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Tu G, Fu T, Zheng G, Xu B, Gou R, Luo D, Wang P, Xue W. Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. J Chem Inf Model 2024; 64:1433-1455. [PMID: 38294194 DOI: 10.1021/acs.jcim.3c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are involved in the transportation of diverse solute ions and small molecules into cells. There are approximately 450 SLCs within the human body, and more than a quarter of them are emerging as attractive therapeutic targets for multiple complex diseases, e.g., depression, cancer, and diabetes. However, only 44 unique transporters (∼9.8% of the SLC superfamily) with 3D structures and specific binding sites have been reported. To design innovative and effective drugs targeting diverse SLCs, there are a number of obstacles that need to be overcome. However, computational chemistry, including physics-based molecular modeling and machine learning- and deep learning-based artificial intelligence (AI), provides an alternative and complementary way to the classical drug discovery approach. Here, we present a comprehensive overview on recent advances and existing challenges of the computational techniques in structure-based drug design of SLCs from three main aspects: (i) characterizing multiple conformations of the proteins during the functional process of transportation, (ii) identifying druggability sites especially the cryptic allosteric ones on the transporters for substrates and drugs binding, and (iii) discovering diverse small molecules or synthetic protein binders targeting the binding sites. This work is expected to provide guidelines for a deep understanding of the structure and function of the SLC superfamily to facilitate rational design of novel modulators of the transporters with the aid of state-of-the-art computational chemistry technologies including artificial intelligence.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Binbin Xu
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610200, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Recław R, Lachowicz M, Chmielowiec K, Chmielowiec J, Strońska-Pluta A, Kowalski MT, Kudliński B, Grzywacz A. Analysis of the Methylation Level of the DAT1 Dopamine Transporter Gene in Patients Addicted to Stimulants, Taking into Account an Analysis of Personality Traits. Int J Mol Sci 2023; 25:532. [PMID: 38203701 PMCID: PMC10779366 DOI: 10.3390/ijms25010532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Drug addiction is a chronic biochemical drug use disorder that affects the human brain and behavior and leads to the uncontrolled use of legal or illicit drugs. It has been shown that three factors are involved in the development of addiction: genetic factors, a diverse environment, and the effect of medication on gene expression. The comprehensive approach and holistic analysis of the problem are due to the multigenic and multifactorial nature of addiction. Dopamine, one of the major neurotransmitters in the brain, is believed to be the "culprit" that leads to a drug abuse-induced "high". That is why, in our research, we focused mainly on the genes related to dopaminergic reuptake. In the present study, we chose methylation of the DAT1 dopamine transporter gene based on molecular reasons related to the dopaminergic theory of addiction. This study included two groups: 226 stimulant-dependent and 290 non-stimulant-dependent subjects. The analysis consisted of a case-control comparison of people addicted to psychostimulants compared to a control group of healthy and non-addicted people. There were differences in the levels of statistical significance between the groups. Our research shows lower methylation of islands 1, 9, and 14 in addicted people and greater methylation of islands 32 and 33. The difference in individual CpG methylation islands of the gene under study provides valuable information about the DNA methylation process in patients addicted to psychostimulants. Pearson's linear correlation analysis in stimulant dependence showed a negative correlation between total methylation island levels and the NEO-FFI Neuroticism scale. In subjects with neuroticism, the methylation level was statistically significantly lower. Pearson's linear correlation analysis of stimulant-dependent subjects showed a positive correlation between total methylation island levels and the NEO-FFI Openness scale and the NEO-FFI Conscientiousness scale.
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Affiliation(s)
- Remigiusz Recław
- Foundation Strong in the Spirit, 60 Sienkiewicza St., 90-058 Łodz, Poland;
| | - Milena Lachowicz
- Department of Psychology, Gdansk University of Physical Education and Sport, Kazimierza Górskiego 1 St., 80-336 Gdansk, Poland;
| | - Krzysztof Chmielowiec
- Department of Hygiene and Epidemiology, Collegium Medicum, University of Zielona Góra, 28 Zyty St., 65-046 Zielona Gora, Poland; (K.C.); (J.C.)
| | - Jolanta Chmielowiec
- Department of Hygiene and Epidemiology, Collegium Medicum, University of Zielona Góra, 28 Zyty St., 65-046 Zielona Gora, Poland; (K.C.); (J.C.)
