compounds were validated as NDRI candidates with high activities, and 4 of them performed acceptable balancing activities acting on hNET and hDAT. This work supplied promising novel NDRIs for treatment of depression with cognitive dysfunction or other related neurodegenerative disorders, and also provided a strategy for highly efficient and cost-effective identification of inhibitors for dual targets with homologous non-targets.
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Affiliation(s)
- Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Fengmei Yan
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Jianghong Dong
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Shengqiang Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Yu Shi
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Mengdan Zhu
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Yuting Zuo
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Hui Ma
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Ruirui Xue
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Dingjie Zhai
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
| | - Xiaoyu Song
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China.
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5
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Occlusion of the human serotonin transporter is mediated by serotonin-induced conformational changes in the bundle domain. J Biol Chem 2022; 298:101613. [PMID: 35065961 PMCID: PMC8867121 DOI: 10.1016/j.jbc.2022.101613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
The human serotonin transporter (hSERT) terminates neurotransmission by removing serotonin (5HT) from the synaptic cleft, an essential process for proper functioning of serotonergic neurons. Structures of the hSERT have revealed its molecular architecture in four conformations, including the outward-open and occluded states, and show the transporter’s engagement with co-transported ions and the binding mode of inhibitors. In this study, we investigated the molecular mechanism by which the hSERT occludes and sequesters the substrate 5HT. This first step of substrate uptake into cells is a structural change consisting of the transition from the outward-open to the occluded state. Inhibitors such as the antidepressants citalopram, fluoxetine, and sertraline inhibit this step of the transport cycle. Using molecular dynamics simulations, we reached a fully occluded state, in which the transporter-bound 5HT becomes fully shielded from both sides of the membrane by two closed hydrophobic gates. Analysis of 5HT-triggered occlusion showed that bound 5HT serves as an essential trigger for transporter occlusion. Moreover, simulations revealed a complex sequence of steps and showed that movements of bundle domain helices are only partially correlated. 5HT-triggered occlusion is initially dominated by movements of transmembrane helix 1b, while in the final step, only transmembrane helix 6a moves and relaxes an intermediate change in its secondary structure.
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6
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Jayaraman K, Das AK, Luethi D, Szöllősi D, Schütz GJ, Reith MEA, Sitte HH, Stockner T. SLC6 transporter oligomerization. J Neurochem 2020; 157:919-929. [PMID: 32767560 PMCID: PMC8247324 DOI: 10.1111/jnc.15145] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
Transporters of the solute carrier 6 (SLC6) family mediate the reuptake of neurotransmitters such as dopamine, norepinephrine, serotonin, GABA, and glycine. SLC6 family members are 12 transmembrane helix‐spanning proteins that operate using the transmembrane sodium gradient for transport. These transporters assume various quaternary arrangements ranging from monomers to complex stoichiometries with multiple subunits. Dopamine and serotonin transporter oligomerization has been implicated in trafficking of newly formed proteins from the endoplasmic reticulum to the plasma membrane with a pre‐fixed assembly. Once at the plasma membrane, oligomers are kept fixed in their quaternary assembly by interaction with phosphoinositides. While it remains unclear how oligomer formation precisely affects physiological transporter function, it has been shown that oligomerization supports the activity of release‐type psychostimulants. Most recently, single molecule microscopy experiments unveiled that the stoichiometry differs between individual members of the SLC6 family. The present overview summarizes our understanding of the influence of plasma membrane constituents on transporter oligomerization, describes the known interfaces between protomers and discusses open questions. ![]()
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Affiliation(s)
- Kumaresan Jayaraman
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Anand K Das
- Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
| | - Dino Luethi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.,Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Gerhard J Schütz
- Institute of Applied Physics, Vienna University of Technology, Vienna, Austria
| | - Maarten E A Reith
- Department of Psychiatry, New York University School of Medicine, New York City, NY, USA
| | - Harald H Sitte
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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7
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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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8
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Wu Z, Alibay I, Newstead S, Biggin PC. Proton Control of Transitions in an Amino Acid Transporter. Biophys J 2019; 117:1342-1351. [PMID: 31500802 PMCID: PMC6818167 DOI: 10.1016/j.bpj.2019.07.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/03/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Amino acid transport into the cell is often coupled to the proton electrochemical gradient, as found in the solute carrier 36 family of proton-coupled amino acid transporters. Although no structure of a human proton-coupled amino acid transporter exists, the crystal structure of a related homolog from bacteria, GkApcT, has recently been solved in an inward-occluded state and allows an opportunity to examine how protons are coupled to amino acid transport. Our working hypothesis is that release of the amino acid substrate is facilitated by the deprotonation of a key glutamate residue (E115) located at the bottom of the binding pocket, which forms part of the intracellular gate, allowing the protein to transition from an inward-occluded to an inward-open conformation. During unbiased molecular dynamics simulations, we observed a transition from the inward-occluded state captured in the crystal structure to a much more open state, which we consider likely to be representative of the inward-open state associated with substrate release. To explore this and the role of protons in these transitions, we have used umbrella sampling to demonstrate that the transition from inward occluded to inward open is more energetically favorable when E115 is deprotonated. That E115 is likely to be protonated in the inward-occluded state and deprotonated in the inward-open state is further confirmed via the use of absolute binding free energies. Finally, we also show, via the use of absolute binding free energy calculations, that the affinity of the protein for alanine is very similar regardless of either the conformational state or the protonation of E115, presumably reflecting the fact that all the key interactions are deep within the binding cavity. Together, our results give a detailed picture of the role of protons in driving one of the major transitions in this transporter.
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Affiliation(s)
- Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Irfan Alibay
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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9
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Quinlan MA, Krout D, Katamish RM, Robson MJ, Nettesheim C, Gresch PJ, Mash DC, Keith Henry L, Blakely RD. Human Serotonin Transporter Coding Variation Establishes Conformational Bias with Functional Consequences. ACS Chem Neurosci 2019; 10:3249-3260. [PMID: 30668912 PMCID: PMC6640095 DOI: 10.1021/acschemneuro.8b00689] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The antidepressant-sensitive serotonin (5-HT) transporter (SERT) dictates rapid, high-affinity clearance of the neurotransmitter in both the brain and periphery. In a study of families with multiple individuals diagnosed with autism spectrum disorder (ASD), we previously identified several, rare, missense coding variants that impart elevated 5-HT transport activity, relative to wild-type SERT, upon heterologous expression as well as in ASD subject lymphoblasts. The most common of these variants, SERT Ala56, located in the transporter's cytosolic N-terminus, has been found to confer in transgenic mice hyperserotonemia, an ASD-associated biochemical trait, an elevated brain 5-HT clearance rate, and ASD-aligned behavioral changes. Hyperfunction of SERT Ala56 has been ascribed to a change in 5-HT KM, though the physical basis of this change has yet to be elucidated. Through assessments of fluorescence resonance energy transfer (FRET) between cytosolic N- and C-termini, sensitivity to methanethiosulfonates, and capacity for N-terminal tryptic digestion, we obtain evidence for mutation-induced conformational changes that support an open-outward 5-HT binding conformation in vitro and in vivo. Aspects of these findings were also evident with another naturally occurring C-terminal SERT coding variant identified in our ASD study, Asn605. We conclude that biased conformations of surface resident transporters that can impact transporter function and regulation are an unappreciated consequence of heritable and disease-associated SERT coding variation.
