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Stampelou M, Ladds G, Kolocouris A. Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A 3 Receptor. J Phys Chem B 2024; 128:914-936. [PMID: 38236582 DOI: 10.1021/acs.jpcb.3c05986] [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: 01/19/2024]
Abstract
A structure-based drug design pipeline that considers both thermodynamic and kinetic binding data of ligands against a receptor will enable the computational design of improved drug molecules. For unresolved GPCR-ligand complexes, a workflow that can apply both thermodynamic and kinetic binding data in combination with alpha-fold (AF)-derived or other homology models and experimentally resolved binding modes of relevant ligands in GPCR-homologs needs to be tested. Here, as test case, we studied a congeneric set of ligands that bind to a structurally unresolved G protein-coupled receptor (GPCR), the inactive human adenosine A3 receptor (hA3R). We tested three available homology models from which two have been generated from experimental structures of hA1R or hA2AR and one model was a multistate alphafold 2 (AF2)-derived model. We applied alchemical calculations with thermodynamic integration coupled with molecular dynamics (TI/MD) simulations to calculate the experimental relative binding free energies and residence time (τ)-random accelerated MD (τ-RAMD) simulations to calculate the relative residence times (RTs) for antagonists. While the TI/MD calculations produced, for the three homology models, good Pearson correlation coefficients, correspondingly, r = 0.74, 0.62, and 0.67 and mean unsigned error (mue) values of 0.94, 1.31, and 0.81 kcal mol-1, the τ-RAMD method showed r = 0.92 and 0.52 for the first two models but failed to produce accurate results for the multistate AF2-derived model. With subsequent optimization of the AF2-derived model by reorientation of the side chain of R1735.34 located in the extracellular loop 2 (EL2) that blocked ligand's unbinding, the computational model showed r = 0.84 for kinetic data and improved performance for thermodynamic data (r = 0.81, mue = 0.56 kcal mol-1). Overall, after refining the multistate AF2 model with physics-based tools, we were able to show a strong correlation between predicted and experimental ligand relative residence times and affinities, achieving a level of accuracy comparable to an experimental structure. The computational workflow used can be applied to other receptors, helping to rank candidate drugs in a congeneric series and enabling the prioritization of leads with stronger binding affinities and longer residence times.
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Affiliation(s)
- Margarita Stampelou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
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2
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Oliva P, Suresh RR, Pasquini S, Salmaso V, Will EJ, Tosh DK, Gao ZG, Liu N, Gavrilova O, Vincenzi F, Varani K, Jacobson KA. 2-Amino-5-arylethynyl-thiophen-3-yl-(phenyl)methanones as A 1 Adenosine Receptor Positive Allosteric Modulators. ACS Med Chem Lett 2023; 14:1640-1646. [PMID: 38116442 PMCID: PMC10726435 DOI: 10.1021/acsmedchemlett.3c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/06/2023] [Indexed: 12/21/2023] Open
Abstract
A1 adenosine receptor (A1AR) agonists have cerebroprotective, cardioprotective, antinociceptive, and other pharmaceutical applications. We explored the structure-activity relationship of 5-arylethynyl aminothiophenes as A1AR positive allosteric modulators (PAMs). The derivatives were compared in binding and functional assays at the human A1AR, indicating that some fluoro-substituted analogues have enhanced PAM activity. We identified substitution of the terminal phenyl ring in 12 (2-F-Ph), 15 (3,4-F2-Ph, MRS7935), and 21 (2-CF3-Ph) as particularly enhancing the PAM activity. 15 was also shown to act as an A1 ago-PAM with EC50 ≈ 2 μM, without activity (30 μM) at other ARs. Molecular modeling indicated that both the 5-arylethynyl and the 4-neopentyl groups are located in a region outside the receptor transmembrane helix bundle that is in contact with the phospholipid bilayer, consistent with the preference for nonpolar substitution of the aryl moiety. Although they are hydrophobic, these PAMs could provide potential drug candidate molecules for engaging protective A1ARs.
