1
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Claff T, Klapschinski TA, Tiruttani Subhramanyam UK, Vaaßen VJ, Schlegel JG, Vielmuth C, Voß JH, Labahn J, Müller CE. Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A 2A Receptor with Preladenant Conjugates. Angew Chem Int Ed Engl 2022; 61:e202115545. [PMID: 35174942 PMCID: PMC9310709 DOI: 10.1002/anie.202115545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 01/08/2023]
Abstract
The G protein-coupled adenosine A2A receptor (A2A AR) is an important new (potential) drug target in immuno-oncology, and for neurodegenerative diseases. Preladenant and its derivatives belong to the most potent A2A AR antagonists displaying exceptional selectivity. While crystal structures of the human A2A AR have been solved, mostly using the A2A -StaR2 protein that bears 9 point mutations, co-crystallization with Preladenant derivatives has so far been elusive. We developed a new A2A AR construct harboring a single point mutation (S913.39 K) which renders it extremely thermostable. This allowed the co-crystallization of two novel Preladenant derivatives, the polyethylene glycol-conjugated (PEGylated) PSB-2113, and the fluorophore-labeled PSB-2115. The obtained crystal structures (2.25 Å and 2.6 Å resolution) provide explanations for the high potency and selectivity of Preladenant derivatives. They represent the first crystal structures of a GPCR in complex with PEG- and fluorophore-conjugated ligands. The applied strategy is predicted to be applicable to further class A GPCRs.
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Affiliation(s)
- Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Tim A Klapschinski
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Udaya K Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.,Research Centre Jülich, Institute of Complex Systems (IBI-7), Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Victoria J Vaaßen
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jonathan G Schlegel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Christin Vielmuth
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jan H Voß
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.,Research Centre Jülich, Institute of Complex Systems (IBI-7), Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
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2
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Claff T, Klapschinski TA, Tiruttani Subhramanyam UK, Vaaßen VJ, Schlegel JG, Vielmuth C, Voß JH, Labahn J, Müller CE. Eine einzige stabilisierende Punktmutation ermöglicht hochaufgelöste Co‐Kristallstrukturen des Adenosin‐A
2A
‐Rezeptors mit Preladenant‐Konjugaten. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias Claff
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Tim A. Klapschinski
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Udaya K. Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB) Notkestraße 85 22607 Hamburg Germany
- Research Centre Jülich Institute of Complex Systems (IBI-7) Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Victoria J. Vaaßen
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jonathan G. Schlegel
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Christin Vielmuth
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jan H. Voß
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB) Notkestraße 85 22607 Hamburg Germany
- Research Centre Jülich Institute of Complex Systems (IBI-7) Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Christa E. Müller
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
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3
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Federico S, Redenti S, Sturlese M, Ciancetta A, Kachler S, Klotz KN, Cacciari B, Moro S, Spalluto G. The Influence of the 1-(3-Trifluoromethyl-Benzyl)-1H-Pyrazole-4-yl Moiety on the Adenosine Receptors Affinity Profile of Pyrazolo[4,3-e][1,2,4]Triazolo[1,5-c]Pyrimidine Derivatives. PLoS One 2015; 10:e0143504. [PMID: 26625265 PMCID: PMC4666649 DOI: 10.1371/journal.pone.0143504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/05/2015] [Indexed: 12/03/2022] Open
Abstract
A new series of pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine (PTP) derivatives has been developed in order to explore their affinity and selectivity profile at the four adenosine receptor subtypes. In particular, the PTP scaffold was conjugated at the C2 position with the 1-(3-trifluoromethyl-benzyl)-1H-pyrazole, a group believed to confer potency and selectivity toward the human (h) A2B adenosine receptor (AR) to the xanthine ligand 8-(1-(3-(trifluoromethyl)benzyl)-1H-pyrazol-4-yl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione (CVT 6975). Interestingly, the synthesized compounds turned out to be inactive at the hA2B AR but they displayed affinity at the hA3 AR in the nanomolar range. The best compound of the series (6) shows both high affinity (hA3 AR Ki = 11 nM) and selectivity (A1/A3 and A2A/A3 > 9090; A2B/A3 > 909) at the hA3 AR. To better rationalize these results, a molecular docking study on the four AR subtypes was performed for all the synthesized compounds. In addition, CTV 6975 and two close analogues have been subjected to the same molecular docking protocol to investigate the role of the 1-(3-trifluoromethyl-benzyl)-1H-pyrazole on the binding at the four ARs.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy
| | - Sara Redenti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Sonja Kachler
- Institut für Pharmakologie und Toxicologie, Universität Würzburg, Würzburg, Germany
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxicologie, Universität Würzburg, Würzburg, Germany
| | - Barbara Cacciari
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Ferrara, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy
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4