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Affiliation(s)
- Meagan A. Quinlan
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN
- Department of Biomedical Science, Charles E. Schmidt College of Medicine
| | - Danielle Krout
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND
| | - Rania M. Katamish
- Department of Biomedical Science, Charles E. Schmidt College of Medicine
| | - Matthew J. Robson
- Division of Pharmaceutical Sciences, University of Cincinnati, Cincinnati, OH
| | | | - Paul J. Gresch
- Department of Biomedical Science, Charles E. Schmidt College of Medicine
- Brain Institute, Florida Atlantic University, Jupiter, FL
| | - Deborah C. Mash
- Dr. Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Davie, FL
| | - L. Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND
| | - Randy D. Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine
- Brain Institute, Florida Atlantic University, Jupiter, FL
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10
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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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11
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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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12
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Schumann-Gillett A, Blyth MT, O’Mara ML. Is protein structure enough? A review of the role of lipids in SLC6 transporter function. Neurosci Lett 2019; 700:64-69. [DOI: 10.1016/j.neulet.2018.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 12/17/2022]
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13
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Möller IR, Slivacka M, Nielsen AK, Rasmussen SGF, Gether U, Loland CJ, Rand KD. Conformational dynamics of the human serotonin transporter during substrate and drug binding. Nat Commun 2019; 10:1687. [PMID: 30976000 PMCID: PMC6459873 DOI: 10.1038/s41467-019-09675-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/22/2019] [Indexed: 12/24/2022] Open
Abstract
The serotonin transporter (SERT), a member of the neurotransmitter:sodium symporter family, is responsible for termination of serotonergic signaling by re-uptake of serotonin (5-HT) into the presynaptic neuron. Its key role in synaptic transmission makes it a major drug target, e.g. for the treatment of depression, anxiety and post-traumatic stress. Here, we apply hydrogen-deuterium exchange mass spectrometry to probe the conformational dynamics of human SERT in the absence and presence of known substrates and targeted drugs. Our results reveal significant changes in dynamics in regions TM1, EL3, EL4, and TM12 upon binding co-transported ions (Na+/K+) and ligand-mediated changes in TM1, EL3 and EL4 upon binding 5-HT, the drugs S-citalopram, cocaine and ibogaine. Our results provide a comprehensive direct view of the conformational response of SERT upon binding both biologically relevant substrate/ions and ligands of pharmaceutical interest, thus advancing our understanding of the structure-function relationship in SERT.
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Affiliation(s)
- Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Marika Slivacka
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ulrik Gether
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark.
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Substrate and inhibitor binding to the serotonin transporter: Insights from computational, crystallographic, and functional studies. Neuropharmacology 2019; 161:107548. [PMID: 30807752 DOI: 10.1016/j.neuropharm.2019.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 02/02/2023]
Abstract
The serotonin transporter (SERT) belongs to the monoamine transporter family, which also includes the dopamine and norepinephrine transporters. SERT is essential for regulating serotonergic signaling by the reuptake of serotonin from the synaptic cleft back into the presynaptic neuron. Dysregulation of SERT has been implicated in several major psychiatric disorders such as major depressive disorder (MDD). MDD was among the top five leading causes of years lived with disease in 2016 and is characterized as a major global burden. Several drugs have been developed to target SERT for use in the treatment of MDD, and their respective binding modes and locations within SERT have been studied. The elucidation of the first structure of a bacterial SERT homologue in 2005 has accelerated crystallographic, computational, and functional studies to further elucidate drug binding and method of action in SERT. Herein, we aim to highlight and compare these studies with an emphasis on what the different experimental methods conclude on substrate and inhibitor binding modes, and the potential caveats of using the different types of studies are discussed. We focus this review on the binding of cognate substrate and drugs belonging to the different families of antidepressants, including tricyclic antidepressants, selective serotonin reuptake inhibitors, serotonin-norepinephrine reuptake inhibitors, and multimodal drugs, as well as illicit drugs such as cocaine, amphetamines, and ibogaine. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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15
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Djikic T, Martí Y, Spyrakis F, Lau T, Benedetti P, Davey G, Schloss P, Yelekci K. Human dopamine transporter: the first implementation of a combined in silico/in vitro approach revealing the substrate and inhibitor specificities. J Biomol Struct Dyn 2018; 37:291-306. [PMID: 29334320 DOI: 10.1080/07391102.2018.1426044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the human dopamine transporter (hDAT) could represent a viable strategy for establishing selective neuroprotection. Molecules able to increase the bioactive amount of extracellular dopamine, thereby enhancing and compensating a loss of dopaminergic neurotransmission, and to exert neuroprotective response because of their accumulation in the cytoplasm, are required. By means of homology modeling, molecular docking, and molecular dynamics simulations, we have generated 3D structure models of hDAT in complex with substrate and inhibitors. Our results clearly reveal differences in binding affinity of these compounds to the hDAT in the open and closed conformations, critical for future drug design. The established in silico approach allowed the identification of promising substrate compounds that were subsequently analyzed for their efficiency in inhibiting hDAT-dependent fluorescent substrate uptake, through in vitro live cell imaging experiments. Taken together, our work presents the first implementation of a combined in silico/in vitro approach enabling the selection of promising dopaminergic neuron-specific substrates.
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Affiliation(s)
- Teodora Djikic
- a Department of Bioinformatics and Genetics , Kadir Has University , Cibali campus, Fatih 34083 , Istanbul , Turkey
| | - Yasmina Martí
- b Hector Institute for Translational Brain Research, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany.,f Biochemical Laboratory, Psychiatry and Psychotherapy Department, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany
| | - Francesca Spyrakis
- c Department of Drug Science and Technology , University of Turin , via P. Giuria 9, Turin 10125 , Italy
| | - Thorsten Lau
- b Hector Institute for Translational Brain Research, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany
| | - Paolo Benedetti
- d Department of Chemistry, Biology and Biotechnology , University of Perugia , via Elce di sotto 8, Perugia 06123 , Italy
| | - Gavin Davey
- e School of Biochemistry and Immunology , Trinity College Dublin , Dublin 2, Ireland
| | - Patrick Schloss
- f Biochemical Laboratory, Psychiatry and Psychotherapy Department, Central Institute of Mental Health, Medical Faculty Mannheim , Heidelberg University , Mannheim J5, 68159 , Germany
| | - Kemal Yelekci
- a Department of Bioinformatics and Genetics , Kadir Has University , Cibali campus, Fatih 34083 , Istanbul , Turkey
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16
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Zeppelin T, Ladefoged LK, Sinning S, Periole X, Schiøtt B. A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition. PLoS Comput Biol 2018; 14:e1005907. [PMID: 29329285 PMCID: PMC5811071 DOI: 10.1371/journal.pcbi.1005907] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/13/2018] [Accepted: 11/29/2017] [Indexed: 01/30/2023] Open
Abstract
Monoamine transporters (MATs) carry out neurotransmitter reuptake from the synaptic cleft, a key step in neurotransmission, which is targeted in the treatment of neurological disorders. Cholesterol (CHOL), a major component of the synaptic plasma membrane, has been shown to exhibit a modulatory effect on MATs. Recent crystal structures of the dopamine transporter (DAT) revealed the presence of two conserved CHOL-like molecules, suggesting a functional protein-CHOL direct interaction. Here, we present extensive atomistic molecular dynamics (MD) simulations of DAT in an outward-facing conformation. In the absence of bound CHOL, DAT undergoes structural changes reflecting early events of dopamine transport: transition to an inward-facing conformation. In contrast, in the presence of bound CHOL, these conformational changes are inhibited, seemingly by an immobilization of the intracellular interface of transmembrane helix 1a and 5 by CHOL. We also provide evidence, from coarse grain MD simulations that the CHOL sites observed in the DAT crystal structures are preserved in all human monoamine transporters (dopamine, serotonin and norepinephrine), suggesting that our findings might extend to the entire family.
