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Du JC, Chang MH, Yeh CJ, Lee MT, Lee HJ, Chuang SH, Chiou LC. Pivotal Role of Slitrk1 in Adult Striatal Cholinergic Neurons in Mice: Implication in Tourette Syndrome. Ann Neurol 2023. [PMID: 37776102 DOI: 10.1002/ana.26805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
OBJECTIVE The SLIT and NTRK-like 1 (SLITRK1) gene mutation and striatal cholinergic interneurons (ChIs) loss are associated with Tourette syndrome (TS). ChIs comprise only 1 to 2% of striatal neurons but project widely throughout the stratum to impact various striatal neurotransmission, including TS-related dopaminergic transmission. Here, we link striatal Slitrk1, ChI function, and dopaminergic transmission and their associations with TS-like tic behaviors. METHODS Slitrk1-KD mice were induced by bilaterally injecting Slitrk1 siRNA into their dorsal striatum. Control mice received scrambled siRNA injection. Their TS-like tic behaviors, prepulse inhibition, sensory-motor function and dopamine-related behaviors were compared. We also compared dopamine and ACh levels in microdialysates, Slitrk protein and dopamine transporter levels, and numbers of Slitrk-positive ChIs and activated ChIs in the striatum between two mouse groups, and electrophysiological properties between Slitrk-positive and Slitrk-negative striatal ChIs. RESULTS Slitrk1-KD mice exhibit TS-like haloperidol-sensitive stereotypic tic behaviors, impaired prepulse inhibition, and delayed sensorimotor response compared with the control group. These TS-like characteristics correlate with lower striatal Slitrk1 protein levels, fewer Slitrk1-containing ChIs, and fewer activated ChIs in Slitrk1-KD mice. Based on their electrophysiological properties, Slitrk1-negative ChIs are less excitable than Slitrk1-positive ChIs. Slitrk1-KD mice have lower evoked acetylcholine and dopamine levels, higher tonic dopamine levels, and downregulated dopamine transporters in the striatum, increased apomorphine-induced climbing behaviors, and impaired methamphetamine-induced hyperlocomotion compared with controls. INTERPRETATION Slitrk1 is pivotal in maintaining striatal ChIs activity and subsequent dopaminergic transmission for normal motor functioning. Furthermore, conditional striatal Slitrk1-KD mice may serve as a translational modality with aspects of TS phenomenology. ANN NEUROL 2023.
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Affiliation(s)
- Jung-Chieh Du
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pediatrics, Taipei City Hospital, Zhongxiao Branch, Taipei, Taiwan
| | - Man-Hsin Chang
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chen-Jiun Yeh
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming Tatt Lee
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
- Center of Research for Mental Health and Wellbeing, UCSI University, Kuala Lumpur, Malaysia
| | - Hsin-Jung Lee
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Hui Chuang
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Lih-Chu Chiou
- Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Acupuncture Science, China Medical University, Taichung, Taiwan
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2
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yousif FA, Alzain AA, Alraih AM, Ibraheem W. Repurposing of approved drugs for targeting CDK4/6 and aromatase protein using molecular docking and molecular dynamics studies. PLoS One 2023; 18:e0291256. [PMID: 37682937 PMCID: PMC10490992 DOI: 10.1371/journal.pone.0291256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Breast cancer is a leading cause of cancer-related morbidity and mortality worldwide, with the highest incidence among women. Among the various subtypes of breast cancer, estrogen-receptor positive (ER+) is the most diagnosed. Estrogen upregulates cyclin D1, which in turn promotes the activity of CDK4/6 and facilitates cell cycle progression. To address this, the first-line treatment for ER+ breast cancer focuses on inhibiting estrogen production by targeting aromatase, the enzyme responsible for the rate-limiting step in estrogen synthesis. Thus, combining CDK4/6 inhibitors with aromatase inhibitors has emerged as a crucial treatment strategy for this type of breast cancer. This approach effectively suppresses estrogen biosynthesis and controls uncontrolled cell proliferation, significantly improving overall survival rates and delayed disease progression. This study aimed to identify compounds that are likely to inhibit CDK4/6 and aromatase simultaneously by using a structure-based drug design strategy. 12,432 approved and investigational drugs were prepared and docked into the active site of CDK6 using HTVS and XP docking modes of Glide resulting in 277 compounds with docking scores ≤ -7 kcal/mol. These compounds were docked into aromatase enzyme using XP mode to give seven drugs with docking scores≤ -6.001 kcal/mol. Furthermore, the shortlisted drugs were docked against CDK4 showing docking scores ranging from -3.254 to -8.254 kcal/mol. Moreover, MM-GBSA for the top seven drugs was calculated. Four drugs, namely ellagic acid, carazolol, dantron, and apomorphine, demonstrated good binding affinity to all three protein targets CDK4/6 and aromatase. Specifically, they exhibited favourable binding free energy with CDK6, with values of -51.92, -53.90, -50.22, and -60.97 kcal/mol, respectively. Among these drugs, apomorphine displayed the most favourable binding free energy with all three protein targets. To further evaluate the stability of the interaction, apomorphine was subjected to a 100 ns molecular dynamics simulation with CDK6. The results indicated the formation of a stable ligand-protein complex. While the results obtained from the MM-GBSA calculation of the binding free energies of the MD conformations of apomorphine showed less favourable binding free energy compared to that obtained post-docking. All these computational findings will provide better structural insight for the development of CDK4/6 and aromatase multi-target inhibitors.
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Affiliation(s)
- Fatima A. yousif
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Abdulrahim A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Alhafez M. Alraih
- Department of Chemistry, College of Science and Arts, Mohail Aseer, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Walaa Ibraheem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
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Shafieenezhad A, Mitra S, Wassall SR, Tristram-Nagle S, Nagle JF, Petrache HI. Location of dopamine in lipid bilayers and its relevance to neuromodulator function. Biophys J 2023; 122:1118-1129. [PMID: 36804668 PMCID: PMC10111280 DOI: 10.1016/j.bpj.2023.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/18/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Dopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.
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Affiliation(s)
- Azam Shafieenezhad
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | - Saheli Mitra
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Stephen R Wassall
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana
| | | | - John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Horia I Petrache
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana.