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Affiliation(s)
- Paola Oliva
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - R. Rama Suresh
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Silvia Pasquini
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Fossato di Mortara 17-19, 44121 Ferrara, Italy
| | - Veronica Salmaso
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Edward J. Will
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Dilip K. Tosh
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Naili Liu
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Oksana Gavrilova
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Fabrizio Vincenzi
- Department
of Translational Medicine, University of
Ferrara, Via Fossato
di Mortara 17-19, 44121 Ferrara, Italy
| | - Katia Varani
- Department
of Translational Medicine, University of
Ferrara, Via Fossato
di Mortara 17-19, 44121 Ferrara, Italy
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry and Mouse Metabolism Core, National
Institute of Diabetes and Digestive and Kidney
Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
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3
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Nguyen ATN, Tran QL, Baltos JA, McNeill SM, Nguyen DTN, May LT. Small molecule allosteric modulation of the adenosine A 1 receptor. Front Endocrinol (Lausanne) 2023; 14:1184360. [PMID: 37435481 PMCID: PMC10331460 DOI: 10.3389/fendo.2023.1184360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the target for approximately a third of FDA-approved small molecule drugs. The adenosine A1 receptor (A1R), one of four adenosine GPCR subtypes, has important (patho)physiological roles in humans. A1R has well-established roles in the regulation of the cardiovascular and nervous systems, where it has been identified as a potential therapeutic target for a number of conditions, including cardiac ischemia-reperfusion injury, cognition, epilepsy, and neuropathic pain. A1R small molecule drugs, typically orthosteric ligands, have undergone clinical trials. To date, none have progressed into the clinic, predominantly due to dose-limiting unwanted effects. The development of A1R allosteric modulators that target a topographically distinct binding site represent a promising approach to overcome current limitations. Pharmacological parameters of allosteric ligands, including affinity, efficacy and cooperativity, can be optimized to regulate A1R activity with high subtype, spatial and temporal selectivity. This review aims to offer insights into the A1R as a potential therapeutic target and highlight recent advances in the structural understanding of A1R allosteric modulation.
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Affiliation(s)
- Anh T. N. Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Quan L. Tran
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Samantha M. McNeill
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Diep T. N. Nguyen
- Department of Information Technology, Faculty of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Lauren T. May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Pasquini S, Contri C, Cappello M, Borea PA, Varani K, Vincenzi F. Update on the recent development of allosteric modulators for adenosine receptors and their therapeutic applications. Front Pharmacol 2022; 13:1030895. [PMID: 36278183 PMCID: PMC9581118 DOI: 10.3389/fphar.2022.1030895] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Adenosine receptors (ARs) have been identified as promising therapeutic targets for countless pathological conditions, spanning from inflammatory diseases to central nervous system disorders, from cancer to metabolic diseases, from cardiovascular pathologies to respiratory diseases, and beyond. This extraordinary therapeutic potential is mainly due to the plurality of pathophysiological actions of adenosine and the ubiquitous expression of its receptors. This is, however, a double-edged sword that makes the clinical development of effective ligands with tolerable side effects difficult. Evidence of this is the low number of AR agonists or antagonists that have reached the market. An alternative approach is to target allosteric sites via allosteric modulators, compounds endowed with several advantages over orthosteric ligands. In addition to the typical advantages of allosteric modulators, those acting on ARs could benefit from the fact that adenosine levels are elevated in pathological tissues, thus potentially having negligible effects on normal tissues where adenosine levels are maintained low. Several A1 and various A3AR allosteric modulators have been identified so far, and some of them have been validated in different preclinical settings, achieving promising results. Less fruitful, instead, has been the discovery of A2A and A2BAR allosteric modulators, although the results obtained up to now are encouraging. Collectively, data in the literature suggests that allosteric modulators of ARs could represent valuable pharmacological tools, potentially able to overcome the limitations of orthosteric ligands.