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Affiliation(s)
- Talia Zeppelin
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Lucy Kate Ladefoged
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
| | - Steffen Sinning
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus C, Denmark
| | - Xavier Periole
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, Denmark
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17
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Wang P, Fu T, Zhang X, Yang F, Zheng G, Xue W, Chen Y, Yao X, Zhu F. Differentiating physicochemical properties between NDRIs and sNRIs clinically important for the treatment of ADHD. Biochim Biophys Acta Gen Subj 2017; 1861:2766-2777. [PMID: 28757337 DOI: 10.1016/j.bbagen.2017.07.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/23/2017] [Accepted: 07/26/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Drugs available for treating attention-deficit hyperactivity disorder (ADHD) are mainly selective norepinephrine (sNRIs) and dual norepinephrine-dopamine (NDRIs) reuptake inhibitors. The major problem of sNRIs lines in their delayed onset of action and partial- or non-responses, which makes NDRIs distinguished in drug efficacy. Understanding of the differential binding modes of these 2 types of drugs to their corresponding targets can give great insights into the discovery of privileged drug-like scaffolds with improved efficacy. So far, no such study has been carried out. METHODS A combinatorial computational strategy, integrating homology modeling, molecular docking, molecular dynamics (MD) and binding free energy calculation, was employed to analyze the binding modes of 8 clinically important ADHD drugs in their targets. RESULTS Binding modes of 2 types of ADHD drugs (sNRIs and NDRIs) in their targets was identified for the first time by MD simulation, and 15 hot spot residues were discovered as crucial for NDRIs' binding in hNET and hDAT. Comparing to sNRIs, a clear reduction in the hydrophobic property of NDRIs' one functional group was observed, and the depth of drugs' aromatic ring stretched into the pocket of both targets was further identified as key contributors to drugs' selectivity. CONCLUSIONS The hydrophobic property of NDRI ADHD drugs' one functional group contributes to their selectivity when bind hNET and hDAT. GENERAL SIGNIFICANCE These results provide insights into NDRI ADHD drugs' binding mechanisms, which could be utilized as structural blueprints for assessing and discovering more efficacious drugs for ADHD therapy.
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Affiliation(s)
- Panpan Wang
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China; School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xiaoyu Zhang
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Fengyuan Yang
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Guoxun Zheng
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China.
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China.
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18
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Jean B, Surratt CK, Madura JD. Molecular dynamics of conformation-specific dopamine transporter-inhibitor complexes. J Mol Graph Model 2017; 76:143-151. [PMID: 28734204 DOI: 10.1016/j.jmgm.2017.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/26/2022]
Abstract
The recreational psychostimulant cocaine inhibits dopamine reuptake from the synapse, resulting in excessive stimulation of postsynaptic dopamine receptors in brain areas associated with reward and addiction. Cocaine binds to and stabilizes the outward- (extracellular-) facing conformation of the dopamine transporter (DAT) protein, while the low abuse potential DAT inhibitor benztropine prefers the inward- (cytoplasmic-) facing conformation. A correlation has been previously postulated between psychostimulant abuse potential and preference for the outward-facing DAT conformation. The 3β-aryltropane cocaine analogs LX10 and LX11, however, differ only in stereochemistry and share a preference for the outward-facing DAT, yet are reported to vary widely in abuse potential in an animal model. In search of the molecular basis for DAT conformation preference, complexes of cocaine, benztropine, LX10 or LX11 bound to each DAT conformation were subjected to 100ns of all-atom molecular dynamics simulation. Results were consistent with previous findings from cysteine accessibility assays used to assess an inhibitor's DAT conformation preference. The respective 2β- and 2α-substituted phenyltropanes of LX10 and LX11 interacted with hydrophobic regions of the DAT S1 binding site that were inaccessible to cocaine. Solvent accessibility measurements also revealed subtle differences in inhibitor positioning within a given DAT conformation. This work serves to advance our understanding of the conformational selectivity of DAT inhibitors and suggests that MD may be useful in antipsychostimulant therapeutic design.
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Affiliation(s)
- Bernandie Jean
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, United States
| | - Christopher K Surratt
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States.
| | - Jeffry D Madura
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282, United States
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19
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Wang P, Zhang X, Fu T, Li S, Li B, Xue W, Yao X, Chen Y, Zhu F. Differentiating Physicochemical Properties between Addictive and Nonaddictive ADHD Drugs Revealed by Molecular Dynamics Simulation Studies. ACS Chem Neurosci 2017; 8:1416-1428. [PMID: 28557437 DOI: 10.1021/acschemneuro.7b00173] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is the most commonly diagnosed mental disorder of children and adolescents. Although psychostimulants are currently the first-line drugs for ADHD, their highly addictive profile raises great abuse concerns. It is known that psychostimulants' addictiveness is largely attributed to their interaction with dopamine transporter (DAT) and their binding modes in DAT can thus facilitate the understanding of the mechanism underlining drugs' addictiveness. However, no DAT residue able to discriminate ADHD drugs' addictiveness is identified, and the way how different drug structures affect their abuse liability is still elusive. In this study, multiple computational methods were integrated to differentiate binding modes between approved psychostimulants and ADHD drugs of little addictiveness. As a result, variation in energy contribution of 8 residues between addictive and nonaddictive drugs was observed, and a reduction in hydrophobicity of drugs' 2 functional groups was identified as the indicator of drugs' addictiveness. This finding agreed well with the physicochemical properties of 8 officially reported controlled substances. The identified variations in binding mode can shed light on the mechanism underlining drugs' addictiveness, which may thus facilitate the discovery of improved ADHD therapeutics with reduced addictive profile.
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Affiliation(s)
- Panpan Wang
- College of Pharmaceutical
Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xiaoyu Zhang
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Shuang Li
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Bo Li
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic
Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Yuzong Chen
- Bioinformatics and
Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Feng Zhu
- College of Pharmaceutical
Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Innovative Drug Research and Bioinformatics
Group, School of Pharmaceutical Sciences and Collaborative Innovation
Center for Brain Science, Chongqing University, Chongqing 401331, China
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20
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Erol I, Aksoydan B, Kantarcioglu I, Salmas RE, Durdagi S. Identification of novel serotonin reuptake inhibitors targeting central and allosteric binding sites: A virtual screening and molecular dynamics simulations study. J Mol Graph Model 2017; 74:193-202. [DOI: 10.1016/j.jmgm.2017.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/26/2017] [Accepted: 02/02/2017] [Indexed: 10/19/2022]
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21
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Kalueff AV, Kaluyeva A, Maillet EL. Anxiolytic-like effects of noribogaine in zebrafish. Behav Brain Res 2017; 330:63-67. [PMID: 28479267 DOI: 10.1016/j.bbr.2017.05.008] [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] [Received: 04/03/2017] [Revised: 04/27/2017] [Accepted: 05/03/2017] [Indexed: 01/09/2023]
Abstract
Noribogaine is the main psychoactive metabolite of the hallucinogenic drug ibogaine, and is a particularly interesting compound potentially useful to treat dependence and various psychiatric disorders. Here, we report the effects of noribogaine on anxiety and locomotion in zebrafish (Danio rerio), a new promising model organism in neurobehavioral and psychopharmacological research. Adult zebrafish were subjected to the 5min novel tank test (NTT) following an acute, 20-min drug immersion in 1, 5 and 10mg/L noribogaine. Overall, noribogaine produced robust anxiolytic-like behavior in zebrafish (increasing the time spent and transitions to the top half compartment and reducing freezing bouts) without overt effects on fish locomotion. Taken together, these results indicate that noribogaine modulates the components of the acute stress response related to emotionality and anxiety behaviors, implicating this drug as a potentially useful non-sedative anxiolytic agent.