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Chen X, Yuan Y, Chen Y, Yu J, Wang J, Chen J, Guo Y, Pu X. Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from μOR/δOR Dimers. J Chem Inf Model 2022; 62:5581-5600. [PMID: 36377848 DOI: 10.1021/acs.jcim.2c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
GPCRs regulate multiple intracellular signaling cascades. Biasedly activating one signaling pathway over the others provides additional clinical utility to optimize GPCR-based therapies. GPCR heterodimers possess different functions from their monomeric states, including their selectivity to different transducers. However, the biased signaling mechanism induced by the heterodimerization remains unclear. Motivated by the issue, we select an important GPCR heterodimer (μOR/δOR heterodimer) as a case and use microsecond Gaussian accelerated molecular dynamics simulation coupled with potential of mean force and protein structure network (PSN) to probe mechanisms regarding the heterodimerization-induced constitutive β-arrestin activity and efficacy change of the agonist DAMGO. The results show that only the lowest energy state of the μOR/δOR heterodimer, which adopts a slightly outward shift of TM6 and an ICL2 conformation close to the receptor core, can selectively accommodate β-arrestins. PSN further reveals important roles of H8, ICL1, and ICL2 in regulating the constitutive β-arrestin-biased activity for the apo μOR/δOR heterodimer. In addition, the heterodimerization can allosterically alter the binding mode of DAMGO mainly by means of W7.35. Consequently, DAMGO transmits the structural signal mainly through TM6 and TM7 in the dimer, rather than TM3 similar to the μOR monomer, thus changing the efficacy of DAMGO from a balanced agonist to the β-arrestin-biased one. On the other side, the binding of DAMGO to the heterodimer can stabilize μOR/δOR heterodimers through a stronger interaction of TM1/TM1 and H8/H8, accordingly enhancing the interaction of μOR with δOR and the binding affinity of the dimer to the β-arrestin. The agonist DAMGO does not change main compositions of the regulation network from the dimer interface to the transducer binding pocket of the μOR protomer, but induces an increase in the structural communication of the network, which should contribute to the enhanced β-arrestin coupling. Our observations, for the first time, reveal the molecular mechanism of the biased signaling induced by the heterodimerization for GPCRs, which should be beneficial to more comprehensively understand the GPCR bias signaling.
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Affiliation(s)
- Xin Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu610041, China
| | - Yichi Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, California92697, United States
| | - Jingzhou Wang
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu610064, China
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Identification of Novel Dopamine D2 Receptor Ligands—A Combined In Silico/In Vitro Approach. Molecules 2022; 27:molecules27144435. [PMID: 35889317 PMCID: PMC9318694 DOI: 10.3390/molecules27144435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Diseases of the central nervous system are an alarming global problem showing an increasing prevalence. Dopamine receptor D2 (D2R) has been shown to be involved in central nervous system diseases. While different D2R-targeting drugs have been approved by the FDA, they all suffer from major drawbacks due to promiscuous receptor activity leading to adverse effects. Increasing the number of potential D2R-targeting drug candidates bears the possibility of discovering molecules with less severe side-effect profiles. In dire need of novel D2R ligands for drug development, combined in silico/in vitro approaches have been shown to be efficient strategies. In this study, in silico pharmacophore models were generated utilizing both ligand- and structure-based approaches. Subsequently, different databases were screened for novel D2R ligands. Selected virtual hits were investigated in vitro, quantifying their binding affinity towards D2R. This workflow successfully identified six novel D2R ligands exerting micro- to nanomolar (most active compound KI = 4.1 nM) activities. Thus, the four pharmacophore models showed prospective true-positive hit rates in between 4.5% and 12%. The developed workflow and identified ligands could aid in developing novel drug candidates for D2R-associated pathologies.
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Chowdhury A, Singh PC. Role of the weak noncovalent interactions in the stability of the aggregated protonated dopamine in the aqueous solution: spectroscopic and quantum chemical calculation studies. J CHEM SCI 2022. [DOI: 10.1007/s12039-021-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kanan T, Kanan D, Al Shardoub EJ, Durdagi S. Transcription factor NF-κB as target for SARS-CoV-2 drug discovery efforts using inflammation-based QSAR screening model. J Mol Graph Model 2021; 108:107968. [PMID: 34311260 PMCID: PMC8219481 DOI: 10.1016/j.jmgm.2021.107968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 01/06/2023]
Abstract
NF-κB is a central regulator of immunity and inflammation. It is suggested that the inflammatory response mediated by SARS-CoV-2 is predominated by NF-κB activation. Thus, NF-κB inhibition is considered a potential therapeutic strategy for COVID-19. The aim of this study was to identify potential anti-inflammation lead molecules that target NF-κB using a quantitative structure-activity relationships (QSAR) model of currently used and investigated anti-inflammatory drugs as the basis for screening. We applied an integrated approach by starting with the inflammation-based QSAR model to screen three libraries containing more than 220,000 drug-like molecules for the purpose of finding potential drugs that target the NF-κB/IκBα p50/p65 (RelA) complex. We also used QSAR models to rule out molecules that were predicted to be toxic. Among screening libraries, 382 molecules were selected as potentially nontoxic and were analyzed further by short and long molecular dynamics (MD) simulations and free energy calculations. We have discovered five hit ligands with highly predicted anti-inflammation activity and nearly no predicted toxicities which had strongly favorable protein-ligand interactions and conformational stability at the binding pocket compared to a known NF-κB inhibitor (procyanidin B2). We propose these hit molecules as potential NF-κB inhibitors which can be further investigated in pre-clinical studies against SARS-CoV-2 and may be used as a scaffold for chemical optimization and drug development efforts.
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Affiliation(s)
- Tarek Kanan
- School of Medicine, Bahcesehir University, Istanbul, Turkey; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Duaa Kanan
- School of Medicine, Bahcesehir University, Istanbul, Turkey; Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Istanbul, Turkey.
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8
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Fenoterol and dobutamine as SARS-CoV-2 main protease inhibitors: A virtual screening study. J Mol Struct 2020; 1228:129449. [PMID: 33071354 PMCID: PMC7550866 DOI: 10.1016/j.molstruc.2020.129449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/19/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022]
Abstract
Global health is under heavy threat by a worldwide pandemic caused by a new type of coronavirus (COVID-19) since its rapid spread in China in 2019 [1]. Currently, there are no approved specific drugs and effective treatment for COVID-19 infection, but several available drugs are known to facilitate tentative treatment. Since drug design, development and testing procedures are time-consuming [2], [1], [2], [3], virtual screening studies with the aid of available drug databases take the initiative at this point and save the time. Besides, drug repurposing strategies promises to identify new agents for the novel diseases in a time-critical fashion. In this study, we used structure based virtual screening method on FDA approved drugs and compounds in clinical trials. As a result of this study we choose three most prominent compounds for further studies. Here we show that these three compounds (dobutamine and its two derivatives) can be considered as promising inhibitors for SARS-CoV-2 main protease and results also demonstrate the possible interactions of dobutamine and its derivatives with SARS-CoV-2 main protease (6W63) [6]. Our efforts in this work directly address current urgency of a new drug discovery against COVID-19.
