1
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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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2
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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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The full activation mechanism of the adenosine A 1 receptor revealed by GaMD and Su-GaMD simulations. Proc Natl Acad Sci U S A 2022; 119:e2203702119. [PMID: 36215480 PMCID: PMC9586258 DOI: 10.1073/pnas.2203702119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The full activation process of G protein-coupled receptor (GPCR) plays an important role in cellular signal transduction. However, it remains challenging to simulate the whole process in which the GPCR is recognized and activated by a ligand and then couples to the G protein on a reasonable simulation timescale. Here, we developed a molecular dynamics (MD) approach named supervised (Su) Gaussian accelerated MD (GaMD) by incorporating a tabu-like supervision algorithm into a standard GaMD simulation. By using this Su-GaMD method, from the active and inactive structure of adenosine A1 receptor (A1R), we successfully revealed the full activation mechanism of A1R, including adenosine (Ado)-A1R recognition, preactivation of A1R, and A1R-G protein recognition, in hundreds of nanoseconds of simulations. The binding of Ado to the extracellular side of A1R initiates conformational changes and the preactivation of A1R. In turn, the binding of Gi2 to the intracellular side of A1R causes a decrease in the volume of the extracellular orthosteric site and stabilizes the binding of Ado to A1R. Su-GaMD could be a useful tool to reconstruct or even predict ligand-protein and protein-protein recognition pathways on a short timescale. The intermediate states revealed in this study could provide more detailed complementary structural characterizations to facilitate the drug design of A1R in the future.
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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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5
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Vincenzi F, Pasquini S, Battistello E, Merighi S, Gessi S, Borea PA, Varani K. A 1 Adenosine Receptor Partial Agonists and Allosteric Modulators: Advancing Toward the Clinic? Front Pharmacol 2020; 11:625134. [PMID: 33362567 PMCID: PMC7756085 DOI: 10.3389/fphar.2020.625134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
- Fabrizio Vincenzi
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Silvia Pasquini
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Enrica Battistello
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Stefania Merighi
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | - Stefania Gessi
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
| | | | - Katia Varani
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy
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Targeting Adenosine Receptors: A Potential Pharmacological Avenue for Acute and Chronic Pain. Int J Mol Sci 2020; 21:ijms21228710. [PMID: 33218074 PMCID: PMC7698931 DOI: 10.3390/ijms21228710] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Adenosine is a purine nucleoside, responsible for the regulation of multiple physiological and pathological cellular and tissue functions by activation of four G protein-coupled receptors (GPCR), namely A1, A2A, A2B, and A3 adenosine receptors (ARs). In recent years, extensive progress has been made to elucidate the role of adenosine in pain regulation. Most of the antinociceptive effects of adenosine are dependent upon A1AR activation located at peripheral, spinal, and supraspinal sites. The role of A2AAR and A2BAR is more controversial since their activation has both pro- and anti-nociceptive effects. A3AR agonists are emerging as promising candidates for neuropathic pain. Although their therapeutic potential has been demonstrated in diverse preclinical studies, no AR ligands have so far reached the market. To date, novel pharmacological approaches such as adenosine regulating agents and allosteric modulators have been proposed to improve efficacy and limit side effects enhancing the effect of endogenous adenosine. This review aims to provide an overview of the therapeutic potential of ligands interacting with ARs and the adenosinergic system for the treatment of acute and chronic pain.
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Deb PK, Deka S, Borah P, Abed SN, Klotz KN. Medicinal Chemistry and Therapeutic Potential of Agonists, Antagonists and Allosteric Modulators of A1 Adenosine Receptor: Current Status and Perspectives. Curr Pharm Des 2020; 25:2697-2715. [PMID: 31333094 DOI: 10.2174/1381612825666190716100509] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/01/2019] [Indexed: 12/28/2022]
Abstract
Adenosine is a purine nucleoside, responsible for the regulation of a wide range of physiological and pathophysiological conditions by binding with four G-protein-coupled receptors (GPCRs), namely A1, A2A, A2B and A3 adenosine receptors (ARs). In particular, A1 AR is ubiquitously present, mediating a variety of physiological processes throughout the body, thus represents a promising drug target for the management of various pathological conditions. Agonists of A1 AR are found to be useful for the treatment of atrial arrhythmia, angina, type-2 diabetes, glaucoma, neuropathic pain, epilepsy, depression and Huntington's disease, whereas antagonists are being investigated for the treatment of diuresis, congestive heart failure, asthma, COPD, anxiety and dementia. However, treatment with full A1 AR agonists has been associated with numerous challenges like cardiovascular side effects, off-target activation as well as desensitization of A1 AR leading to tachyphylaxis. In this regard, partial agonists of A1 AR have been found to be beneficial in enhancing insulin sensitivity and subsequently reducing blood glucose level, while avoiding severe CVS side effects and tachyphylaxis. Allosteric enhancer of A1 AR is found to be potent for the treatment of neuropathic pain, culminating the side effects related to off-target tissue activation of A1 AR. This review provides an overview of the medicinal chemistry and therapeutic potential of various agonists/partial agonists, antagonists and allosteric modulators of A1 AR, with a particular emphasis on their current status and future perspectives in clinical settings.