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Affiliation(s)
- Allan V Kalueff
- School of Pharmaceutical Sciences, Southwest University, Chongqing 400700, China; ZENEREI Research Center, 309 Palmer Court, Slidell, LA 70458, USA; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell 70458, LA, USA; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia; Ural Federal University, Yekaterinburg, 620020, Russia.
| | - Aleksandra Kaluyeva
- ZENEREI Research Center, 309 Palmer Court, Slidell, LA 70458, USA; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell 70458, LA, USA
| | - Emeline L Maillet
- DemeRx, Inc., R&D Laboratory, University of Miami Life Science and Tech Park. Blg 1, 1951 NW 7th Ave, Suite 300, Miami, FL 33136, USA.
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22
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Razavi AM, Khelashvili G, Weinstein H. A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter. Sci Rep 2017; 7:40076. [PMID: 28059145 PMCID: PMC5216462 DOI: 10.1038/srep40076] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/30/2016] [Indexed: 12/24/2022] Open
Abstract
The dopamine transporter (DAT) belongs to the neurotransmitter:sodium symporter (NSS) family of membrane proteins that are responsible for reuptake of neurotransmitters from the synaptic cleft to terminate a neuronal signal and enable subsequent neurotransmitter release from the presynaptic neuron. The release of one sodium ion from the crystallographically determined sodium binding site Na2 had been identified as an initial step in the transport cycle which prepares the transporter for substrate translocation by stabilizing an inward-open conformation. We have constructed Markov State Models (MSMs) from extensive molecular dynamics simulations of human DAT (hDAT) to explore the mechanism of this sodium release. Our results quantify the release process triggered by hydration of the Na2 site that occurs concomitantly with a conformational transition from an outward-facing to an inward-facing state of the transporter. The kinetics of the release process are computed from the MSM, and transition path theory is used to identify the most probable sodium release pathways. An intermediate state is discovered on the sodium release pathway, and the results reveal the importance of various modes of interaction of the N-terminus of hDAT in controlling the pathways of release.
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Affiliation(s)
- Asghar M Razavi
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA.,Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY 10065, USA
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23
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Ferraro M, Masetti M, Recanatini M, Cavalli A, Bottegoni G. Mapping Cholesterol Interaction Sites on Serotonin Transporter through Coarse-Grained Molecular Dynamics. PLoS One 2016; 11:e0166196. [PMID: 27907003 PMCID: PMC5132266 DOI: 10.1371/journal.pone.0166196] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022] Open
Abstract
Serotonin transporter (SERT) modulates serotonergic signaling via re-uptake of serotonin in pre-synaptic cells. The inclusion in cholesterol-enriched membrane domains is crucial for SERT activity, suggesting a cross-talk between the protein and the sterol. Here, we develop a protocol to identify potential cholesterol interaction sites coupling statistical analysis to multi-microsecond coarse-grained molecular dynamics simulations of SERT in a previously validated raft-like membrane model. Six putative sites were found, including a putative CRAC motif on TM4 and a CARC motif on TM10. Among them, four hot-spots near regions related to ion binding, transport, and inhibition were detected. Our results encourage prospective studies to unravel mechanistic features of the transporter and related drug discovery implications.
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Affiliation(s)
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - Università di Bologna, Bologna, Italy
- * E-mail: (MM); (GB)
| | - Maurizio Recanatini
- Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, Genova, Italy
- Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - Università di Bologna, Bologna, Italy
| | - Giovanni Bottegoni
- CompuNet, Istituto Italiano di Tecnologia, Genova, Italy
- BiKi Technologies s.r.l., Genova, Italy
- * E-mail: (MM); (GB)
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24
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Hasenhuetl PS, Freissmuth M, Sandtner W. Electrogenic Binding of Intracellular Cations Defines a Kinetic Decision Point in the Transport Cycle of the Human Serotonin Transporter. J Biol Chem 2016; 291:25864-25876. [PMID: 27756841 PMCID: PMC5207061 DOI: 10.1074/jbc.m116.753319] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/13/2016] [Indexed: 12/02/2022] Open
Abstract
The plasmalemmal monoamine transporters clear the extracellular space from their cognate substrates and sustain cellular monoamine stores even during neuronal activity. In some instances, however, the transporters enter a substrate-exchange mode, which results in release of intracellular substrate. Understanding what determines the switch between these two transport modes demands time-resolved measurements of intracellular (co-)substrate binding and release. Here, we report an electrophysiological investigation of intracellular solute-binding to the human serotonin transporter (SERT) expressed in HEK-293 cells. We measured currents induced by rapid application of serotonin employing varying intracellular (co-)substrate concentrations and interpreted the data using kinetic modeling. Our measurements revealed that the induction of the substrate-exchange mode depends on both voltage and intracellular Na+ concentrations because intracellular Na+ release occurs before serotonin release and is highly electrogenic. This voltage dependence was blunted by electrogenic binding of intracellular K+ and, notably, also H+. In addition, our data suggest that Cl− is bound to SERT during the entire catalytic cycle. Our experiments, therefore, document an essential role of electrogenic binding of K+ or of H+ to the inward-facing conformation of SERT in (i) cancelling out the electrogenic nature of intracellular Na+ release and (ii) in selecting the forward-transport over the substrate-exchange mode. Finally, the kinetics of intracellular Na+ release and K+ (or H+) binding result in a voltage-independent rate-limiting step where SERT may return to the outward-facing state in a KCl- or HCl-bound form.
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Affiliation(s)
- Peter S Hasenhuetl
- From the Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University Vienna, Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
| | - Michael Freissmuth
- From the Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University Vienna, Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
| | - Walter Sandtner
- From the Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University Vienna, Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
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25
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Chandran A, Vishveshwara S. Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket. Protein Sci 2016; 25:1989-2005. [PMID: 27515410 DOI: 10.1002/pro.3012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/07/2016] [Indexed: 11/06/2022]
Abstract
Ligand-regulated pregnane X receptor (PXR), a member of the nuclear receptor superfamily, plays a central role in xenobiotic metabolism. Despite its critical role in drug metabolism, PXR activation can lead to adverse drug-drug interactions and early stage metabolism of drugs. Activated PXR can induce cancer drug resistance and enhance the onset of malignancy. Since promiscuity in ligand binding makes it difficult to develop competitive inhibitors targeting PXR ligand binding pocket (LBP), it is essential to identify allosteric sites for effective PXR antagonism. Here, molecular dynamics (MD) simulation studies unravelled the existence of two different conformational states, namely "expanded" and "contracted", in apo PXR ligand binding domain (LBD). Ligand binding events shifted this conformational equilibrium and locked the LBD in a single "ligand-adaptable" conformational state. Ensemble-based computational solvent mapping identified a transiently open potential small molecule binding pocket between α5 and α8 helices, named "α8 pocket", whose opening-closing mechanism directly correlated with the conformational shift in LBD. A virtual hit identified through structure-based virtual screening against α8 pocket locks the pocket in its open conformation. MD simulations further revealed that the presence of small molecule at allosteric site disrupts the LBD dynamics and locks the LBD in a "tightly-contracted" conformation. The molecular details provided here could guide new structural studies to understand PXR activation and antagonism.