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9
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Aguayo-Cerón KA, Calzada-Mendoza CC, Méndez-Bolaina E, Romero-Nava R, Ocharan-Hernández ME. The regulatory effect of bromocriptine on cardiac hypertrophy by prolactin and D2 receptor modulation. Clin Exp Hypertens 2020; 42:675-679. [PMID: 32478610 DOI: 10.1080/10641963.2020.1772814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Bromocriptine, a dopamine agonist, used for the treatment of hyperprolactinemia, type 2 diabetes, ovarian hyper-stimulation syndrome, has also effects on the cardiac remodeling process, but the mechanism of action is unknown. The aim of this work was to determinate the effect during hypertrophic process through molecular mechanisms that include prolactin receptor (Prlr) and receptor of dopamine 2 (D2 r) expression. METHODS We used a model of cardiac hypertrophy induced by an aortocaval fistula (ACF) surgery in rats. Protein concentrations of D2 r and Prlr were determined by western blotting. The treatment consisted in water (control), captopril (50 mg/kg/day), bromocriptine (3 mg/kg/day), and ACF group (n = 6 per group). RESULTS Our results showed that bromocriptine treatment decreases the hypertrophy index. Treatment with bromocriptine increases the protein expression of Prlr and D2 r in the cardiac tissue of rats with cardiac hypertrophy. CONCLUSIONS We concluded that bromocriptine has a protective effect on cardiac hypertrophy, and due to this effect, it may modulate the expression of Prlr and D2 r, which are involved in the development of cardiac hypertrophy.
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Affiliation(s)
- Karla Aidee Aguayo-Cerón
- Sección de Estudios de Posgrado e Investigación, Escuela Superior De Medicina, Instituto Politécnico Nacional-Escuela Superior de Medicina , México City, México
| | - Claudia Camelia Calzada-Mendoza
- Sección de Estudios de Posgrado e Investigación, Escuela Superior De Medicina, Instituto Politécnico Nacional-Escuela Superior de Medicina , México City, México
| | | | - Rodrigo Romero-Nava
- Sección de Estudios de Posgrado e Investigación, Escuela Superior De Medicina, Instituto Politécnico Nacional-Escuela Superior de Medicina , México City, México.,Departamento de Farmacología, Hospital Infantil de México Federico Gómez (HIMFG) , México City, México
| | - María Esther Ocharan-Hernández
- Sección de Estudios de Posgrado e Investigación, Escuela Superior De Medicina, Instituto Politécnico Nacional-Escuela Superior de Medicina , México City, México
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Lee JY, Ham J, Lim W, Song G. Apomorphine facilitates loss of respiratory chain activity in human epithelial ovarian cancer and inhibits angiogenesis in vivo. Free Radic Biol Med 2020; 154:95-104. [PMID: 32437927 DOI: 10.1016/j.freeradbiomed.2020.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
Apomorphine, a therapeutic agent for neurological diseases, is structurally similar to dopamine, and thereby holds potential in cancer therapy. However, there are no reports regarding its anti-cancer effects on human epithelial ovarian cancers (EOCs); therefore, we aimed to elucidate the mechanism underlying its action after drug repositioning. Apomorphine inhibited the proliferation of ES2 and OV90 EOC cells by inducing caspase activation and mitochondrion-associated apoptosis; it also promoted endoplasmic reticulum stress and mitochondrial dysfunction through mitochondrial membrane potential depolarization and mitochondrial calcium overload. Moreover, following apomorphine treatment, we noted the loss of respiratory chain activity by reduction of oxidative phosphorylation and energy-production shift in EOC cells. Further, we verified the anti-angiogenic capacity of apomorphine using fli:eGFP transgenic zebrafish. As a preclinical assessment, we demonstrated the synergistic anti-cancer effects of apomorphine and paclitaxel combination.
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Affiliation(s)
- Jin-Young Lee
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jiyeon Ham
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Whasun Lim
- Department of Food and Nutrition, Kookmin University, Seoul, 02707, Republic of Korea.
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology and Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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Tosso RD, Parravicini O, Zarycz MNC, Angelina E, Vettorazzi M, Peruchena N, Andujar S, Enriz RD. Conformational and electronic study of dopamine interacting with theD2dopamine receptor. J Comput Chem 2020; 41:1898-1911. [DOI: 10.1002/jcc.26361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/10/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Rodrigo D. Tosso
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Oscar Parravicini
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - M. Natalia C. Zarycz
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y PropiedadesFacultad de Ciencias Exactas y Naturales y Agrimensura Corrientes Argentina
- Instituto de Química Básica y Aplicada (IQUIBA‐NEA)CONICET Corrientes Argentina
| | - Marcela Vettorazzi
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Nélida Peruchena
- Laboratorio de Estructura Molecular y PropiedadesFacultad de Ciencias Exactas y Naturales y Agrimensura Corrientes Argentina
- Instituto de Química Básica y Aplicada (IQUIBA‐NEA)CONICET Corrientes Argentina
| | - Sebastián Andujar
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
| | - Ricardo D. Enriz
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO‐SL)CONICET San Luis Argentina
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Tutumlu G, Dogan B, Avsar T, Orhan MD, Calis S, Durdagi S. Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2. Front Chem 2020; 8:167. [PMID: 32328476 PMCID: PMC7160371 DOI: 10.3389/fchem.2020.00167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Antiapoptotic members of B-cell leukemia/lymphoma-2 (BCL-2) family proteins are one of the overexpressed proteins in cancer cells that are oncogenic targets. As such, targeting of BCL-2 family proteins raises hopes for new therapeutic discoveries. Thus, we used multistep screening and filtering approaches that combine structure and ligand-based drug design to identify new, effective BCL-2 inhibitors from a small molecule database (Specs SC), which includes more than 210,000 compounds. This database is first filtered based on binary “cancer-QSAR” model constructed with 886 training and 167 test set compounds and common 26 toxicity quantitative structure-activity relationships (QSAR) models. Predicted non-toxic compounds are considered for target-driven studies. Here, we applied two different approaches to filter and select hit compounds for further in vitro biological assays and human cell line experiments. In the first approach, a molecular docking and filtering approach is used to rank compounds based on their docking scores and only a few top-ranked molecules are selected for further long (100-ns) molecular dynamics (MD) simulations and in vitro tests. While docking algorithms are promising in predicting binding poses, they can be less prone to precisely predict ranking of compounds leading to decrease in the success rate of in silico studies. Hence, in the second approach, top-docking poses of each compound filtered through QSAR studies are subjected to initially short (1 ns) MD simulations and their binding energies are calculated via molecular mechanics generalized Born surface area (MM/GBSA) method. Then, the compounds are ranked based on their average MM/GBSA energy values to select hit molecules for further long MD simulations and in vitro studies. Additionally, we have applied text-mining approaches to identify molecules that contain “indol” phrase as many of the approved drugs contain indole and indol derivatives. Around 2700 compounds are filtered based on “cancer-QSAR” model and are then docked into BCL-2. Short MD simulations are performed for the top-docking poses for each compound in complex with BCL-2. The complexes are again ranked based on their MM/GBSA values to select hit molecules for further long MD simulations and in vitro studies. In total, seven molecules are subjected to biological activity tests in various human cancer cell lines as well as Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay. Inhibitory concentrations are evaluated, and biological activities and apoptotic potentials are assessed by cell culture studies. Four molecules are found to be limiting the proliferation capacity of cancer cells while increasing the apoptotic cell fractions.