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Affiliation(s)
- Silvia Pasquini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Contri
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Martina Cappello
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | | | - Katia Varani
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- *Correspondence: Katia Varani,
| | - Fabrizio Vincenzi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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6
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Adenosine Receptors in Neuropsychiatric Disorders: Fine Regulators of Neurotransmission and Potential Therapeutic Targets. Int J Mol Sci 2022; 23:ijms23031219. [PMID: 35163142 PMCID: PMC8835915 DOI: 10.3390/ijms23031219] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/16/2022] Open
Abstract
Adenosine exerts an important role in the modulation of central nervous system (CNS) activity. Through the interaction with four G-protein coupled receptor (GPCR) subtypes, adenosine subtly regulates neurotransmission, interfering with the dopaminergic, glutamatergic, noradrenergic, serotoninergic, and endocannabinoid systems. The inhibitory and facilitating actions of adenosine on neurotransmission are mainly mediated by A1 and A2A adenosine receptors (ARs), respectively. Given their role in the CNS, ARs are promising therapeutic targets for neuropsychiatric disorders where altered neurotransmission represents the most likely etiological hypothesis. Activating or blocking ARs with specific pharmacological agents could therefore restore the balance of altered neurotransmitter systems, providing the rationale for the potential treatment of these highly debilitating conditions. In this review, we summarize and discuss the most relevant studies concerning AR modulation in psychotic and mood disorders such as schizophrenia, bipolar disorders, depression, and anxiety, as well as neurodevelopment disorders such as autism spectrum disorder (ASD), fragile X syndrome (FXS), attention-deficit hyperactivity disorder (ADHD), and neuropsychiatric aspects of neurodegenerative disorders.
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Lutsenko RV. ON THE QUESTION OF ADENOSINE SYSTEM PARTICIPATION IN THE PATHOGENESIS OF NEUROSES. BULLETIN OF PROBLEMS BIOLOGY AND MEDICINE 2022. [DOI: 10.29254/2077-4214-2022-4-167-76-83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Deganutti G, Barkan K, Ladds G, Reynolds CA. Multisite Model of Allosterism for the Adenosine A1 Receptor. J Chem Inf Model 2021; 61:2001-2015. [PMID: 33779168 DOI: 10.1021/acs.jcim.0c01331] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite being a target for about one-third of approved drugs, G protein-coupled receptors (GPCRs) still represent a tremendous reservoir for therapeutic strategies against diseases. For example, several cardiovascular and central nervous system conditions could benefit from clinical agents that activate the adenosine 1 receptor (A1R); however, the pursuit of A1R agonists for clinical use is usually impeded by both on- and off-target side effects. One of the possible strategies to overcome this issue is the development of positive allosteric modulators (PAMs) capable of selectively enhancing the effect of a specific receptor subtype and triggering functional selectivity (a phenomenon also referred to as bias). Intriguingly, besides enforcing the effect of agonists upon binding to an allosteric site, most of the A1R PAMs display intrinsic partial agonism and orthosteric competition with antagonists. To rationalize this behavior, we simulated the binding of the prototypical PAMs PD81723 and VCP171, the full-agonist NECA, the antagonist 13B, and the bitopic agonist VCP746. We propose that a single PAM can bind several A1R sites rather than a unique allosteric pocket, reconciling the structure-activity relationship and the mutagenesis results.
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Affiliation(s)
- Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Alison Gingell Building, Coventry CV1 5FB, U.K
| | - Kerry Barkan
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Christopher A Reynolds
- Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Alison Gingell Building, Coventry CV1 5FB, U.K
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The Detrimental Action of Adenosine on Glutamate-Induced Cytotoxicity in PC12 Cells Can Be Shifted towards a Neuroprotective Role through A 1AR Positive Allosteric Modulation. Cells 2020; 9:cells9051242. [PMID: 32443448 PMCID: PMC7290574 DOI: 10.3390/cells9051242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/22/2022] Open
Abstract
Glutamate cytotoxicity is implicated in neuronal death in different neurological disorders including stroke, traumatic brain injury, and neurodegenerative diseases. Adenosine is a nucleoside that plays an important role in modulating neuronal activity and its receptors have been identified as promising therapeutic targets for glutamate cytotoxicity. The purpose of this study is to elucidate the role of adenosine and its receptors on glutamate-induced injury in PC12 cells and to verify the protective effect of the novel A1 adenosine receptor positive allosteric modulator, TRR469. Flow cytometry experiments to detect apoptosis revealed that adenosine has a dual role in glutamate cytotoxicity, with A2A and A2B adenosine receptor (AR) activation exacerbating and A1 AR activation improving glutamate-induced cell injury. The overall effect of endogenous adenosine in PC12 cells resulted in a facilitating action on glutamate cytotoxicity, as demonstrated by the use of adenosine deaminase and selective antagonists. However, enhancing the action of endogenous adenosine on A1ARs by TRR469 completely abrogated glutamate-mediated cell death, caspase 3/7 activation, ROS production, and mitochondrial membrane potential loss. Our results indicate a novel potential therapeutic strategy against glutamate cytotoxicity based on the positive allosteric modulation of A1ARs.