| | - Aleksandra Strońska-Pluta
- Independent Laboratory of Health Promotion, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 St., 70-111 Szczecin, Poland;
| | - Michał Tomasz Kowalski
- Clinical Department of Cardiology, Nowa Sól Multidisciplinary Hospital, 67-100 Nowa Sol, Poland;
| | - Bartosz Kudliński
- Department of Emergency Medicine, Anesthesiology and Intensive Care in K. Marcinkowski University Hospital, Collegium Medicum, University of Zielona Góra, 65-046 Zielona Gora, Poland;
| | - Anna Grzywacz
- Independent Laboratory of Health Promotion, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich 72 St., 70-111 Szczecin, Poland;
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Sahai M, Opacka-Juffry J. Molecular mechanisms of action of stimulant novel psychoactive substances that target the high-affinity transporter for dopamine. Neuronal Signal 2021; 5:NS20210006. [PMID: 34888062 PMCID: PMC8630395 DOI: 10.1042/ns20210006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 11/17/2022] Open
Abstract
Drug misuse is a significant social and public health problem worldwide. Misused substances exert their neurobehavioural effects through changing neural signalling within the brain, many of them leading to substance dependence and addiction in the longer term. Among drugs with addictive liability, there are illicit classical stimulants such as cocaine and amphetamine, and their more recently available counterparts known as novel psychoactive substances (NPS). Stimulants normally increase dopamine availability in the brain, including the pathway implicated in reward-related behaviour. This pattern is observed in both animal and human brain. The main biological target of stimulants, both classical and NPS, is the dopamine transporter (DAT) implicated in the dopamine-enhancing effects of these drugs. This article aims at reviewing research on the molecular mechanisms underpinning the interactions between stimulant NPS, such as benzofurans, cathinones or piperidine derivatives and DAT, to achieve a greater understanding of the core phenomena that decide about the addictive potential of stimulant NPS. As the methodology is essential in the process of experimental research in this area, we review the applications of in vitro, in vivo and in silico approaches. The latter, including molecular dynamics, attracts the focus of the present review as the method of choice in molecular and atomistic investigations of the mechanisms of addiction of stimulant NPS. Research of this kind is of interest to not only scientists but also health professionals as updated knowledge of NPS, their modes of action and health risks, is needed to tackle the challenges posed by NPS misuse.
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Affiliation(s)
- Michelle A. Sahai
- School of Life and Health Sciences, University of Roehampton, London SW15 4JD, U.K
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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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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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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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Hsu SY, Lin HC, Chen TB, Du WC, Hsu YH, Wu YC, Tu PW, Huang YH, Chen HY. Feasible Classified Models for Parkinson Disease from 99mTc-TRODAT-1 SPECT Imaging. SENSORS 2019; 19:s19071740. [PMID: 30978990 PMCID: PMC6480576 DOI: 10.3390/s19071740] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 11/16/2022]
Abstract
The neuroimaging techniques such as dopaminergic imaging using Single Photon Emission Computed Tomography (SPECT) with 99mTc-TRODAT-1 have been employed to detect the stages of Parkinson’s disease (PD). In this retrospective study, a total of 202 99mTc-TRODAT-1 SPECT imaging were collected. All of the PD patient cases were separated into mild (HYS Stage 1 to Stage 3) and severe (HYS Stage 4 and Stage 5) PD, according to the Hoehn and Yahr Scale (HYS) standard. A three-dimensional method was used to estimate six features of activity distribution and striatal activity volume in the images. These features were skewness, kurtosis, Cyhelsky’s skewness coefficient, Pearson’s median skewness, dopamine transporter activity volume, and dopamine transporter activity maximum. Finally, the data were modeled using logistic regression (LR) and support vector machine (SVM) for PD classification. The results showed that SVM classifier method produced a higher accuracy than LR. The sensitivity, specificity, PPV, NPV, accuracy, and AUC with SVM method were 0.82, 1.00, 0.84, 0.67, 0.83, and 0.85, respectively. Additionally, the Kappa value was shown to reach 0.68. This claimed that the SVM-based model could provide further reference for PD stage classification in medical diagnosis. In the future, more healthy cases will be expected to clarify the false positive rate in this classification model.