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Affiliation(s)
- Gurbet Tutumlu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Timucin Avsar
- Department of Medical Biology, Bahcesehir University, School of Medicine, Istanbul, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Muge Didem Orhan
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Seyma Calis
- Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey.,Molecular Biology, Genetics and Biotechnology Graduate Program, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
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13
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Qu L, Zhang X, Wang J, Zhou H, Hou T, Wei L, Xu F, Liang X. Phenotypic assessment and ligand screening of ETA/ETB receptors with label-free dynamic mass redistribution assay. Naunyn Schmiedebergs Arch Pharmacol 2019; 393:937-950. [PMID: 31781785 DOI: 10.1007/s00210-019-01756-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/23/2019] [Indexed: 01/16/2023]
Abstract
Endothelin receptors, consisting of two subtypes, ETA and ETB, are expressed in various tissues and widely regulate cardiovascular systems. The two receptors show distinct biological characteristics and are involved in different downstream pathways. Hence, to evaluate the ETA and ETB receptors on the same platform is helpful to display their pharmacological features. In this study, we developed a label-free dynamic mass redistribution (DMR) assay to investigate the phenotypic features of the ETA and ETB receptors in native cell lines. Meanwhile, specific agonists and antagonists were investigated for their pharmacological parameters. Results indicated that the DMR response of endothelin 1 (ET-1, an endogenous ETA/ETB agonist) was cell line dependent on ETA receptors and this ligand generated a biphasic dose-response curve in SH-SY5Y as well as PC3 cell lines. ET-1 and IRL 1620 (an ETB agonist) showed different DMR responses in U251 cells. IC50 values of antagonists were consistent with the Ki values previously reported. Furthermore, a list of compounds was screened on the ETA and ETB receptor models established by the high-throughput DMR assays. This study demonstrated that the DMR assay had great potential in the phenotypic-based investigation and ligand screening of GPCRs.
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Affiliation(s)
- Lala Qu
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiuli Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215006, China.
- Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Jixia Wang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Han Zhou
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tao Hou
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lai Wei
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fangfang Xu
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinmiao Liang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, China.
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14
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Sahin K, Zengin Kurt B, Sonmez F, Durdagi S. Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays. J Biomol Struct Dyn 2019; 38:3342-3358. [PMID: 31462153 DOI: 10.1080/07391102.2019.1660218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the current work, we developed a computational pipeline method for predicting the binding affinities of studied compounds at the specific target sites. Since many approved therapeutic compounds involve indole or indole-derivative rings, in the current study we focused compounds including these fingerprints. Initially, 212520 compounds were retrieved from Specs-SC library and after the conversion of IUPAC text file format, compounds that include 'indol' keyword (5194 compounds) were used in binary QSAR-based models to screen against a defined therapeutic activity "Alzheimer's disease" (AD). The molecules that have higher AD therapeutic activity values (>0.5) were then used in the 26 different toxicity-QSAR models. Binary QSAR models resulted 89 hits that have high AD therapeutic activity and no toxicity. Selected 89 molecules were then screened against acetylcholinesterase (AChE) targets using molecular docking and top-docking poses of compounds were used in initially short (10 ns) molecular dynamics (MD) simulations. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations were performed for 89 ligands and tightly bound 17 ligands based on average MM/GBSA scores were selected for long (100 ns) MD simulations. The same protocol was also applied for the known 4 AChE inhibitors. Selected hits were also docked to the binding pocket of butyrylcholinesterase (BChE). Finally, based on MM/GBSA scores, as well as their corresponding docking scores and metabolite production profiles, 7 compounds were selected and their in vitro tests were performed. Out of 7 compounds, 6 of them showed μM-level inhibition for both AChE and BChE targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Belma Zengin Kurt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, Turkey
| | - Fatih Sonmez
- Pamukova Vocational High School, Sakarya University of Applied Sciences, Sakarya, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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15
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Chagas C, Alisaraie L. Metabolites of Vinca Alkaloid Vinblastine: Tubulin Binding and Activation of Nausea-Associated Receptors. ACS OMEGA 2019; 4:9784-9799. [PMID: 31460070 PMCID: PMC6648052 DOI: 10.1021/acsomega.9b00652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/22/2019] [Indexed: 05/16/2023]
Abstract
Vinblastine (VLB) is an antimitotic drug that binds to the vinca site of tubulin. The molecule possesses a high molecular weight and a complex chemical structure with many possibilities of metabolization. Despite advances in drug discovery research in reducing drug toxicity, the cause and mechanism of VLB-induced adverse drug reactions (ADRs) remains poorly understood. VLB is metabolized to at least 35 known metabolites, which have been identified and collected in this present work. This study also explores how VLB metabolites affect nausea-associated receptors such as muscarinic, dopaminergic, and histaminic. The metabolites have stronger binding interactions than acetylcholine (ACh) for muscarinic M1, M4, and M5 receptors and demonstrate similar binding profiles to that of the natural substrate, ACh. The affinities of VLB metabolites to dopaminergic and histaminic receptors, their absorption, distribution, metabolism, excretion, toxicity properties, and the superiority of VLB to ACh for binding to M5R, indicate their potential to trigger activation of nausea-associated receptors during chemotherapy with VLB. It has been shown that metabolite 20-hydroxy-VLB (metabolite 10) demonstrates a stronger binding affinity to the vinca site of tubulin than VLB; however, they have similar modes of action. VLB and metabolite 10 have similar gastric solubility (FaSSGF), intestinal solubility (FeSSIF), and log P values. Metabolite 10 has a more acceptable pharmacokinetic profile than VLB, a better gastric and intestinal solubility. Furthermore, metabolite 10 was found to be less bound to plasma proteins than VLB. These are desired and essential features for effective drug bioavailability. Metabolite 10 is not a substrate of CYP2D6 and thus is less likely to cause drug-drug interactions and ADRs compared to its parent drug. The hydroxyl group added upon metabolism of VLB suggests that it can also be a reasonable starting compound for designing the next generation of antimitotic drugs to overcome P-glycoprotein-mediated multidrug resistance, which is often observed with vinca alkaloids.