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Affiliation(s)
- Aneesh Chandran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.,Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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26
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Forsyth B, Machado L, Jowett T, Jakobi H, Garbe K, Winter H, Glue P. Effects of low dose ibogaine on subjective mood state and psychological performance. JOURNAL OF ETHNOPHARMACOLOGY 2016; 189:10-13. [PMID: 27180314 DOI: 10.1016/j.jep.2016.05.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 04/30/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Root bark from Tabernanthe iboga has been used traditionally in West Africa as a psychoactive substance in religious rituals. In smaller doses it is reported anecdotally to have stimulant properties. AIM OF THE STUDY To evaluate the influence of a single 20mg ibogaine dose on psychological variables reflecting subjective mood state and a range of cognitive functions. MATERIALS AND METHODS 21 healthy male volunteers received single 20mg doses of ibogaine after 6 days pretreatment with double-blind paroxetine or placebo. We compared responses to a battery of psychometric tests and subjective mood ratings performed before and 2h after ibogaine dosing, and assessed relationships between changes in test scores and concentrations of active moiety (the sum of molar noribogaine and ibogaine concentrations). Psychological tests were chosen based on responsiveness to opioid and serotonergic ligands. RESULTS Ibogaine had minimal influence on psychological tests and mood ratings. The ability to selectively ignore distracting spatial information showed some evidence of modulation; however because this effect was limited to the less challenging condition calls into question the reliability of this result. CONCLUSION We were unable to identify stimulant effects after single 20mg doses of ibogaine. Future research is needed to confirm whether active moiety concentrations impact selective attention abilities while leaving other cognitive functions and mood state unaffected.
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Affiliation(s)
- Bridget Forsyth
- Department of Psychology, University of Otago, Dunedin, New Zealand.
| | - Liana Machado
- Department of Psychology, University of Otago, Dunedin, New Zealand.
| | - Tim Jowett
- Department of Mathematics, University of Otago, Dunedin, New Zealand.
| | - Hannah Jakobi
- Department of Psychological Medicine, University of Otago, Dunedin, New Zealand; University of Heidelberg, Heidelberg, Germany.
| | - Kira Garbe
- Department of Psychological Medicine, University of Otago, Dunedin, New Zealand; University of Heidelberg, Heidelberg, Germany.
| | - Helen Winter
- Departments of Pharmacy, University of Otago, Dunedin, New Zealand.
| | - Paul Glue
- Department of Psychological Medicine, University of Otago, Dunedin, New Zealand.
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27
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Khelashvili G, Schmidt SG, Shi L, Javitch JA, Gether U, Loland CJ, Weinstein H. Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290. J Biol Chem 2016; 291:19786-99. [PMID: 27474737 DOI: 10.1074/jbc.m116.731455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 01/06/2023] Open
Abstract
Ions play key mechanistic roles in the gating dynamics of neurotransmitter:sodium symporters (NSSs). In recent microsecond scale molecular dynamics simulations of a complete model of the dopamine transporter, a NSS protein, we observed a partitioning of K(+) ions from the intracellular side toward the unoccupied Na2 site of dopamine transporter following the release of the Na2-bound Na(+) Here we evaluate with computational simulations and experimental measurements of ion affinities under corresponding conditions, the consequences of K(+) binding in the Na2 site of LeuT, a bacterial homolog of NSS, when both Na(+) ions and substrate have left, and the transporter prepares for a new cycle. We compare the results with the consequences of binding Na(+) in the same apo system. Analysis of >50-μs atomistic molecular dynamics and enhanced sampling trajectories of constructs with Glu(290), either charged or neutral, point to the Glu(290) protonation state as a main determinant in the structural reconfiguration of the extracellular vestibule of LeuT in which a "water gate" opens through coordinated motions of residues Leu(25), Tyr(108), and Phe(253) The resulting water channel enables the binding/dissociation of the Na(+) and K(+) ions that are prevalent, respectively, in the extracellular and intracellular environments.
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Affiliation(s)
- George Khelashvili
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065,
| | - Solveig Gaarde Schmidt
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Lei Shi
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224
| | - Jonathan A Javitch
- the Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, New York, New York 10032, Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, and
| | - Ulrik Gether
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- the Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Harel Weinstein
- From the Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, the Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065
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28
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Vermaas JV, Trebesch N, Mayne CG, Thangapandian S, Shekhar M, Mahinthichaichan P, Baylon JL, Jiang T, Wang Y, Muller MP, Shinn E, Zhao Z, Wen PC, Tajkhorshid E. Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation. Methods Enzymol 2016; 578:373-428. [PMID: 27497175 PMCID: PMC6404235 DOI: 10.1016/bs.mie.2016.05.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Membrane transporters mediate one of the most fundamental processes in biology. They are the main gatekeepers controlling active traffic of materials in a highly selective and regulated manner between different cellular compartments demarcated by biological membranes. At the heart of the mechanism of membrane transporters lie protein conformational changes of diverse forms and magnitudes, which closely mediate critical aspects of the transport process, most importantly the coordinated motions of remotely located gating elements and their tight coupling to chemical processes such as binding, unbinding and translocation of transported substrate and cotransported ions, ATP binding and hydrolysis, and other molecular events fueling uphill transport of the cargo. An increasing number of functional studies have established the active participation of lipids and other components of biological membranes in the function of transporters and other membrane proteins, often acting as major signaling and regulating elements. Understanding the mechanistic details of these molecular processes require methods that offer high spatial and temporal resolutions. Computational modeling and simulations technologies empowered by advanced sampling and free energy calculations have reached a sufficiently mature state to become an indispensable component of mechanistic studies of membrane transporters in their natural environment of the membrane. In this article, we provide an overview of a number of major computational protocols and techniques commonly used in membrane transporter modeling and simulation studies. The article also includes practical hints on effective use of these methods, critical perspectives on their strengths and weak points, and examples of their successful applications to membrane transporters, selected from the research performed in our own laboratory.
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Affiliation(s)
- J V Vermaas
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - N Trebesch
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - C G Mayne
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - S Thangapandian
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - M Shekhar
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Mahinthichaichan
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J L Baylon
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - T Jiang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Wang
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - M P Muller
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Shinn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Z Zhao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P-C Wen
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; University of Illinois at Urbana-Champaign, Urbana, IL, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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29
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Synthesis and inhibitory evaluation of 3-linked imipramines for the exploration of the S2 site of the human serotonin transporter. Bioorg Med Chem 2016; 24:2725-38. [PMID: 27160055 DOI: 10.1016/j.bmc.2016.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/16/2016] [Accepted: 04/20/2016] [Indexed: 01/10/2023]
Abstract
The human serotonin transporter is the primary target of several antidepressant drugs, and the importance of a primary, high affinity binding site (S1) for antidepressant binding is well documented. The existence of a lower affinity, secondary binding site (S2) has, however, been debated. Herein we report the synthesis of 3-position coupled imipramine ligands from clomipramine using a copper free Sonogashira reaction. Ligand design was inspired by results from docking and steered molecular dynamics simulations, and the ligands were utilized in a structure-activity relationship study of the positional relationship between the S1 and S2 sites. The computer simulations suggested that the S2 site does indeed exist although with lower affinity for imipramine than observed within the S1 site. Additionally, it was possible to dock the 3-linked imipramine analogs into positions which occupy the S1 and the S2 site simultaneously. The structure activity relationship study showed that the shortest ligands were the most potent, and mutations enlarging the proposed S2 site were found to affect the larger ligands positively, while the smaller ligands were mostly unaffected.