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Affiliation(s)
- Shih-Yen Hsu
- Department of Information Engineering, I-Shou University, No.1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung City 84001, Taiwan.
| | - Hsin-Chieh Lin
- Department of Chinese Medicine, E-Da Cancer Hospital, No.1, Yida Rd., Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
- School of Chinese Medicine for Post-Baccalaureate, I-Shou University, No.8, Yida Rd., Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
| | - Tai-Been Chen
- Department of Medical Imaging and Radiological Science, I-Shou University, No.8, Yida Rd., Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
| | - Wei-Chang Du
- Department of Information Engineering, I-Shou University, No.1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung City 84001, Taiwan.
| | - Yun-Hsuan Hsu
- Department of Nuclear Medicine, E-Da Hospital, I-Shou University, No.1, Yida Rd, Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
| | - Yi-Chen Wu
- Department of Information Engineering, I-Shou University, No.1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung City 84001, Taiwan.
- Department of Nuclear Medicine, E-Da Hospital, I-Shou University, No.1, Yida Rd, Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
| | - Po-Wei Tu
- Department of Nuclear Medicine, E-Da Hospital, I-Shou University, No.1, Yida Rd, Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
| | - Yung-Hui Huang
- Department of Medical Imaging and Radiological Science, I-Shou University, No.8, Yida Rd., Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
| | - Huei-Yung Chen
- Department of Nuclear Medicine, E-Da Hospital, I-Shou University, No.1, Yida Rd, Jiaosu Village, Yanchao District, Kaohsiung City 82445, Taiwan.
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Modulation of Hippocampal Antioxidant Defense System in Chronically Stressed Rats by Lithium. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8745376. [PMID: 30911352 PMCID: PMC6398005 DOI: 10.1155/2019/8745376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/05/2018] [Accepted: 12/02/2018] [Indexed: 01/09/2023]
Abstract
This study examined the effects of lithium on gene expression and activity of the antioxidant enzymes copper zinc superoxide dismutase (SOD1), manganese superoxide dismutase (SOD2), catalase (CAT), glutathione peroxidase (GPx), and glutathione reductase (GR) in the hippocampus of chronically stressed rats. In addition, we examined the effects of lithium on anxiety behaviors, hippocampal concentrations of dopamine (DA) and malondialdehyde (MDA), protein levels of brain-derived neurotrophic factor (BDNF), tyrosine hydroxylase (TH), dopamine transporter (DAT), and catechol-O-methyltransferase (COMT), as well as activity of monoamine oxidase (MAO) in chronically stressed rats. The investigated parameters were quantified by real-time RT-PCR, Western blot analyses, and assays of enzyme activities. We found that lithium did not change gene expression of SOD1, CAT, GPx, and GR but decreased gene expression of SOD2 in chronically stressed rats. A very important result in this study was that lithium treatment decreased the enzyme activities of SOD1 and SOD2 but increased the enzyme activities of GPx and GR in stress condition, which indicates the control of redox balance. The reduced concentration of MDA confirms this. In addition, we found that lithium treatment decreased high protein levels of BDNF and DAT in chronically stressed rats to the level found in unstressed animals. Also, lithium treatment increased the expression of TH but decreased the enzyme activity of MAO B, which contributed to the increase of hippocampal concentration of DA in chronically stressed rats to the level of unstressed animals. Finally, lithium treatment in animals exposed to chronic stress increased the time spent in open arms. Lithium-induced modulation of hippocampal antioxidant status and attenuation of oxidative stress stabilized behavior in animals with high anxiety index. In addition, reduced oxidative stress was followed by the changes of both turnover of DA and levels of BDNF protein in chronically stressed rats treated with lithium. These findings may be important in preclinical research of the effects of lithium on oxidative stress level in pathological conditions.