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Affiliation(s)
- Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University, PO Box - 1, 19392, Amman, Jordan
| | - Satyendra Deka
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Sara N Abed
- Faculty of Pharmacy, Philadelphia University, PO Box - 1, 19392, Amman, Jordan
| | - Karl-Norbert Klotz
- University of Würzburg, Department of Pharmacology and Toxicology Versbacher Str. 9, D-97078 Würzburg, Germany
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Lagarias P, Barkan K, Tzortzini E, Stampelou M, Vrontaki E, Ladds G, Kolocouris A. Insights to the Binding of a Selective Adenosine A 3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis. J Chem Inf Model 2019; 59:5183-5197. [PMID: 31725294 DOI: 10.1021/acs.jcim.9b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adenosine A3 receptor (A3R) is a promising drug target cancer and for a number of other conditions like inflammatory diseases, including asthma and rheumatoid arthritis, glaucoma, chronic obstructive pulmonary disease, and ischemic injury. Currently, there is no experimentally determined structure of A3R. We explored the binding profile of O4-{[3-(2,6-dichlorophenyl)-5-methylisoxazol-4-yl]carbonyl}-2-methyl-1,3-thiazole-4-carbohydroximamide (K18), which is a new specific and competitive antagonist at the orthosteric binding site of A3R. MD simulations and MM-GBSA calculations of the WT A3R in complex with K18 combined with in vitro mutagenic studies show that the most plausible binding conformation for the dichlorophenyl group of K18 is oriented toward trans-membrane helices (TM) 5, 6 and reveal important residues for binding. Further, MM-GBSA calculations distinguish mutations that reduce or maintain or increase antagonistic activity. Our studies show that selectivity of K18 toward A3R is defined not only by direct interactions with residues within the orthosteric binding area but also by remote residues playing a significant role. Although V1695.30 is considered to be a selectivity filter for A3R binders, when it was mutated to glutamic acid, K18 maintained antagonistic potency, in agreement with our previous results obtained for agonists binding profile investigation. Mutation of the direct interacting residue L903.32 in the low region and the remote L2647.35 in the middle/upper region to alanine increases antagonistic potency, suggesting an empty space in the orthosteric area available for increasing antagonist potency. These results approve the computational model for the description of K18 binding at A3R, which we previously performed for agonists binding to A3R, and the design of more effective antagonists based on K18.
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Affiliation(s)
- Panagiotis Lagarias
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupolis-Zografou , 15771 Athens , Greece
| | - Kerry Barkan
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Eva Tzortzini
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupolis-Zografou , 15771 Athens , Greece
| | - Margarita Stampelou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupolis-Zografou , 15771 Athens , Greece
| | - Eleni Vrontaki
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupolis-Zografou , 15771 Athens , Greece
| | - Graham Ladds
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , United Kingdom
| | - Antonios Kolocouris
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimioupolis-Zografou , 15771 Athens , Greece
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Li Y, Wang M, Gao N, Li D, Lin J. The effect of dimerization on the activation and conformational dynamics of adenosine A 1 receptor. Phys Chem Chem Phys 2019; 21:22763-22773. [PMID: 31595279 DOI: 10.1039/c9cp04060a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adenosine A1 receptor (A1R) is one of four adenosine receptors in humans, which are involved in the function of the cardiovascular, respiratory and central nervous systems. Experimental results indicate that A1R can form a homodimer and that the protomer-protomer interaction in the A1R dimer is related to certain pharmacological characteristics of A1R activation. In this work, we performed docking, metadynamics simulation, conventional molecular dynamics simulations, Gaussian-accelerated molecular dynamics simulations, potential of mean force calculations, dynamic cross-correlation motions analysis and community network analysis to study the binding mode of 5'-N-ethylcarboxamidoadenosine (NECA) to A1R and the effect of dimerization on the activation of A1R. Our results show that NECA binds to A1R in a similar mode to adenosine in the A1R crystal structure and NECA in the A2AR crystal structure. The A1R homodimer can be activated by one or two agonists with NECA occupying its orthosteric pockets in one (which we call the NECA-A1R system) or both protomers (which we call the dNECA-A1R system). In the NECA-A1R system, activation is predicated in the protomer without NECA bound. In the dNECA-A1R system, only one protomer achieves the active state. These findings suggest an asymmetrical activation mechanism of the homodimer and a negative cooperativity between the two protomers. We envision that our results may further facilitate the drug development of A1R.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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10
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Deb PK. Progress in the Development of Agonists, Antagonists and Allosteric Modulators of Adenosine Receptors. Curr Pharm Des 2019; 25:2695-2696. [DOI: 10.2174/138161282525190916100149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University, PO Box 1, 19392, Amman, Jordan
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Shaik K, Deb PK, Mailavaram RP, Chandrasekaran B, Kachler S, Klotz K, Jaber AMY. 7‐Amino‐2‐aryl/hetero‐aryl‐5‐oxo‐5,8‐dihydro[1,2,4]triazolo[1,5‐a]pyridine‐6‐carbonitriles: Synthesis and adenosine receptor binding studies. Chem Biol Drug Des 2019; 94:1568-1573. [DOI: 10.1111/cbdd.13528] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/26/2019] [Accepted: 03/17/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Khasim Shaik