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30
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Andersen J, Ladefoged LK, Wang D, Kristensen TNB, Bang-Andersen B, Kristensen AS, Schiøtt B, Strømgaard K. Binding of the multimodal antidepressant drug vortioxetine to the human serotonin transporter. ACS Chem Neurosci 2015; 6:1892-900. [PMID: 26389667 DOI: 10.1021/acschemneuro.5b00225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Selective inhibitors of the human serotonin transporter (hSERT) have been first-line treatment against depression for several decades. Recently, vortioxetine was approved as a new therapeutic option for the treatment of depression. Vortioxetine represents a new class of antidepressant drugs with a multimodal pharmacological profile that in addition to potent inhibition of hSERT include agonistic or antagonistic effects at different serotonin receptors. We used a combination of computational, chemical, and biological methods to decipher the molecular basis for high affinity binding of vortioxetine in hSERT. X-ray crystal structures of the bacterial amino acid transporter LeuT and the Drosophila melanogaster dopamine transporter were used to build homology models of hSERT. Comparative modeling and ligand docking suggest that vortioxetine can adopt several distinct binding modes within the central binding site of hSERT. To distinguish between the identified binding modes, we determined the effect of 57 functional hSERT point mutants on vortioxetine potency and characterized seven structurally related analogs of vortioxetine in a subset of the point mutants. This allowed us to determine the orientation of vortioxetine within the central binding site and showed that only one of the proposed binding modes is functionally relevant. The findings provide important new insight about the molecular basis for high affinity recognition of vortioxetine in hSERT, which is essential for future structure-based drug discovery of novel multimodal drugs with fine-tuned selectivity across different transporter and receptor proteins in the human brain.
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Affiliation(s)
- Jacob Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lucy Kate Ladefoged
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Danyang Wang
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Trine N. Bjerre Kristensen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Benny Bang-Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Lundbeck Research Denmark, H. Lundbeck A/S, Ottiliavej 9, DK-2500 Valby, Denmark
| | - Anders S. Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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31
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Khelashvili G, Stanley N, Sahai MA, Medina J, LeVine MV, Shi L, De Fabritiis G, Weinstein H. Spontaneous inward opening of the dopamine transporter is triggered by PIP2-regulated dynamics of the N-terminus. ACS Chem Neurosci 2015; 6:1825-37. [PMID: 26255829 PMCID: PMC4653762 DOI: 10.1021/acschemneuro.5b00179] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
![]()
We
present the dynamic mechanism of concerted motions in a full-length
molecular model of the human dopamine transporter (hDAT), a member
of the neurotransmitter/sodium symporter (NSS) family, involved in
state-to-state transitions underlying function. The findings result
from an analysis of unbiased atomistic molecular dynamics simulation
trajectories (totaling >14 μs) of the hDAT molecule immersed
in lipid membrane environments with or without phosphatidylinositol
4,5-biphosphate (PIP2) lipids. The N-terminal region of
hDAT (N-term) is shown to have an essential mechanistic role in correlated
rearrangements of specific structural motifs relevant to state-to-state
transitions in the hDAT. The mechanism involves PIP2-mediated
electrostatic interactions between the N-term and the intracellular
loops of the transporter molecule. Quantitative analyses of collective
motions in the trajectories reveal that these interactions correlate
with the inward-opening dynamics of hDAT and are allosterically coupled
to the known functional sites of the transporter. The observed large-scale
motions are enabled by specific reconfiguration of the network of
ionic interactions at the intracellular end of the protein. The isomerization
to the inward-facing state in hDAT is accompanied by concomitant movements
in the extracellular vestibule and results in the release of an Na+ ion from the Na2 site and destabilization of the substrate
dopamine in the primary substrate binding S1 site. The dynamic mechanism
emerging from the findings highlights the involvement of the PIP2-regulated interactions between the N-term and the intracellular
loop 4 in the functionally relevant conformational transitions that
are also similar to those found to underlie state-to-state transitions
in the leucine transporter (LeuT), a prototypical bacterial homologue
of the NSS.
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Affiliation(s)
- George Khelashvili
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Nathaniel Stanley
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona
Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Michelle A. Sahai
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Jaime Medina
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Michael V. LeVine
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
| | - Lei Shi
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
- HRH
Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational
Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Gianni De Fabritiis
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona
Biomedical Research Park (PRBB), C/Doctor Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Harel Weinstein
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York 10065, United States
- HRH
Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational
Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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Grouleff J, Ladefoged LK, Koldsø H, Schiøtt B. Monoamine transporters: insights from molecular dynamics simulations. Front Pharmacol 2015; 6:235. [PMID: 26528185 PMCID: PMC4607855 DOI: 10.3389/fphar.2015.00235] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/01/2015] [Indexed: 01/31/2023] Open
Abstract
The human monoamine transporters (MATs) facilitate the reuptake of the neurotransmitters serotonin, dopamine, and norepinephrine from the synaptic cleft. Imbalance in monoaminergic neurotransmission is linked to various diseases including major depression, attention deficit hyperactivity disorder, schizophrenia, and Parkinson's disease. Inhibition of the MATs is thus an important strategy for treatment of such diseases. The MATs are sodium-coupled transport proteins belonging to the neurotransmitter/Na(+) symporter (NSS) family, and the publication of the first high-resolution structure of a NSS family member, the bacterial leucine transporter LeuT, in 2005, proved to be a major stepping stone for understanding this family of transporters. Structural data allows for the use of computational methods to study the MATs, which in turn has led to a number of important discoveries. The process of substrate translocation across the membrane is an intrinsically dynamic process. Molecular dynamics simulations, which can provide atomistic details of molecular motion on ns to ms timescales, are therefore well-suited for studying transport processes. In this review, we outline how molecular dynamics simulations have provided insight into the large scale motions associated with transport of the neurotransmitters, as well as the presence of external and internal gates, the coupling between ion and substrate transport, and differences in the conformational changes induced by substrates and inhibitors.
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Affiliation(s)
- Julie Grouleff
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University Aarhus, Denmark
| | - Lucy Kate Ladefoged
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University Aarhus, Denmark
| | - Heidi Koldsø
- Department of Biochemistry, University of Oxford Oxford, UK
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University Aarhus, Denmark
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Koldsø H, Grouleff J, Schiøtt B. Insights to ligand binding to the monoamine transporters-from homology modeling to LeuBAT and dDAT. Front Pharmacol 2015; 6:208. [PMID: 26441663 PMCID: PMC4585151 DOI: 10.3389/fphar.2015.00208] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2015] [Indexed: 11/20/2022] Open
Abstract
Understanding of drug binding to the human biogenic amine transporters (BATs) is essential to explain the mechanism of action of these pharmaceuticals but more importantly to be able to develop new and improved compounds to be used in the treatment of depression or drug addiction. Until recently no high resolution structure was available of the BATs and homology modeling was a necessity. Various studies have revealed experimentally validated binding modes of numerous ligands to the BATs using homology modeling. Here we examine and discuss the similarities between the binding models of substrates, antidepressants, psychostimulants, and mazindol in homology models of the human BATs and the recently published crystal structures of the Drosophila dopamine transporter and the engineered protein, LeuBAT. The comparison reveals that careful computational modeling combined with experimental data can be utilized to predict binding of molecules to proteins that agree very well with crystal structures.