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Krout D, Pramod AB, Dahal RA, Tomlinson MJ, Sharma B, Foster JD, Zou MF, Boatang C, Newman AH, Lever JR, Vaughan RA, Henry LK. Inhibitor mechanisms in the S1 binding site of the dopamine transporter defined by multi-site molecular tethering of photoactive cocaine analogs. Biochem Pharmacol 2017; 142:204-215. [PMID: 28734777 DOI: 10.1016/j.bcp.2017.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints. Understanding the molecular mechanisms governing the pharmacological inhibition of DAT is therefore key for understanding the requisite interactions for behavioral modulation and addiction. Previously, we leveraged complementary computational docking, mutagenesis, peptide mapping, and substituted cysteine accessibility strategies to identify the specific adduction site and binding pose for the crosslinkable, photoactive cocaine analog, RTI 82, which contains a photoactive azide attached at the 2β position of the tropane pharmacophore. Here, we utilize similar methodology with a different cocaine analog N-[4-(4-azido-3-I-iodophenyl)-butyl]-2-carbomethoxy-3-(4-chlorophenyl)tropane, MFZ 2-24, where the photoactive azide is attached to the tropane nitrogen. In contrast to RTI 82, which crosslinked into residue Phe319 of transmembrane domain (TM) 6, our findings show that MFZ 2-24 adducts to Leu80 in TM1 with modeling and biochemical data indicating that MFZ 2-24, like RTI 82, occupies the central S1 binding pocket with the (+)-charged tropane ring nitrogen coordinating with the (-)-charged carboxyl side chain of Asp79. The superimposition of the tropane ring in the three-dimensional binding poses of these two distinct ligands provides strong experimental evidence for cocaine binding to DAT in the S1 site and the importance of the tropane moiety in competitive mechanisms of DA uptake inhibition. These findings set a structure-function baseline for comparison of typical and atypical DAT inhibitors and how their interactions with DAT could lead to the loss of cocaine-like behaviors.
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Affiliation(s)
- Danielle Krout
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Akula Bala Pramod
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Rejwi Acharya Dahal
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Michael J Tomlinson
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Babita Sharma
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - James D Foster
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA
| | - Mu-Fa Zou
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - Comfort Boatang
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - Amy Hauck Newman
- Medicinal Chemistry Section, National Institute on Drug Abuse - Intramural Research Program, Baltimore, MD 21224, USA
| | - John R Lever
- Research Service, Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; Department of Radiology and Radiopharmaceutical Sciences Institute, University of Missouri, Columbia, MO 65211, USA
| | - Roxanne A Vaughan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA.
| | - L Keith Henry
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, 1301 North Columbia Road, Grand Forks, ND 58202, USA.
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Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to. J Mol Graph Model 2017; 71:233-241. [DOI: 10.1016/j.jmgm.2016.11.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023]
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Sohail A, Jayaraman K, Venkatesan S, Gotfryd K, Daerr M, Gether U, Loland CJ, Wanner KT, Freissmuth M, Sitte HH, Sandtner W, Stockner T. The Environment Shapes the Inner Vestibule of LeuT. PLoS Comput Biol 2016; 12:e1005197. [PMID: 27835643 PMCID: PMC5105988 DOI: 10.1371/journal.pcbi.1005197] [Citation(s) in RCA: 13] [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: 06/26/2016] [Accepted: 10/12/2016] [Indexed: 12/27/2022] Open
Abstract
Human neurotransmitter transporters are found in the nervous system terminating synaptic signals by rapid removal of neurotransmitter molecules from the synaptic cleft. The homologous transporter LeuT, found in Aquifex aeolicus, was crystallized in different conformations. Here, we investigated the inward-open state of LeuT. We compared LeuT in membranes and micelles using molecular dynamics simulations and lanthanide-based resonance energy transfer (LRET). Simulations of micelle-solubilized LeuT revealed a stable and widely open inward-facing conformation. However, this conformation was unstable in a membrane environment. The helix dipole and the charged amino acid of the first transmembrane helix (TM1A) partitioned out of the hydrophobic membrane core. Free energy calculations showed that movement of TM1A by 0.30 nm was driven by a free energy difference of ~15 kJ/mol. Distance measurements by LRET showed TM1A movements, consistent with the simulations, confirming a substantially different inward-open conformation in lipid bilayer from that inferred from the crystal structure. Crystal structures of the bacterial small amino acid transporter LeuT provided structural evidence for the alternating access model. Thereby, these structures shaped our understanding of the mechanisms underlying substrate translocation by neurotransmitter transporters. However, it has been questioned, if the crystallized inward-open conformation of LeuT can exist in the membrane environment. Here we show that, while stable in detergent micelles, the inward-open conformation of LeuT is of high energy and undergoes structural readjustments. We use a multi-faceted approach including molecular dynamics simulations, scintillation proximity assays, free energy calculations and apply for the first time lanthanide resonance energy transfer measurements to verify the in silico predictions. In silico and in vitro approaches using the same conditions allowed us to combine the macroscopic experimental data with microscopic all atom results from simulations to identify the underlying driving forces: partitioning of charged and polar groups from the hydrophobic membrane interior to the hydrophilic environment. We propose that the inward-facing state shows a much smaller movement of TM1A, but large enough to create an access path to the S1 substrate binding site from the vestibule.