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Affiliation(s)
- Caroline
Manto Chagas
- School
of Pharmacy, Memorial University of Newfoundland, 300 Prince Philip Dr., A1B 3V6 St. John’s, Newfoundland, Canada
| | - Laleh Alisaraie
- School
of Pharmacy, Memorial University of Newfoundland, 300 Prince Philip Dr., A1B 3V6 St. John’s, Newfoundland, Canada
- Department
of Chemistry, Memorial University of Newfoundland, A1B 3X7 St. John’s, Newfoundland, Canada
- E-mail:
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16
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Silva AR, Grosso C, Delerue-Matos C, Rocha JM. Comprehensive review on the interaction between natural compounds and brain receptors: Benefits and toxicity. Eur J Med Chem 2019; 174:87-115. [PMID: 31029947 DOI: 10.1016/j.ejmech.2019.04.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023]
Abstract
Given their therapeutic activity, natural products have been used in traditional medicines throughout the centuries. The growing interest of the scientific community in phytopharmaceuticals, and more recently in marine products, has resulted in a significant number of research efforts towards understanding their effect in the treatment of neurodegenerative diseases, such as Alzheimer's (AD), Parkinson (PD) and Huntington (HD). Several studies have shown that many of the primary and secondary metabolites of plants, marine organisms and others, have high affinities for various brain receptors and may play a crucial role in the treatment of diseases affecting the central nervous system (CNS) in mammalians. Actually, such compounds may act on the brain receptors either by agonism, antagonism, allosteric modulation or other type of activity aimed at enhancing a certain effect. The current manuscript comprehensively reviews the state of the art on the interactions between natural compounds and brain receptors. This information is of foremost importance when it is intended to investigate and develop cutting-edge drugs, more effective and with alternative mechanisms of action to the conventional drugs presently used for the treatment of neurodegenerative diseases. Thus, we reviewed the effect of 173 natural products on neurotransmitter receptors, diabetes related receptors, neurotrophic factor related receptors, immune system related receptors, oxidative stress related receptors, transcription factors regulating gene expression related receptors and blood-brain barrier receptors.
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Affiliation(s)
- Ana R Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology (DB), University of Minho (UM), Campus Gualtar, P-4710-057, Braga, Portugal
| | - Clara Grosso
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida, 431, P-4249-015, Porto, Portugal.
| | - Cristina Delerue-Matos
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida, 431, P-4249-015, Porto, Portugal
| | - João M Rocha
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology (DB), University of Minho (UM), Campus Gualtar, P-4710-057, Braga, Portugal; REQUIMTE/LAQV, Grupo de investigação de Química Orgânica Aplicada (QUINOA), Laboratório de polifenóis alimentares, Departamento de Química e Bioquímica (DQB), Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre, s/n, P-4169-007, Porto, Portugal
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17
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Current status of multiscale simulations on GPCRs. Curr Opin Struct Biol 2019; 55:93-103. [DOI: 10.1016/j.sbi.2019.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/19/2019] [Accepted: 02/27/2019] [Indexed: 01/14/2023]
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18
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Bueschbell B, Barreto CAV, Preto AJ, Schiedel AC, Moreira IS. A Complete Assessment of Dopamine Receptor- Ligand Interactions through Computational Methods. Molecules 2019; 24:E1196. [PMID: 30934701 PMCID: PMC6479630 DOI: 10.3390/molecules24071196] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/21/2019] [Accepted: 03/23/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Selectively targeting dopamine receptors (DRs) has been a persistent challenge in the last years for the development of new treatments to combat the large variety of diseases involving these receptors. Although, several drugs have been successfully brought to market, the subtype-specific binding mode on a molecular basis has not been fully elucidated. Methods: Homology modeling and molecular dynamics were applied to construct robust conformational models of all dopamine receptor subtypes (D₁-like and D₂-like). Fifteen structurally diverse ligands were docked. Contacts at the binding pocket were fully described in order to reveal new structural findings responsible for selective binding to DR subtypes. Results: Residues of the aromatic microdomain were shown to be responsible for the majority of ligand interactions established to all DRs. Hydrophobic contacts involved a huge network of conserved and non-conserved residues between three transmembrane domains (TMs), TM2-TM3-TM7. Hydrogen bonds were mostly mediated by the serine microdomain. TM1 and TM2 residues were main contributors for the coupling of large ligands. Some amino acid groups form electrostatic interactions of particular importance for D₁R-like selective ligands binding. Conclusions: This in silico approach was successful in showing known receptor-ligand interactions as well as in determining unique combinations of interactions, which will support mutagenesis studies to improve the design of subtype-specific ligands.
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Affiliation(s)
- Beatriz Bueschbell
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, D-53121 Bonn, Germany.
| | - Carlos A V Barreto
- Center for Neuroscience and Cell Biology, UC- Biotech Parque Tecnológico de Cantanhede, Núcleo 04, Lote B, 3060-197 Cantanhede, Portugal.
| | - António J Preto
- Center for Neuroscience and Cell Biology, UC- Biotech Parque Tecnológico de Cantanhede, Núcleo 04, Lote B, 3060-197 Cantanhede, Portugal.
| | - Anke C Schiedel
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, D-53121 Bonn, Germany.
| | - Irina S Moreira
- Center for Neuroscience and Cell Biology, UC- Biotech Parque Tecnológico de Cantanhede, Núcleo 04, Lote B, 3060-197 Cantanhede, Portugal.
- Institute for Interdisciplinary Research, University of Coimbra, 3004-531 Coimbra, Portugal.