- Pharmaceutical Chemistry Department Shri Vishnu College of Pharmacy Bhimavaram, West Godavari India
| | | | - Raghu Prasad Mailavaram
- Pharmaceutical Chemistry Department Shri Vishnu College of Pharmacy Bhimavaram, West Godavari India
| | | | - Sonja Kachler
- Department of Pharmacology and Toxicology University of Würzburg Würzburg Germany
| | - Karl‐Norbert Klotz
- Department of Pharmacology and Toxicology University of Würzburg Würzburg Germany
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12
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Lagarias P, Vrontaki E, Lambrinidis G, Stamatis D, Convertino M, Ortore G, Mavromoustakos T, Klotz KN, Kolocouris A. Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode. J Chem Inf Model 2018; 58:794-815. [PMID: 29485875 DOI: 10.1021/acs.jcim.7b00455] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An intense effort is made by pharmaceutical and academic research laboratories to identify and develop selective antagonists for each adenosine receptor (AR) subtype as potential clinical candidates for "soft" treatment of various diseases. Crystal structures of subtypes A2A and A1ARs offer exciting opportunities for structure-based drug design. In the first part of the present work, Maybridge HitFinder library of 14400 compounds was utilized to apply a combination of structure-based against the crystal structure of A2AAR and ligand-based methodologies. The docking poses were rescored by CHARMM energy minimization and calculation of the desolvation energy using Poisson-Boltzmann equation electrostatics. Out of the eight selected and tested compounds, five were found positive hits (63% success). Although the project was initially focused on targeting A2AAR, the identified antagonists exhibited low micromolar or micromolar affinity against A2A/A3, ARs, or A3AR, respectively. Based on these results, 19 compounds characterized by novel chemotypes were purchased and tested. Sixteen of them were identified as AR antagonists with affinity toward combinations of the AR family isoforms (A2A/A3, A1/A3, A1/A2A/A3, and A3). The second part of this work involves the performance of hundreds of molecular dynamics (MD) simulations of complexes between the ARs and a total of 27 ligands to resolve the binding interactions of the active compounds, which were not achieved by docking calculations alone. This computational work allowed the prediction of stable and unstable complexes which agree with the experimental results of potent and inactive compounds, respectively. Of particular interest is that the 2-amino-thiophene-3-carboxamides, 3-acylamino-5-aryl-thiophene-2-carboxamides, and carbonyloxycarboximidamide derivatives were found to be selective and possess a micromolar to low micromolar affinity for the A3 receptor.
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Affiliation(s)
- Panagiotis Lagarias
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Eleni Vrontaki
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - George Lambrinidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Dimitrios Stamatis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Marino Convertino
- Department of Biochemistry & Biophysics , University of North Carolina at Chapel Hill , 120 Mason Farm Road , Chapel Hill , North Carolina 27599 , United States
| | - Gabriella Ortore
- Department of Pharmacy , University of Pisa , 56126 Pisa , Italy
| | - Thomas Mavromoustakos
- Division of Organic Chemistry, Department of Chemistry, School of Science , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Karl-Norbert Klotz
- Institute of Pharmacology and Toxicology , University of Würzburg Versbacher Str. 9 , 97078 Würzburg , Germany
| | - Antonios Kolocouris
- Division 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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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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14
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Rossi M, Fasciani I, Marampon F, Maggio R, Scarselli M. The First Negative Allosteric Modulator for Dopamine D 2 and D 3 Receptors, SB269652 May Lead to a New Generation of Antipsychotic Drugs. Mol Pharmacol 2017; 91:586-594. [PMID: 28265019 DOI: 10.1124/mol.116.107607] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/02/2017] [Indexed: 12/15/2022] Open
Abstract
D2 and D3 dopamine receptors belong to the largest family of cell surface proteins in eukaryotes, the G protein-coupled receptors (GPCRs). Considering their crucial physiologic functions and their relatively accessible cellular locations, GPCRs represent one of the most important classes of therapeutic targets. Until recently, the only strategy to develop drugs regulating GPCR activity was through the identification of compounds that directly acted on the orthosteric sites for endogenous ligands. However, many efforts have recently been made to identify small molecules that are able to interact with allosteric sites. These sites are less well-conserved, therefore allosteric ligands have greater selectivity on the specific receptor. Strikingly, the use of allosteric modulators can provide specific advantages, such as an increased selectivity for GPCR subunits and the ability to introduce specific beneficial therapeutic effects without disrupting the integrity of complex physiologically regulated networks. In 2010, our group unexpectedly found that N-[(1r,4r)-4-[2-(7-cyano-1,2,3,4-tetrahydroisoquinolin-2-yl)ethyl]cyclohexyl]-1H-indole-2-carboxamide (SB269652), a compound supposed to interact with the orthosteric binding site of dopamine receptors, was actually a negative allosteric modulator of D2- and D3-receptor dimers, thus identifying the first allosteric small molecule acting on these important therapeutic targets. This review addresses the progress in understanding the molecular mechanisms of interaction between the negative modulator SB269652 and D2 and D3 dopamine receptor monomers and dimers, and surveys the prospects for developing new dopamine receptor allosteric drugs with SB269652 as the leading compound.