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Affiliation(s)
- Azmat Sohail
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kumaresan Jayaraman
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Santhoshkannan Venkatesan
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Kamil Gotfryd
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
- University of Copenhagen, Faculty of Health Sciences Denmark, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Markus Daerr
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Ulrik Gether
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Claus J. Loland
- University of Copenhagen, Faculty of Health and Medical Sciences Denmark, Department of Neuroscience and Pharmacology, Copenhagen, Denmark
| | - Klaus T. Wanner
- Ludwig Maximilians University Munich, Department of Pharmacy, Center of Drug Research, Munich, Germany
| | - Michael Freissmuth
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Harald H. Sitte
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
- * E-mail:
| | - Walter Sandtner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Vienna, Austria
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Grouleff J, Søndergaard S, Koldsø H, Schiøtt B. Properties of an inward-facing state of LeuT: conformational stability and substrate release. Biophys J 2016; 108:1390-1399. [PMID: 25809252 DOI: 10.1016/j.bpj.2015.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 01/12/2023] Open
Abstract
The leucine transporter (LeuT) is a bacterial homolog of the human monoamine transporters, which are important pharmaceutical targets. There are no high-resolution structures of the human transporters available; however, LeuT has been crystallized in several different conformational states. Recently, an inward-facing conformation of LeuT was solved revealing an unexpectedly large movement of transmembrane helix 1a (TM1a). We have performed molecular dynamics simulations of the mutated and wild-type transporter, with and without the cocrystallized Fab antibody fragment, to investigate the properties of this inward-facing conformation in relation to transport by LeuT within the membrane environment. In all of the simulations, local conformational changes with respect to the crystal structure are consistently observed, especially in TM1a. Umbrella sampling revealed a soft potential for TM1a tilting. Furthermore, simulations of inward-facing LeuT with Na(+) ions and substrate bound suggest that one of the Na(+) ion binding sites is fully disrupted. Release of alanine and the second Na(+) ion is also observed, giving insight into the final stage of the translocation process in atomistic detail.
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Affiliation(s)
- Julie Grouleff
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Siri Søndergaard
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Heidi Koldsø
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark.
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13
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Xue W, Wang P, Li B, Li Y, Xu X, Yang F, Yao X, Chen YZ, Xu F, Zhu F. Identification of the inhibitory mechanism of FDA approved selective serotonin reuptake inhibitors: an insight from molecular dynamics simulation study. Phys Chem Chem Phys 2016; 18:3260-71. [DOI: 10.1039/c5cp05771j] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The binding mode shared by 4 FDA approved SSRIs treating major depression was identified by integrating multiple computational methods.