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19
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Kiriakidi S, Kolocouris A, Liapakis G, Ikram S, Durdagi S, Mavromoustakos T. Effects of Cholesterol on GPCR Function: Insights from Computational and Experimental Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1135:89-103. [DOI: 10.1007/978-3-030-14265-0_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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20
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Montgomery D, Campbell A, Sullivan HJ, Wu C. Molecular dynamics simulation of biased agonists at the dopamine D2 receptor suggests the mechanism of receptor functional selectivity. J Biomol Struct Dyn 2018; 37:3206-3225. [PMID: 30124143 DOI: 10.1080/07391102.2018.1513378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The dopamine D2 receptor (D2R) is the primary target for antipsychotic drugs. Besides schizophrenia, this receptor is linked to dementia, Parkinson's disease, and depression. Recent studies have shown that β-arrestin biased agonists at this receptor treat schizophrenia with less side effects. Although the high resolution structure of this receptor exists, the mechanism of biased agonism at the receptor is unknown. In this study, dopamine, the endogenous unbiased G-protein agonist, MLS1547, a G-protein biased agonist, and UNC9975, a G-protein antagonist and a β-arrestin biased agonist, were docked to a homology model of the whole D2R including all flexible loops, and molecular dynamics simulations were conducted to study the potential mechanisms of biased agonism. Our thorough analysis on the protein-ligand interaction, secondary structure, tertiary structure, structure dynamics, and molecular switches of all three systems indicates that ligand binding to transmembrane 3 might be essential for G-protein recruitment, while ligand binding to transmembrane 6 might be essential for β-arrestin recruitment. Our analysis also suggests changes in both the secondary and the tertiary structures of TM5 and TM7, molecular switches and ICL3 flexibility are important in biased signaling. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- David Montgomery
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
| | - Alexandra Campbell
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
| | - Holli-Joi Sullivan
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
| | - Chun Wu
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
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21
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de Witte WEA, Versfelt JW, Kuzikov M, Rolland S, Georgi V, Gribbon P, Gul S, Huntjens D, van der Graaf PH, Danhof M, Fernández-Montalván A, Witt G, de Lange ECM. In vitro and in silico analysis of the effects of D 2 receptor antagonist target binding kinetics on the cellular response to fluctuating dopamine concentrations. Br J Pharmacol 2018; 175:4121-4136. [PMID: 30051456 PMCID: PMC6177617 DOI: 10.1111/bph.14456] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 06/17/2018] [Accepted: 06/25/2018] [Indexed: 12/27/2022] Open
Abstract
Background and Purpose Target binding kinetics influence the time course of the drug effect (pharmacodynamics) both (i) directly, by affecting the time course of target occupancy, driven by the pharmacokinetics of the drug, competition with endogenous ligands and target turnover, and (ii) indirectly, by affecting signal transduction and homeostatic feedback. For dopamine D2 receptor antagonists, it has been hypothesized that fast receptor binding kinetics cause fewer side effects, because part of the dynamics of the dopaminergic system is preserved by displacement of these antagonists. Experimental Approach Target binding kinetics of D2 receptor antagonists and signal transduction after dopamine and D2 receptor antagonist exposure were measured in vitro. These data were integrated by mechanistic modelling, taking into account competitive binding of endogenous dopamine and the antagonist, the turnover of the second messenger cAMP and negative feedback by PDE turnover. Key Results The proposed signal transduction model successfully described the cellular cAMP response for 17 D2 receptor antagonists with widely different binding kinetics. Simulation of the response to fluctuating dopamine concentrations revealed that a significant effect of the target binding kinetics on the dynamics of the signalling only occurs at endogenous dopamine concentration fluctuations with frequencies below 1 min−1. Conclusions and Implications Signal transduction and feedback are important determinants of the time course of drug effects. The effect of the D2 receptor antagonist dissociation rate constant (koff) is limited to the maximal rate of fluctuations in dopamine signalling as determined by the dopamine koff and the cAMP turnover.
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Affiliation(s)
- Wilhelmus E A de Witte
- Department of Pharmacology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Joost W Versfelt
- Department of Pharmacology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Maria Kuzikov
- ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology, Hamburg, Germany
| | - Solene Rolland
- Global Drug Discovery, Bayer Healthcare Pharmaceuticals, Berlin, Germany
| | - Victoria Georgi
- Global Drug Discovery, Bayer Healthcare Pharmaceuticals, Berlin, Germany
| | - Philip Gribbon
- ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology, Hamburg, Germany
| | - Sheraz Gul
- ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology, Hamburg, Germany
| | | | - Piet Hein van der Graaf
- Department of Pharmacology, Leiden Academic Centre for Drug Research, Leiden, Netherlands.,QSP, Certara, Canterbury, UK
| | - Meindert Danhof
- Department of Pharmacology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
| | - Amaury Fernández-Montalván
- Global Drug Discovery, Bayer Healthcare Pharmaceuticals, Berlin, Germany.,Servier Research Institute, Croissy-sur-Seine, France
| | - Gesa Witt
- ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology, Hamburg, Germany
| | - Elizabeth C M de Lange
- Department of Pharmacology, Leiden Academic Centre for Drug Research, Leiden, Netherlands
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22
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Salmas RE, Seeman P, Stein M, Durdagi S. Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2 HighR and D2 LowR States. J Chem Inf Model 2018. [PMID: 29537837 DOI: 10.1021/acs.jcim.7b00722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The active (D2HighR) and inactive (D2LowR) states of dimeric dopamine D2 receptor (D2R) models were investigated to clarify the binding mechanisms of the dopamine agonist bromocriptine, using Molecular Dynamics (MD) simulation. The aim of this comprehensive study was to investigate the critical effects of bromocriptine binding on each distinct receptor conformation. The different binding modes of the bromocriptine ligand in the active and inactive states have a significant effect on the conformational changes of the receptor. Based on the MM/GBSA approach, the calculated binding enthalpies of bromocriptine demonstrated selectivity toward the D2HighR active state. There is good agreement between the calculated and experimentally measured D2HighR selectivity. In the ligand-binding site, the key amino acids identified for D2HighR were Asp114(3.32) and Glu95(2.65), and for D2LowR, it was Ser193(5.42). Moreover, analysis of replicate MD trajectories demonstrated that the bromocriptine structure was more rigid at the D2HighR state and more flexible at the D2LowR state. However, the side chains of the ligand-receptor complex of D2HighR showed larger variations relative to the corresponding regions of D2LowR. The present study is part of an ongoing research program to study D2R conformational changes during ligand activation and to evaluate the conformational state selectivity for ligand binding.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey
| | - Philip Seeman
- Departments of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605 , M5P 3L6 Toronto , Ontario , Canada
| | - Matthias Stein
- Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1 , 39106 Magdeburg , Germany
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey.,Neuroscience Program, Graduate School of Health Sciences , Bahcesehir University , Istanbul 34349 , Turkey
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23
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Durdagi S, Erol I, Salmas RE, Aksoydan B, Kantarcioglu I. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors. Neurosci Lett 2018; 700:30-37. [PMID: 29684528 DOI: 10.1016/j.neulet.2018.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022]
Abstract
G Protein-Coupled Receptors (GPCRs) can form homo- and heterodimers or constitute higher oligomeric clusters with other heptahelical GPCRs. In this article, multiscale molecular modeling approaches as well as experimental techniques which are used to study oligomerization of GPCRs are reviewed. In particular, the effect of dimerization/oligomerization to the ligand binding affinity of individual protomers and also on the efficacy of the oligomer are discussed by including diverse examples from the literature. In addition, possible allosteric effects that may emerge upon interaction of GPCRs with membrane components, like cholesterol, is also discussed. Investigation of these above-mentioned interactions may greatly contribute to the candidate molecule screening studies and development of novel therapeutics with fewer adverse effects.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
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24
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Aksoydan B, Kantarcioglu I, Erol I, Salmas RE, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. J Mol Graph Model 2017; 79:103-117. [PMID: 29156380 DOI: 10.1016/j.jmgm.2017.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Angiotensin II receptor type 1 (AT1) antagonists are the most recent drug class against hypertension. Recently first crystal structure of AT1 receptor is deposited to the protein data bank (PDB ID: 4YAY). In this work, several molecular screening methods such as molecular docking and de novo design studies were performed and it is found that oxazolone and imidazolone derivatives reveal similar/better interaction energy profiles compared to the FDA approved sartan molecules at the binding site of the AT1 receptor. A database consisting of 3500-fragments were used to enumerate de novo designed imidazolone and oxazolone derivatives and hereby more than 50000 novel small molecules were generated. These derivatives were then used in high throughput virtual screening simulations (Glide/HTVS) to find potent hit molecules. In addition, virtual screening of around 18 million small drug-like compounds from ZINC database were screened at the binding pocket of the AT1 receptor via Glide/HTVS method. Filtered structures were then used in more sophisticated molecular docking simulations protocols (i.e., Glide/SP; Glide/XP; Glide/IFD; Glide/QPLD, and GOLD). However, the K+ ion channel/drug interactions should also be considered in studies implemented in molecular level against their cardiovascular risks. Thus, selected compounds with high docking scores via all diverse docking algorithms are also screened at the pore domain regions of human ether-a-go-go-related gene (hERG1) K+ channel to remove the high affinity hERG1 blocking compounds. High docking scored compounds at the AT1 with low hERG1 affinity is considered for long molecular dynamics (MD) simulations. Post-processing analysis of MD simulations assisted for better understanding of molecular mechanism of studied compounds at the binding cavity of AT1 receptor. Results of this study can be useful for designing of novel and safe AT1 inhibitors.