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Bhattarai A, Wang J, Miao Y. Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor. Biochim Biophys Acta Gen Subj 2020; 1864:129615. [PMID: 32298791 DOI: 10.1016/j.bbagen.2020.129615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/26/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Ensemble docking has proven useful in drug discovery and development. It increases the hit rate by incorporating receptor flexibility into molecular docking as demonstrated on important drug targets including G-protein-coupled receptors (GPCRs). Adenosine A1 receptor (A1AR) is a key GPCR that has been targeted for treating cardiac ischemia-reperfusion injuries, neuropathic pain and renal diseases. Development of allosteric modulators, compounds binding to distinct and less conserved GPCR target sites compared with agonists and antagonists, has attracted increasing interest for designing selective drugs of the A1AR. Despite significant advances, more effective approaches are needed to discover potent and selective allosteric modulators of the A1AR. METHODS Ensemble docking that integrates Gaussian accelerated molecular dynamic (GaMD) simulations and molecular docking using Autodock has been implemented for retrospective docking of known positive allosteric modulators (PAMs) in the A1AR. RESULTS Ensemble docking outperforms docking of the receptor cryo-EM structure. The calculated docking enrichment factors (EFs) and the area under the receiver operating characteristic curves (AUC) are significantly increased. CONCLUSIONS Receptor ensembles generated from GaMD simulations are able to increase the success rate of discovering PAMs of A1AR. It is important to account for receptor flexibility through GaMD simulations and flexible docking. GENERAL SIGNIFICANCE Ensemble docking is a promising approach for drug discovery targeting flexible receptors.
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Affiliation(s)
- Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA.
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Martire A, Lambertucci C, Pepponi R, Ferrante A, Benati N, Buccioni M, Dal Ben D, Marucci G, Klotz KN, Volpini R, Popoli P. Neuroprotective potential of adenosine A 1 receptor partial agonists in experimental models of cerebral ischemia. J Neurochem 2019; 149:211-230. [PMID: 30614535 DOI: 10.1111/jnc.14660] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 01/16/2023]
Abstract
Cerebral ischemia is the second most common cause of death and a major cause of disability worldwide. Available therapies are based only on anticoagulants or recombinant tissue plasminogen activator. Extracellular adenosine increases during ischemia and acts as a neuroprotective endogenous agent mainly by activating adenosine A1 receptors (A1 Rs) which control calcium influx, glutamate release, membrane potential, and metabolism. Accordingly, in many experimental paradigms it has been already demonstrated that the stimulation of A1 R with full agonists is able to reduce ischemia-related structural and functional brain damage; unfortunately, cardiovascular side effects and desensitization of A1 R induced by these compounds have strongly limited their exploitation in stroke therapy so far. Among the newly emerging compounds, A1 R partial agonists could be almost free of side effects and equally effective. Therefore, we decided to evaluate the neuroprotective potential of two A1 R partial agonists, namely 2'-dCCPA and 3'-dCCPA, in in vitro and ex vivo experimental models of cerebral ischemia. Within the experimental paradigm of oxygen-glucose deprivation in vitro in human neuroblastoma (SH-SY5Y) cells both A1 R partial agonists increased cell viability. Considering the high level of expression of A1 Rs in the hippocampus and the susceptibility of CA1 region to hypoxia, we performed electrophysiological experiments in this subfield. The application of 7 min of oxygen-glucose deprivation constantly produces an irreversible synaptic failure in all the C57Bl/6 mice hippocampal slices evaluated; both tested compounds allowed a significant recovery of synaptic transmission. These findings demonstrate that A1 R and its partial agonists are still of interest for cerebral ischemia therapy. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Alberto Martire
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Catia Lambertucci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Rita Pepponi
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Antonella Ferrante
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Nicholas Benati
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Michela Buccioni
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Diego Dal Ben
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Gabriella Marucci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxikologie, Universität Würzburg, Würzburg, Germany
| | - Rosaria Volpini
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Camerino, Italy
| | - Patrizia Popoli
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