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Bonet I, Franco-Montero P, Rivero V, Teijeira M, Borges F, Uriarte E, Morales Helguera A. Classifier ensemble based on feature selection and diversity measures for predicting the affinity of A(2B) adenosine receptor antagonists. J Chem Inf Model 2013; 53:3140-55. [PMID: 24289249 DOI: 10.1021/ci300516w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A(2B) adenosine receptor antagonists may be beneficial in treating diseases like asthma, diabetes, diabetic retinopathy, and certain cancers. This has stimulated research for the development of potent ligands for this subtype, based on quantitative structure-affinity relationships. In this work, a new ensemble machine learning algorithm is proposed for classification and prediction of the ligand-binding affinity of A(2B) adenosine receptor antagonists. This algorithm is based on the training of different classifier models with multiple training sets (composed of the same compounds but represented by diverse features). The k-nearest neighbor, decision trees, neural networks, and support vector machines were used as single classifiers. To select the base classifiers for combining into the ensemble, several diversity measures were employed. The final multiclassifier prediction results were computed from the output obtained by using a combination of selected base classifiers output, by utilizing different mathematical functions including the following: majority vote, maximum and average probability. In this work, 10-fold cross- and external validation were used. The strategy led to the following results: i) the single classifiers, together with previous features selections, resulted in good overall accuracy, ii) a comparison between single classifiers, and their combinations in the multiclassifier model, showed that using our ensemble gave a better performance than the single classifier model, and iii) our multiclassifier model performed better than the most widely used multiclassifier models in the literature. The results and statistical analysis demonstrated the supremacy of our multiclassifier approach for predicting the affinity of A(2B) adenosine receptor antagonists, and it can be used to develop other QSAR models.
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Affiliation(s)
- Isis Bonet
- Escuela de Ingeniería de Antioquia, Envigado, 055428 Antioquia, Colombia
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5
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Bacilieri M, Ciancetta A, Paoletta S, Federico S, Cosconati S, Cacciari B, Taliani S, Da Settimo F, Novellino E, Klotz KN, Spalluto G, Moro S. Revisiting a receptor-based pharmacophore hypothesis for human A(2A) adenosine receptor antagonists. J Chem Inf Model 2013; 53:1620-37. [PMID: 23705857 DOI: 10.1021/ci300615u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The application of both structure- and ligand-based design approaches represents to date one of the most useful strategies in the discovery of new drug candidates. In the present paper, we investigated how the application of docking-driven conformational analysis can improve the predictive ability of 3D-QSAR statistical models. With the use of the crystallographic structure in complex with the high affinity antagonist ZM 241385 (4-(2-[7-amino-2-(2-furyl)[1,2,4]-triazolo[2,3-a][1,3,5]triazin-5-ylamino]ethyl)phenol), we revisited a general pharmacophore hypothesis for the human A(2A) adenosine receptor of a set of 751 known antagonists, by applying an integrated ligand- and structure-based approach. Our novel pharmacophore hypothesis has been validated by using an external test set of 29 newly synthesized human adenosine receptor antagonists.
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Affiliation(s)
- Magdalena Bacilieri
- Molecular Modeling Section-MMS, Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, Padova, Italy
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6
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Synthesis and anti-bacterial activities of some novel pyrazolobenzothiazine-based chalcones and their pyrimidine derivatives. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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7
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Cheong SL, Dolzhenko AV, Paoletta S, Lee EPR, Kachler S, Federico S, Klotz KN, Dolzhenko AV, Spalluto G, Moro S, Pastorin G. Does the combination of optimal substitutions at the C2-, N5- and N8-positions of the pyrazolo-triazolo-pyrimidine scaffold guarantee selective modulation of the human A3 adenosine receptors? Bioorg Med Chem 2011; 19:6120-34. [DOI: 10.1016/j.bmc.2011.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Revised: 08/10/2011] [Accepted: 08/11/2011] [Indexed: 10/17/2022]
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8
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Pharmacophore elucidation for a new series of 2-aryl-pyrazolo-triazolo-pyrimidines as potent human A3 adenosine receptor antagonists. Bioorg Med Chem Lett 2011; 21:2898-905. [DOI: 10.1016/j.bmcl.2011.03.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 03/17/2011] [Accepted: 03/18/2011] [Indexed: 11/18/2022]
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9
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Pyrazolo derivatives as potent adenosine receptor antagonists: an overview on the structure-activity relationships. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2011; 2011:480652. [PMID: 25954519 PMCID: PMC4411897 DOI: 10.1155/2011/480652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 02/10/2011] [Indexed: 11/17/2022]
Abstract
In the past few decades, medicinal chemistry research towards potent and selective antagonists of human adenosine receptors (namely, A1, A2A, A2B, and A3) has been evolving rapidly. These antagonists are deemed therapeutically beneficial in several pathological conditions including neurological and renal disorders, cancer, inflammation, and glaucoma. Up to this point, many classes of compounds have been successfully synthesized and identified as potent human adenosine receptor antagonists. In this paper, an overview of the structure-activity relationship (SAR) profiles of promising nonxanthine pyrazolo derivatives is reported and discussed. We have emphasized the SAR for some representative structures such as pyrazolo-[4,3-e]-1,2,4-triazolo-[1,5-c]pyrimidines; pyrazolo-[3,4-c] or -[4,3-c]quinolines; pyrazolo-[4,3-d]pyrimidinones; pyrazolo-[3,4-d]pyrimidines and pyrazolo-[1,5-a]pyridines. This overview not only clarifies the structural requirements deemed essential for affinity towards individual adenosine receptor subtypes, but it also sheds light on the rational design and optimization of existing structural templates to allow us to conceive new, more potent adenosine receptor antagonists.