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Affiliation(s)
- Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.
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Akıncıoğlu A, Kocaman E, Akıncıoğlu H, Salmas RE, Durdagi S, Gülçin İ, Supuran CT, Göksu S. The synthesis of novel sulfamides derived from β-benzylphenethylamines as acetylcholinesterase, butyrylcholinesterase and carbonic anhydrase enzymes inhibitors. Bioorg Chem 2017; 74:238-250. [DOI: 10.1016/j.bioorg.2017.08.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 10/19/2022]
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26
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Publisher's note. J Mol Graph Model 2017; 77:240-249. [DOI: 10.1016/j.jmgm.2017.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/17/2022]
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Ekhteiari Salmas R, Serhat Is Y, Durdagi S, Stein M, Yurtsever M. A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R). J Biomol Struct Dyn 2017; 36:2668-2677. [DOI: 10.1080/07391102.2017.1365772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Yusuf Serhat Is
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
- Vocational School Department of Chemistry Technology, Istanbul Gedik University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Molecular Simulations and Design Group, Max-Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
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Salmas RE, Seeman P, Aksoydan B, Erol I, Kantarcioglu I, Stein M, Yurtsever M, Durdagi S. Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chem Neurosci 2017; 8:1404-1415. [PMID: 28272861 DOI: 10.1021/acschemneuro.7b00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2HighR and D2LowR dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2HighR and D2LowR targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2HighR and D2LowR with binding affinities (Ki) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [3H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2HighR. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2HighR binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2LowR. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, Toronto, Ontario M5P 3L6, Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Department
of Chemistry, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Isik Kantarcioglu
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Matthias Stein
- Max-Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
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Ekhteiari Salmas R, Seeman P, Aksoydan B, Stein M, Yurtsever M, Durdagi S. Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor. ACS Chem Neurosci 2017; 8:826-836. [PMID: 28001043 DOI: 10.1021/acschemneuro.6b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The dopamine D2 receptor (D2R) plays an important part in the human central nervous system and it is considered to be a focal target of antipsychotic agents. It is structurally modeled in active and inactive states, in which homodimerization reaction of the D2R monomers is also applied. The ASP2314 (also known as ACR16) ligand, a D2R stabilizer, is used in tests to evaluate how dimerization and conformational changes may alter the ligand binding space and to provide information on alterations in inhibitory mechanisms upon activation. The administration of the D2R agonist ligand ACR16 [3H](+)-4-propyl-3,4,4a,5,6,10b-hexahydro-2H-naphtho[1,2-b][1,4]oxazin-9-ol ((+)PHNO) revealed Ki values of 32 nM for the D2highR and 52 μM for the D2lowR. The calculated binding affinities of ACR16 with post processing molecular dynamics (MD) simulations analyses using MM/PBSA for the monomeric and homodimeric forms of the D2highR were -9.46 and -8.39 kcal/mol, respectively. The data suggests that the dimerization of the D2R leads negative cooperativity for ACR16 binding. The dimerization reaction of the D2highR is energetically favorable by -22.95 kcal/mol. The dimerization reaction structurally and thermodynamically stabilizes the D2highR conformation, which may be due to the intermolecular forces formed between the TM4 of each monomer, and the result strongly demonstrates dimerization essential for activation of the D2R.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, M5P 3L6 Toronto, Ontario Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Max-Planck
Institute
for Dynamics of Complex Technical Systems, Molecular Simulations and
Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34467 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
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Ekhteiari Salmas R, Durdagi S, Gulhan MF, Duruyurek M, Abdullah HI, Selamoglu Z. The effects of pollen, propolis, and caffeic acid phenethyl ester on tyrosine hydroxylase activity and total RNA levels in hypertensive rats caused by nitric oxide synthase inhibition: experimental, docking and molecular dynamic studies. J Biomol Struct Dyn 2017; 36:609-620. [DOI: 10.1080/07391102.2017.1288660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Mehmet Fuat Gulhan
- Department of Medicinal and Aromatic Plants, Vocational School of Technical Sciences, Aksaray, Turkey
| | - Merve Duruyurek
- Faculty of Arts and Science, Department of Biotechnology, Omer Halisdemir University, Nigde 51240, Turkey
| | - Huda I. Abdullah
- Department of Pharmacology, New York Medical College, Valhalla 10595, NY, USA
| | - Zeliha Selamoglu
- Faculty of Arts and Science, Department of Biotechnology, Omer Halisdemir University, Nigde 51240, Turkey
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Synthesis, anticholinesterase activity and molecular modeling study of novel carbamate-substituted thymol/carvacrol derivatives. Bioorg Med Chem 2017; 25:1352-1363. [DOI: 10.1016/j.bmc.2016.12.037] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022]
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Kaczor AA, Jörg M, Capuano B. The dopamine D2 receptor dimer and its interaction with homobivalent antagonists: homology modeling, docking and molecular dynamics. J Mol Model 2016; 22:203. [PMID: 27491852 PMCID: PMC5023759 DOI: 10.1007/s00894-016-3065-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/03/2016] [Indexed: 01/11/2023]
Abstract
In order to apply structure-based drug design techniques to G protein-coupled receptor complexes, it is essential to model their 3D structure and to identify regions that are suitable for selective drug binding. For this purpose, we have developed and tested a multi-component protocol to model the inactive conformation of the dopamine D2 receptor dimer, suitable for interaction with homobivalent antagonists. Our approach was based on protein-protein docking, applying the Rosetta software to obtain populations of dimers as present in membranes with all the main possible interfaces. Consensus scoring based on the values and frequencies of best interfaces regarding four scoring parameters, Rosetta interface score, interface area, free energy of binding and energy of hydrogen bond interactions indicated that the best scored dimer model possesses a TM4-TM5-TM7-TM1 interface, which is in agreement with experimental data. This model was used to study interactions of the previously published dopamine D2 receptor homobivalent antagonists based on clozapine,1,4-disubstituted aromatic piperidines/piperazines and arylamidoalkyl substituted phenylpiperazine pharmacophores. It was found that the homobivalent antagonists stabilize the receptor-inactive conformation by maintaining the ionic lock interaction, and change the dimer interface by disrupting a set of hydrogen bonds and maintaining water- and ligand-mediated hydrogen bonds in the extracellular and intracellular part of the interface. Graphical Abstract Structure of the final model of the dopamine D2 receptor homodimer, indicating the distancebetween Tyr37 and Tyr 5.42 in the apo form (left) and in the complex with the ligand (right).