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Wold EA, Chen J, Cunningham KA, Zhou J. Allosteric Modulation of Class A GPCRs: Targets, Agents, and Emerging Concepts. J Med Chem 2019; 62:88-127. [PMID: 30106578 PMCID: PMC6556150 DOI: 10.1021/acs.jmedchem.8b00875] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-protein-coupled receptors (GPCRs) have been tractable drug targets for decades with over one-third of currently marketed drugs targeting GPCRs. Of these, the class A GPCR superfamily is highly represented, and continued drug discovery for this family of receptors may provide novel therapeutics for a vast range of diseases. GPCR allosteric modulation is an innovative targeting approach that broadens the available small molecule toolbox and is proving to be a viable drug discovery strategy, as evidenced by recent FDA approvals and clinical trials. Numerous class A GPCR allosteric modulators have been discovered recently, and emerging trends such as the availability of GPCR crystal structures, diverse functional assays, and structure-based computational approaches are improving optimization and development. This Perspective provides an update on allosterically targeted class A GPCRs and their disease indications and the medicinal chemistry approaches toward novel allosteric modulators and highlights emerging trends and opportunities in the field.
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Affiliation(s)
- Eric A. Wold
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jianping Chen
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Kathryn A. Cunningham
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
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Miao Y, Bhattarai A, Nguyen ATN, Christopoulos A, May LT. Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A 1 Receptor. Sci Rep 2018; 8:16836. [PMID: 30442899 PMCID: PMC6237911 DOI: 10.1038/s41598-018-35266-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022] Open
Abstract
Despite intense interest in designing positive allosteric modulators (PAMs) as selective drugs of the adenosine A1 receptor (A1AR), structural binding modes of the receptor PAMs remain unknown. Using the first X-ray structure of the A1AR, we have performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) technique to determine binding modes of the A1AR allosteric drug leads. Two prototypical PAMs, PD81723 and VCP171, were selected. Each PAM was initially placed at least 20 Å away from the receptor. Extensive GaMD simulations using the AMBER and NAMD simulation packages at different acceleration levels captured spontaneous binding of PAMs to the A1AR. The simulations allowed us to identify low-energy binding modes of the PAMs at an allosteric site formed by the receptor extracellular loop 2 (ECL2), which are highly consistent with mutagenesis experimental data. Furthermore, the PAMs stabilized agonist binding in the receptor. In the absence of PAMs at the ECL2 allosteric site, the agonist sampled a significantly larger conformational space and even dissociated from the A1AR alone. In summary, the GaMD simulations elucidated structural binding modes of the PAMs and provided important insights into allostery in the A1AR, which will greatly facilitate the receptor structure-based drug design.
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Affiliation(s)
- Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA.
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Anh T N Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, 3052, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, 3052, Australia
| | - Lauren T May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, VIC, 3052, Australia
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2-Aminothiophene scaffolds: Diverse biological and pharmacological attributes in medicinal chemistry. Eur J Med Chem 2017; 140:465-493. [PMID: 28987607 DOI: 10.1016/j.ejmech.2017.09.039] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/19/2017] [Indexed: 12/30/2022]
Abstract
2-Aminothiophenes are important five-membered heterocyclic building blocks in organic synthesis, and the chemistry of these small molecules is still developing based on the discovery of cyclization by Gewald. Another attractive feature of 2-aminothiophene scaffolds is their ability to act as synthons for the synthesis of biological active thiophene-containing heterocycles, conjugates and hybrids. Currently, the biological actions of 2-aminothiophenes or their 2-N-substituted analogues are still being investigated because of their various mechanisms of action (e.g., pharmacophore and pharmacokinetic properties). Likewise, the 2-aminothiophene family is used as diverse promising selective inhibitors, receptors, and modulators in medicinal chemistry, and these compounds even exhibit effective pharmacological properties in the various clinical phases of appropriate diseases. In this review, major biological and pharmacological reports on 2-aminothiophenes and related compounds have been highlighted; most perspective drug-candidate hits were selected for discussion and described, along with additional synthetic pathways. In addition, we focused on the literature dedicated to 2-aminothiophenes and 2-N-substituted derivatives, which have been published from 2010 to 2017.