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Affiliation(s)
- Mario Rossi
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (M.R.); Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy (I.F., F.M., R.M.); Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy (M.S.)
| | - Irene Fasciani
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (M.R.); Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy (I.F., F.M., R.M.); Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy (M.S.)
| | - Francesco Marampon
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (M.R.); Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy (I.F., F.M., R.M.); Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy (M.S.)
| | - Roberto Maggio
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (M.R.); Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy (I.F., F.M., R.M.); Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy (M.S.)
| | - Marco Scarselli
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (M.R.); Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy (I.F., F.M., R.M.); Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy (M.S.)
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Nguyen ATN, Vecchio EA, Thomas T, Nguyen TD, Aurelio L, Scammells PJ, White PJ, Sexton PM, Gregory KJ, May LT, Christopoulos A. Role of the Second Extracellular Loop of the Adenosine A1 Receptor on Allosteric Modulator Binding, Signaling, and Cooperativity. Mol Pharmacol 2016; 90:715-725. [PMID: 27683013 DOI: 10.1124/mol.116.105015] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/27/2016] [Indexed: 02/05/2023] Open
Abstract
Allosteric modulation of adenosine A1 receptors (A1ARs) offers a novel therapeutic approach for the treatment of numerous central and peripheral disorders; however, despite decades of research, there is a relative paucity of structural information regarding the A1AR allosteric site and mechanisms governing cooperativity with orthosteric ligands. We combined alanine-scanning mutagenesis of the A1AR second extracellular loop (ECL2) with radioligand binding and functional interaction assays to quantify effects on allosteric ligand affinity, cooperativity, and efficacy. Docking and molecular dynamics (MD) simulations were performed using an A1AR homology model based on an agonist-bound A2AAR structure. Substitution of E172ECL2 for alanine reduced the affinity of the allosteric modulators PD81723 and VCP171 for the unoccupied A1AR. Residues involved in cooperativity with the orthosteric agonist NECA were different in PD81723 and VCP171; positive cooperativity between PD81723 and NECA was reduced on alanine substitution of a number of ECL2 residues, including E170ECL2 and K173ECL2, whereas mutation of W146ECL2 and W156ECL2 decreased VCP171 cooperativity with NECA. Molecular modeling localized a likely allosteric pocket for both modulators to an extracellular vestibule that overlaps with a region used by orthosteric ligands as they transit into the canonical A1AR orthosteric site. MD simulations confirmed a key interaction between E172ECL2 and both modulators. Bound PD81723 is flanked by another residue, E170ECL2, which forms hydrogen bonds with adjacent K168ECL2 and K173ECL2. Collectively, our data suggest E172ECL2 is a key allosteric ligand-binding determinant, whereas hydrogen-bonding networks within the extracellular vestibule may facilitate the transmission of cooperativity between orthosteric and allosteric sites.
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Affiliation(s)
- Anh T N Nguyen
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Elizabeth A Vecchio
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Trayder Thomas
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Toan D Nguyen
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Peter J Scammells
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Paul J White
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Patrick M Sexton
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Karen J Gregory
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Lauren T May
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
| | - Arthur Christopoulos
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., E.A.V., T.T., L.A., P.J.S., P.J.W., P.M.S., K.J.G., L.T.M., A.C.), Monash e-Research Centre (T.D.N.), and Department of Pharmacology (A.T.N.N., E.A.V., P.M.S., K.J.G., L.T.M., A.C), Monash University, Victoria, Australia
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