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14
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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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15
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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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Kordi-Tamandani DM, Tajoddini S, Salimi F. Promoter Methylation and BDNF and DAT1 Gene Expression Profiles in Patients with Drug Addiction. Pathobiology 2015; 82:94-9. [DOI: 10.1159/000430465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
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Dahal RA, Pramod AB, Sharma B, Krout D, Foster JD, Cha JH, Cao J, Newman AH, Lever JR, Vaughan RA, Henry LK. Computational and biochemical docking of the irreversible cocaine analog RTI 82 directly demonstrates ligand positioning in the dopamine transporter central substrate-binding site. J Biol Chem 2014; 289:29712-27. [PMID: 25179220 PMCID: PMC4207985 DOI: 10.1074/jbc.m114.571521] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/09/2014] [Indexed: 12/20/2022] Open
Abstract
The dopamine transporter (DAT) functions as a key regulator of dopaminergic neurotransmission via re-uptake of synaptic dopamine (DA). Cocaine binding to DAT blocks this activity and elevates extracellular DA, leading to psychomotor stimulation and addiction, but the mechanisms by which cocaine interacts with DAT and inhibits transport remain incompletely understood. Here, we addressed these questions using computational and biochemical methodologies to localize the binding and adduction sites of the photoactivatable irreversible cocaine analog 3β-(p-chlorophenyl)tropane-2β-carboxylic acid, 4'-azido-3'-iodophenylethyl ester ([(125)I]RTI 82). Comparative modeling and small molecule docking indicated that the tropane pharmacophore of RTI 82 was positioned in the central DA active site with an orientation that juxtaposed the aryliodoazide group for cross-linking to rat DAT Phe-319. This prediction was verified by focused methionine substitution of residues flanking this site followed by cyanogen bromide mapping of the [(125)I]RTI 82-labeled mutants and by the substituted cysteine accessibility method protection analyses. These findings provide positive functional evidence linking tropane pharmacophore interaction with the core substrate-binding site and support a competitive mechanism for transport inhibition. This synergistic application of computational and biochemical methodologies overcomes many uncertainties inherent in other approaches and furnishes a schematic framework for elucidating the ligand-protein interactions of other classes of DA transport inhibitors.
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Affiliation(s)
- Rejwi Acharya Dahal
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Akula Bala Pramod
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Babita Sharma
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Danielle Krout
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - James D Foster
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203
| | - Joo Hwan Cha
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - Jianjing Cao
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - Amy Hauck Newman
- the Medicinal Chemistry Section, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland 21224
| | - John R Lever
- the Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, Missouri 65201, and the Department of Radiology, Radiopharmaceutical Sciences Institute, and Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, Missouri 65211
| | - Roxanne A Vaughan
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203,
| | - L Keith Henry
- From the Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203,
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Pattison LP, McIntosh S, Sexton T, Childers SR, Hemby SE. Changes in dopamine transporter binding in nucleus accumbens following chronic self-administration cocaine: heroin combinations. Synapse 2014; 68:437-44. [PMID: 24916769 DOI: 10.1002/syn.21755] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/20/2014] [Accepted: 06/04/2014] [Indexed: 01/10/2023]
Abstract
Concurrent use of cocaine and heroin (speedball) has been shown to exert synergistic effects on dopamine neurotransmission in the nucleus accumbens (NAc), as observed by significant increases in extracellular dopamine levels and compensatory elevations in the maximal reuptake rate of dopamine. The present studies were undertaken to determine whether chronic self-administration of cocaine, heroin or a combination of cocaine:heroin led to compensatory changes in the abundance and/or affinity of high- and low-affinity DAT binding sites. Saturation binding of the cocaine analog [(125) I] 3β-(4-iodophenyl)tropan-2β-carboxylic acid methyl ester ([(125) I]RTI-55) in rat NAc membranes resulted in binding curves that were best fit to two-site binding models, allowing calculation of dissociation constant (Kd ) and binding density (Bmax ) values corresponding to high- and low-affinity DAT binding sites. Scatchard analysis of the saturation binding curves clearly demonstrate the presence of high- and low- affinity binding sites in the NAc, with low-affinity sites comprising 85 to 94% of the binding sites. DAT binding analyses revealed that self-administration of cocaine and a cocaine:heroin combination increased the affinity of the low-affinity site for the cocaine congener RTI-55 compared to saline. These results indicate that the alterations observed following chronic speedball self-administration are likely due to the cocaine component alone; thus further studies are necessary to elaborate upon the synergistic effect of cocaine:heroin combinations on the dopamine system in the NAc.
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Affiliation(s)
- Lindsey P Pattison
- Graduate Program in Neuroscience, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157; Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston-Salem, North Carolina, 27157
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Thomas JR, Gedeon PC, Madura JD. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis. Proteins 2014; 82:2289-302. [PMID: 24753369 DOI: 10.1002/prot.24588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/29/2014] [Accepted: 04/10/2014] [Indexed: 01/28/2023]
Abstract
The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30-D404, Y108-F253, and R5-D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport.
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Affiliation(s)
- James R Thomas
- Department of Chemistry and Biochemistry and the Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania; Mylan School of Pharmacy, Duquesne University, Pittsburgh, Pennsylvania
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