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Varani K, Vincenzi F, Merighi S, Gessi S, Borea PA. Biochemical and Pharmacological Role of A1 Adenosine Receptors and Their Modulation as Novel Therapeutic Strategy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1051:193-232. [DOI: 10.1007/5584_2017_61] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Schmidt J, Ferk P. Safety issues of compounds acting on adenosinergic signalling. ACTA ACUST UNITED AC 2017; 69:790-806. [PMID: 28397249 DOI: 10.1111/jphp.12720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/04/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Much research has been performed on the field of identifying the roles of adenosine and adenosinergic signalling, but a relatively low number of marketing authorizations have been granted for adenosine receptor (AdR) ligands. In part, this could be related to their safety issues; therefore, our aim was to examine the toxicological and adverse effects data of different compounds acting on adenosinergic signalling, including different AdR ligands and compounds resembling the structure of adenosine. We also wanted to present recent pharmaceutical developments of experimental compounds that showed promising results in clinical trial setting. KEY FINDINGS Safety issues of compounds modulating adenosinergic signalling were investigated, and different mechanisms were presented. Structurally different classes of compounds act on AdRs, the most important being adenosine, adenosine derivatives and other non-nucleoside compounds. Many of them are either not selective enough or are targeting other targets of adenosinergic signalling such as metabolizing enzymes that regulate adenosine levels. Many other targets are also involved that are not part of adenosinergic signalling system such as GABA receptors, different channels, enzymes and others. Some synthetic AdR ligands even showed to be genotoxic. SUMMARY Current review presents safety data of adenosine, adenosine derivatives and other non-nucleoside compounds that modulate adenosinergic signalling. We have presented different mechanisms that participate to an adverse effect or toxic outcome. A separate section also deals with possible organ-specific toxic effects on different in-vitro and in-vivo models.
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Affiliation(s)
- Jan Schmidt
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Polonca Ferk
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
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Fronik P, Gaiser BI, Sejer Pedersen D. Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry. J Med Chem 2017; 60:4126-4134. [DOI: 10.1021/acs.jmedchem.6b01601] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Philipp Fronik
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Birgit I. Gaiser
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
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Pigulski B, Męcik P, Cichos J, Szafert S. Use of Stable Amine-Capped Polyynes in the Regioselective Synthesis of Push–Pull Thiophenes. J Org Chem 2017; 82:1487-1498. [DOI: 10.1021/acs.joc.6b02685] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bartłomiej Pigulski
- Department of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Patrycja Męcik
- Department of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Jakub Cichos
- Department of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Sławomir Szafert
- Department of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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Vincenzi F, Ravani A, Pasquini S, Merighi S, Gessi S, Romagnoli R, Baraldi PG, Borea PA, Varani K. Positive allosteric modulation of A1 adenosine receptors as a novel and promising therapeutic strategy for anxiety. Neuropharmacology 2016; 111:283-292. [DOI: 10.1016/j.neuropharm.2016.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 11/16/2022]
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Guo D, Heitman LH, IJzerman AP. Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors. Chem Rev 2016; 117:38-66. [DOI: 10.1021/acs.chemrev.6b00025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Abstract
Adenosine is an ubiquitous nucleoside involved in various physiological and pathological functions by stimulating A1, A2A, A2B and A3 adenosine receptors (ARs). Allosteric enhancers to A1ARs may represent novel therapeutic agents because they increase the activity of these receptors by mediating a shift to their active form in the A1AR-G protein ternary complex. In this manner, they are able to amplify the action of endogenous adenosine, which is produced in high concentrations under conditions of metabolic stress. A1AR allosteric enhancers could be used as a justifiable alternative to the exogenous agonists that are characterized by receptor desensitization and downregulation. In this review, an analysis of some of the most interesting allosteric modulators of A1ARs has been reported.
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