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy with Division for Medical Analytics, Medical University of Lublin, 4A Chodźki St., 20059, Lublin, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, PO Box 1627, 70211, Kuopio, Finland.
| | - Manuela Jörg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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Salmas RE, Stein M, Yurtsever M, Seeman P, Erol I, Mestanoglu M, Durdagi S. The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands. J Biomol Struct Dyn 2016; 35:2040-2048. [PMID: 27367058 DOI: 10.1080/07391102.2016.1206487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G-protein-coupled receptors (GPCRs) are targets of more than 30% of marketed drugs. Investigation on the GPCRs may shed light on upcoming drug design studies. In the present study, we performed a combination of receptor- and ligand-based analysis targeting the dopamine D2 receptor (D2R). The signaling pathway of D2R activation and the construction of universal pharmacophore models for D2R ligands were also studied. The key amino acids, which contributed to the regular activation of the D2R, were in detail investigated by means of normal mode analysis (NMA). A derived cross-correlation matrix provided us an understanding of the degree of pair residue correlations. Although negative correlations were not observed in the case of the inactive D2R state, a high degree of correlation appeared between the residues in the active state. NMA results showed that the cytoplasmic side of the TM5 plays a significant role in promoting of residue-residue correlations in the active state of D2R. Tracing motions of the amino acids Arg219, Arg220, Val223, Asn224, Lys226, and Ser228 in the position of the TM5 are found to be critical in signal transduction. Complementing the receptor-based modeling, ligand-based modeling was also performed using known D2R ligands. The top-scored pharmacophore models were found as 5-sited (AADPR.671, AADRR.1398, AAPRR.3900, and ADHRR.2864) hypotheses from PHASE modeling from a pool consisting of more than 100 initial candidates. The constructed models using 38 D2R ligands (in the training set) were validated with 15 additional test set compounds. The resulting model correctly predicted the pIC50 values of an additional test set compounds as true unknowns.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Matthias Stein
- b Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical System , Sandtorstrasse 1, 39106 Magdeburg , Germany
| | - Mine Yurtsever
- c Department of Chemistry , Istanbul Technical University , Istanbul , Turkey
| | - Philip Seeman
- d Department of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605, M5P 3L6 Toronto , Ontario , Canada
| | - Ismail Erol
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.,e Department of Chemistry , Gebze Technical University , Gebze , Turkey
| | - Mert Mestanoglu
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Serdar Durdagi
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
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Ekhteiari Salmas R, Unlu A, Bektaş M, Yurtsever M, Mestanoglu M, Durdagi S. Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies. J Biomol Struct Dyn 2016; 35:1899-1915. [DOI: 10.1080/07391102.2016.1199328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Ayhan Unlu
- Faculty of Medicine, Department of Biophysics, Trakya University, Edirne, Turkey
| | - Muhammet Bektaş
- Istanbul Faculty of Medicine, Department of Biophysics, Istanbul University, Istanbul, Turkey
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Caravaggio F, Kegeles LS, Wilson AA, Remington G, Borlido C, Mamo DC, Graff-Guerrero A. Estimating the effect of endogenous dopamine on baseline [(11) C]-(+)-PHNO binding in the human brain. Synapse 2016; 70:453-60. [PMID: 27341789 DOI: 10.1002/syn.21920] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/03/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022]
Abstract
Endogenous dopamine (DA) levels at dopamine D2/3 receptors (D2/3 R) have been quantified in the living human brain using the agonist radiotracer [(11) C]-(+)-PHNO. As an agonist radiotracer, [(11) C]-(+)-PHNO is more sensitive to endogenous DA levels than antagonist radiotracers. We sought to determine the proportion of the variance in baseline [(11) C]-(+)-PHNO binding to D2/3 Rs which can be accounted for by variation in endogenous DA levels. This was done by computing the Pearson's coefficient for the correlation between baseline binding potential (BPND ) and the change in BPND after acute DA depletion, using previously published data. All correlations were inverse, and the proportion of the variance in baseline [(11) C]-(+)-PHNO BPND that can be accounted for by variation in endogenous DA levels across the striatal subregions ranged from 42-59%. These results indicate that lower baseline values of [(11) C]-(+)-PHNO BPND reflect greater stimulation by endogenous DA. To further validate this interpretation, we sought to examine whether these data could be used to estimate the dissociation constant (Kd) of DA at D2/3 R. In line with previous in vitro work, we estimated the in vivo Kd of DA to be around 20 nM. In summary, the agonist radiotracer [(11) C]-(+)-PHNO can detect the impact of endogenous DA levels at D2/3 R in the living human brain from a single baseline scan, and may be more sensitive to this impact than other commonly employed radiotracers.
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Affiliation(s)
- Fernando Caravaggio
- Centre for Addiction and Mental Health, Research Imaging Centre, Toronto, Ontario, M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Lawrence S Kegeles
- Department of Psychiatry and Radiology, Columbia University College of Physicians and Surgeons, New York State Psychiatric Institute, New York
| | - Alan A Wilson
- Centre for Addiction and Mental Health, Research Imaging Centre, Toronto, Ontario, M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Psychiatry, University of Toronto, Ontario, M5T 1R8, Canada
| | - Gary Remington
- Centre for Addiction and Mental Health, Research Imaging Centre, Toronto, Ontario, M5T 1R8, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Psychiatry, University of Toronto, Ontario, M5T 1R8, Canada
| | - Carol Borlido
- Centre for Addiction and Mental Health, Research Imaging Centre, Toronto, Ontario, M5T 1R8, Canada
| | - David C Mamo
- Department of Psychiatry, Faculties of Medicine and Health Science, University of Malta, Msida, Malta
| | - Ariel Graff-Guerrero
- Centre for Addiction and Mental Health, Research Imaging Centre, Toronto, Ontario, M5T 1R8, Canada. .,Institute of Medical Science, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. .,Department of Psychiatry, University of Toronto, Ontario, M5T 1R8, Canada.
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