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10
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Cheong SL, Dolzhenko A, Kachler S, Paoletta S, Federico S, Cacciari B, Dolzhenko A, Klotz KN, Moro S, Spalluto G, Pastorin G. The significance of 2-furyl ring substitution with a 2-(para-substituted) aryl group in a new series of pyrazolo-triazolo-pyrimidines as potent and highly selective hA(3) adenosine receptors antagonists: new insights into structure-affinity relationship and receptor-antagonist recognition. J Med Chem 2010; 53:3361-75. [PMID: 20307065 DOI: 10.1021/jm100049f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the heterocyclic structures identified as potent human A(3) (hA(3)) adenosine receptor's antagonists, we have demonstrated that the new pyrazolo-triazolo-pyrimidines, bearing an aryl group in replacement of the C(2)-furyl ring, not only confer a good pharmacological profile (with significantly enhanced selectivity against other adenosine receptor subytpes) but also overcome the metabolic transformation of the furan ring into toxic intermediates. All the synthesized [2-(para-substituted) phenyl]-pyrazolo-triazolo-pyrimidines showed affinity at the hA(3) receptor in the low nanomolar range. The most potent derivative of the series presented better affinity and excellent selectivity (compound 31, K(i) hA(3) = 0.108 nM; hA(1)/hA(3) = 5200; hA(2A)/hA(3) = 7200), in comparison to the C(2)-furyl counterpart. A receptor-driven molecular modeling investigation, based on a recently proposed model of A(3) receptor derived from the crystallographic structure of human A(2A) receptor, has been carried out in order to support the experimental binding data and to justify the enhanced selectivity against the other receptor subtypes.
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Affiliation(s)
- Siew Lee Cheong
- Department of Pharmacy, National University of Singapore, 3 Science Drive 2, Block S15, no. 05-PI-03, Singapore 117543
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11
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Michielan L, Federico S, Terfloth L, Hristozov D, Cacciari B, Klotz KN, Spalluto G, Gasteiger J, Moro S. Exploring Potency and Selectivity Receptor Antagonist Profiles Using a Multilabel Classification Approach: The Human Adenosine Receptors as a Key Study. J Chem Inf Model 2009; 49:2820-36. [DOI: 10.1021/ci900311j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa Michielan
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Stephanie Federico
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Lothar Terfloth
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Dimitar Hristozov
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Barbara Cacciari
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Karl-Norbert Klotz
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Giampiero Spalluto
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Johann Gasteiger
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
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12
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Combining selectivity and affinity predictions using an integrated Support Vector Machine (SVM) approach: An alternative tool to discriminate between the human adenosine A(2A) and A(3) receptor pyrazolo-triazolo-pyrimidine antagonists binding sites. Bioorg Med Chem 2009; 17:5259-74. [PMID: 19501513 DOI: 10.1016/j.bmc.2009.05.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 05/08/2009] [Accepted: 05/14/2009] [Indexed: 11/21/2022]
Abstract
G Protein-coupled receptors (GPCRs) selectivity is an important aspect of drug discovery process, and distinguishing between related receptor subtypes is often the key to therapeutic success. Nowadays, very few valuable computational tools are available for the prediction of receptor subtypes selectivity. In the present study, we present an alternative application of the Support Vector Machine (SVM) and Support Vector Regression (SVR) methodologies to simultaneously describe both A(2A)R versus A(3)R subtypes selectivity profile and the corresponding receptor binding affinities. We have implemented an integrated application of SVM-SVR approach, based on the use of our recently reported autocorrelated molecular descriptors encoding for the Molecular Electrostatic Potential (autoMEP), to simultaneously discriminate A(2A)R versus A(3)R antagonists and to predict their binding affinity to the corresponding receptor subtype of a large dataset of known pyrazolo-triazolo-pyrimidine analogs. To validate our approach, we have synthetized 51 new pyrazolo-triazolo-pyrimidine derivatives anticipating both A(2A)R/A(3)R subtypes selectivity and receptor binding affinity profiles.