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Affiliation(s)
- Heidi Koldsø
- Department of Biochemistry, University of Oxford , Oxford, UK ; inSPIN and iNANO Centers, Department of Chemistry, Aarhus University , Aarhus C, Denmark
| | - Julie Grouleff
- inSPIN and iNANO Centers, Department of Chemistry, Aarhus University , Aarhus C, Denmark
| | - Birgit Schiøtt
- inSPIN and iNANO Centers, Department of Chemistry, Aarhus University , Aarhus C, Denmark
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Söderhielm PC, Andersen J, Munro L, Nielsen AT, Kristensen AS. Substrate and Inhibitor-Specific Conformational Changes in the Human Serotonin Transporter Revealed by Voltage-Clamp Fluorometry. Mol Pharmacol 2015; 88:676-88. [PMID: 26174773 DOI: 10.1124/mol.115.099911] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/13/2015] [Indexed: 01/05/2023] Open
Abstract
The serotonin transporter (SERT) regulates neurotransmission by the biogenic monoamine neurotransmitter serotonin (5-HT, 5-hydroxytryptamine) in the central nervous system, and drugs inhibiting SERT are widely used for the treatment of a variety of central nervous system diseases. The conformational dynamics of SERT transport function and inhibition is currently poorly understood. We used voltage-clamp fluorometry to study conformational changes in human SERT (hSERT) during 5-HT transport and inhibitor binding. Cys residues were introduced at 12 positions in hSERT to enable covalent attachment of a rhodamine-based fluorophore. Transport-associated changes in fluorescence from fluorophore-labeled hSERT expressed in Xenopus oocytes could be robustly detected at four positions in hSERT: endogenous Cys109 in the top of transmembrane domain (TM) 1b, Cys substituted for Thr323 in the top of TM6, Ala419 in the interface between TM8 and extracellular loop (EL) 4, and Leu481 in EL5. The reporter positions were used for time-resolved measurement of conformational changes during 5-HT transport and binding of cocaine and the selective serotonin reuptake inhibitors fluoxetine and escitalopram. At all reporter positions, fluorescence changes observed upon substrate application were distinctly different from those observed upon inhibitor application, with respect to relative amplitude or direction. Furthermore, escitalopram, fluoxetine, and cocaine induced a very similar pattern of fluorescent changes overall, which included movements within or around TM1b, EL4, and EL5. Taken together, our data lead us to suggest that competitive inhibitors stabilize hSERT in a state that is different from the apo outward-open conformation as well as inward-facing conformations.
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Affiliation(s)
- Pella C Söderhielm
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Lachlan Munro
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Anne T Nielsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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Functional mechanisms of neurotransmitter transporters regulated by lipid-protein interactions of their terminal loops. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1765-74. [PMID: 25847498 DOI: 10.1016/j.bbamem.2015.03.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 01/28/2023]
Abstract
The physiological functions of neurotransmitter:sodium symporters (NSS) in reuptake of neurotransmitters from the synapse into the presynaptic nerve have been shown to be complemented by their involvement, together with non-plasma membrane neurotransmitter transporters, in the reverse transport of substrate (efflux) in response to psychostimulants. Recent experimental evidence implicates highly anionic phosphatidylinositol 4,5-biphosphate (PIP(2)) lipids in such functions of the serotonin (SERT) and dopamine (DAT) transporters. Thus, for both SERT and DAT, neurotransmitter efflux has been shown to be strongly regulated by the presence of PIP(2) lipids in the plasma membrane, and the electrostatic interaction of the N-terminal region of DAT with the negatively charged PIP(2) lipids. We examine the experimentally established phenotypes in a structural context obtained from computational modeling based on recent crystallographic data. The results are shown to set the stage for a mechanistic understanding of physiological actions of neurotransmitter transporters in the NSS family of membrane proteins. This article is part of a Special Issue entitled: Lipid-protein interactions.
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36
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Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends Biotechnol 2015; 33:237-46. [DOI: 10.1016/j.tibtech.2015.02.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/02/2015] [Indexed: 02/06/2023]
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37
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Glue P, Lockhart M, Lam F, Hung N, Hung CT, Friedhoff L. Ascending-dose study of noribogaine in healthy volunteers: Pharmacokinetics, pharmacodynamics, safety, and tolerability. J Clin Pharmacol 2014; 55:189-94. [DOI: 10.1002/jcph.404] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/26/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Paul Glue
- University of Otago; Dunedin New Zealand
| | | | - Fred Lam
- Zenith Technology Ltd; Dunedin New Zealand
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38
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Kell DB. What would be the observable consequences if phospholipid bilayer diffusion of drugs into cells is negligible? Trends Pharmacol Sci 2014; 36:15-21. [PMID: 25458537 DOI: 10.1016/j.tips.2014.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 10/11/2014] [Accepted: 10/14/2014] [Indexed: 12/27/2022]
Abstract
For drug transport across (i.e., through) an intact biological membrane, two main routes are possible: drugs may cross (i) through the phospholipid bilayer portion of the membrane, and/or (ii) via proteinaceous pores or transporters. Perhaps surprisingly, there is in fact no direct scientific evidence that the first of these takes place at any significant rate because, in the experiments performed to date, it has neither been varied as an independent variable nor measured directly as a dependent variable. Using a standard hypothetico-deductive framework, I assess the intellectual and observable consequences of assuming that, for drugs, phospholipid bilayer diffusion is negligible - 'PBIN' - (i.e., may be neglected, relative to transporter-mediated transmembrane fluxes). Predictions and postdictions of the PBIN hypothesis are not refuted by available experimental evidence.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Kell DB, Oliver SG. How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol 2014; 5:231. [PMID: 25400580 PMCID: PMC4215795 DOI: 10.3389/fphar.2014.00231] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022] Open
Abstract
One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Cambridge Systems Biology Centre, University of Cambridge Cambridge, UK
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40
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Nolan TL, Geffert LM, Kolber BJ, Madura JD, Surratt CK. Discovery of novel-scaffold monoamine transporter ligands via in silico screening with the S1 pocket of the serotonin transporter. ACS Chem Neurosci 2014; 5:784-92. [PMID: 25003748 PMCID: PMC4176318 DOI: 10.1021/cn500133b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
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Discovery of new inhibitors of the
plasmalemmal monoamine transporters
(MATs) continues to provide pharmacotherapeutic options for depression,
addiction, attention deficit disorders, psychosis, narcolepsy, and
Parkinson’s disease. The windfall of high-resolution MAT structural
information afforded by X-ray crystallography has enabled the construction
of credible computational models. Elucidation of lead compounds, creation
of compound structure–activity series, and pharmacologic testing
are staggering expenses that could be reduced by using a MAT computational
model for virtual screening (VS) of structural libraries containing
millions of compounds. Here, VS of the PubChem small molecule structural
database using the S1 (primary substrate) ligand pocket of a serotonin
transporter homology model yielded 19 prominent “hit”
compounds. In vitro pharmacology of these VS hits revealed four structurally
unique MAT substrate uptake inhibitors with high nanomolar affinity
at one or more of the three MATs. In vivo characterization of three
of these hits revealed significant activity in a mouse model of acute
depression at doses that did not elicit untoward locomotor effects.
This constitutes the first report of MAT inhibitor discovery using
exclusively the primary substrate pocket as a VS tool. Novel-scaffold
MAT inhibitors offer hope of new medications that lack the many classic
adverse effects of existing antidepressant drugs.
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Affiliation(s)
- Tammy L. Nolan
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Laura M. Geffert
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Benedict J. Kolber
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffry D. Madura
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Christopher K. Surratt
- Division of Pharmaceutical Sciences,
Mylan School of Pharmacy, ‡Departments of Chemistry
and Biochemistry, Center for Computational Sciences,
and §Department of Biological
Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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41
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Hansen SK, Vestergaard M, Thøgersen L, Schiøtt B, Nielsen NC, Vosegaard T. Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations. J Phys Chem B 2014; 118:5119-29. [DOI: 10.1021/jp5000304] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sara K. Hansen
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Vestergaard
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Lea Thøgersen
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
- Center
for Membrane Pumps in Cells and Diseases, Bioinformatics Research
Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Birgit Schiøtt
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Niels Chr. Nielsen
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center
for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience
Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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42
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LeVine MV, Weinstein H. NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT. PLoS Comput Biol 2014; 10:e1003603. [PMID: 24785005 PMCID: PMC4006702 DOI: 10.1371/journal.pcbi.1003603] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/24/2014] [Indexed: 11/23/2022] Open
Abstract
Complex networks of interacting residues and microdomains in the structures of biomolecular systems underlie the reliable propagation of information from an input signal, such as the concentration of a ligand, to sites that generate the appropriate output signal, such as enzymatic activity. This information transduction often carries the signal across relatively large distances at the molecular scale in a form of allostery that is essential for the physiological functions performed by biomolecules. While allosteric behaviors have been documented from experiments and computation, the mechanism of this form of allostery proved difficult to identify at the molecular level. Here, we introduce a novel analysis framework, called N-body Information Theory (NbIT) analysis, which is based on information theory and uses measures of configurational entropy in a biomolecular system to identify microdomains and individual residues that act as (i)-channels for long-distance information sharing between functional sites, and (ii)-coordinators that organize dynamics within functional sites. Application of the new method to molecular dynamics (MD) trajectories of the occluded state of the bacterial leucine transporter LeuT identifies a channel of allosteric coupling between the functionally important intracellular gate and the substrate binding sites known to modulate it. NbIT analysis is shown also to differentiate residues involved primarily in stabilizing the functional sites, from those that contribute to allosteric couplings between sites. NbIT analysis of MD data thus reveals rigorous mechanistic elements of allostery underlying the dynamics of biomolecular systems. We developed the new information theory-based analysis framework presented here, NbIT analysis, for the study of allosteric mechanisms in biomolecular systems from Molecular Dynamics trajectories. The illustrative application of NbIT to the analysis of the occluded state in the bacterial transporter LeuT, produced a quantitative representation of the allosteric behavior, and identified intramolecular channels that enable the long-distance information transmission. Our findings, identifying the roles of specific residues in the communication of the allosteric information, were validated by the recognition of residues that have been previously shown to play functional roles in this very well studied system. In addition, we show that application of NbIT analysis leads to the discrimination of functional roles by differentiating between residues that are essential to the dynamics within functional sites (e.g., the substrate binding sites), and residues whose role is to communicate between such functional sites. These results demonstrate that the information theoretical analysis presented here is a powerful tool for quantifying complex allosteric behavior in biomolecular systems and for identifying the crucial components underlying those behaviors.
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Affiliation(s)
- Michael V. LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University (WCMC), New York, New York, United States of America
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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43
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Andersen J, Stuhr-Hansen N, Zachariassen LG, Koldsø H, Schiøtt B, Strømgaard K, Kristensen AS. Molecular basis for selective serotonin reuptake inhibition by the antidepressant agent fluoxetine (Prozac). Mol Pharmacol 2014; 85:703-14. [PMID: 24516100 DOI: 10.1124/mol.113.091249] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inhibitors of the serotonin transporter (SERT) are widely used antidepressant agents, but the structural mechanism for inhibitory activity and selectivity over the closely related norepinephrine transporter (NET) is not well understood. Here we use a combination of chemical, biological, and computational methods to decipher the molecular basis for high-affinity recognition in SERT and selectivity over NET for the prototypical antidepressant drug fluoxetine (Prozac; Eli Lilly, Indianapolis, IN). We show that fluoxetine binds within the central substrate site of human SERT, in agreement with recent X-ray crystal structures of LeuBAT, an engineered monoamine-like version of the bacterial amino acid transporter LeuT. However, the binding orientation of fluoxetine is reversed in our experimentally supported model compared with the LeuBAT structures, emphasizing the need for careful experimental verification when extrapolating findings from crystal structures of bacterial transporters to human relatives. We find that the selectivity of fluoxetine and nisoxetine, a NET selective structural congener of fluoxetine, is controlled by residues in different regions of the transporters, indicating a complex mechanism for selective recognition of structurally similar compounds in SERT and NET. Our findings add important new information on the molecular basis for SERT/NET selectivity of antidepressants, and provide the first assessment of the potential of LeuBAT as a model system for antidepressant binding in human transporters, which is essential for future structure-based drug development of antidepressant drugs with fine-tuned transporter selectivity.
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Affiliation(s)
- Jacob Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (J.A., N.S.-H., L.G.Z., K.S., A.S.K.); and Center for Insoluble Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Aarhus, Denmark (H.K., B.S.)
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44
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Gaffaney JD, Shetty M, Felts B, Pramod AB, Foster JD, Henry LK, Vaughan RA. Antagonist-induced conformational changes in dopamine transporter extracellular loop two involve residues in a potential salt bridge. Neurochem Int 2013; 73:16-26. [PMID: 24269640 DOI: 10.1016/j.neuint.2013.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 10/26/2022]
Abstract
Ligand-induced changes in the conformation of extracellular loop (EL) 2 in the rat (r) dopamine transporter (DAT) were examined using limited proteolysis with endoproteinase Asp-N and detection of cleavage products by epitope-specific immunoblotting. The principle N-terminal fragment produced by Asp-N was a 19kDa peptide likely derived by proteolysis of EL2 residue D174, which is present just past the extracellular end of TM3. Production of this fragment was significantly decreased by binding of cocaine and other uptake blockers, but was not affected by substrates or Zn(2+), indicating the presence of a conformational change at D174 that may be related to the mechanism of transport inhibition. DA transport activity and cocaine analog binding were decreased by Asp-N treatment, suggesting a requirement for EL2 integrity in these DAT functions. In a previous study we demonstrated that ligand-induced protease resistance also occurred at R218 on the C-terminal side of rDAT EL2. Here using substituted cysteine accessibility analysis of human (h) DAT we confirm cocaine-induced alterations in reactivity of the homologous R219 and identify conformational sensitivity of V221. Focused molecular modeling of D174 and R218 based on currently available Aquifex aeolicus leucine transporter crystal structures places these residues within 2.9Å of one another, suggesting their proximity as a structural basis for their similar conformational sensitivities and indicating their potential to form a salt bridge. These findings extend our understanding of DAT EL2 and its role in transport and binding functions.
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Affiliation(s)
- Jon D Gaffaney
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - Madhur Shetty
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - Bruce Felts
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - Akula-Bala Pramod
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - James D Foster
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States
| | - L Keith Henry
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States.
| | - Roxanne A Vaughan
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, United States.
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45
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Severinsen K, Koldsø H, Thorup KAV, Schjøth-Eskesen C, Møller PT, Wiborg O, Jensen HH, Sinning S, Schiøtt B. Binding of Mazindol and Analogs to the Human Serotonin and Dopamine Transporters. Mol Pharmacol 2013; 85:208-17. [DOI: 10.1124/mol.113.088922] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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