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13
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Abstract
The development of potent and selective agonists and antagonists of adenosine receptors (ARs) has been a target of medicinal chemistry research for several decades, and recently the US Food and Drug Administration has approved Lexiscan, an adenosine derivative substituted at the 2 position, for use as a pharmacologic stress agent in radionuclide myocardial perfusion imaging. Currently, some other adenosine A(2A) receptor (A(2A)AR) agonists and antagonists are undergoing preclinical testing and clinical trials. While agonists are potent antiinflammatory agents also showing hypotensive effects, antagonists are being developed for the treatment of Parkinson's disease.However, since there are still major problems in this field, including side effects, low brain penetration (for the targeting of CNS diseases), short half-life, or lack of in vivo effects, the design and development of new AR ligands is a hot research topic.This review presents an update on the medicinal chemistry of A(2A)AR agonists and antagonists, and stresses the strong need for more selective ligands at the human A(2A)AR subtype, in particular in the case of agonists.
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Affiliation(s)
- Gloria Cristalli
- Dipartimento di Scienze Chimiche, Università di Camerino, 62032 Camerino (MC), Italy.
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14
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Cristalli G, Cacciari B, Dal Ben D, Lambertucci C, Moro S, Spalluto G, Volpini R. Highlights on the development of A(2A) adenosine receptor agonists and antagonists. ChemMedChem 2008; 2:260-81. [PMID: 17177231 DOI: 10.1002/cmdc.200600193] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although significant progress has been made in the past few decades demonstrating that adenosine modulates a variety of physiological and pathophysiological processes through the interaction with four subtypes of a family of cell-surface G-protein-coupled receptors, clinical evaluation of some adenosine receptor ligands has been discontinued. Major problems include side effects due to the wide distribution of adenosine receptors, low brain penetration (which is important for the targeting of CNS diseases), short half-life of compounds, or a lack of effects, in some cases perhaps due to receptor desensitization or to low receptor density in the targeted tissue. Currently, three A(2A) adenosine receptor agonists have begun phase III studies. Two of them are therapeutically evaluated as pharmacologic stress agents and the third proved to be effective in the treatment of acute spinal cord injury (SCI), while avoiding the adverse effects of steroid agents. On the other hand, the great interest in the field of A(2A) adenosine receptor antagonists is related to their application in neurodegenerative disorders, in particular, Parkinson's disease, and some of them are currently in various stages of evaluation. This review presents an update of medicinal chemistry and molecular recognition of A(2A) adenosine receptor agonists and antagonists, and stresses the strong need for more selective ligands at the A(2A) human subtype.
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Affiliation(s)
- Gloria Cristalli
- Dipartimento di Scienze Chimiche, Università di Camerino, Via S. Agostino 1, 62032 Camerino, Italy.
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15
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González MP, Terán C, Teijeira M. Search for new antagonist ligands for adenosine receptors from QSAR point of view. How close are we? Med Res Rev 2008; 28:329-71. [PMID: 17668454 DOI: 10.1002/med.20108] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In view of the large libraries of nucleoside analogues that are now being handled in organic synthesis, the identification of drug biological activity is advisable prior to synthesis and this can be achieved by employing predictive biological property methods. In this sense, Quantitative Structure-Activity Relationships (QSAR) or docking approaches have emerged as promising tools. Although a large number of in silico approaches have been described in the literature for the prediction of different biological activities, the use of QSAR applications to develop adenosine receptor (AR) antagonists is not common as for the case of the antibiotics and anticancer compounds for instance. The intention of this review is to summarize the present knowledge concerning computational predictions of new molecules as adenosine receptor antagonists.
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16
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Beukers MW, Meurs I, Ijzerman AP. Structure-affinity relationships of adenosine A2B receptor ligands. Med Res Rev 2007; 26:667-98. [PMID: 16847822 DOI: 10.1002/med.20069] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many selective and high affinity agonists and antagonists have been developed for the adenosine A(1), A(2A), and A(3) receptors. Very recently such compounds have been identified for the adenosine A(2B) receptors. This review presents an overview of the structure-affinity relationships of antagonists and agonists for this receptor subtype as published in the scientific and patent literature. To date the most selective >370-fold, high affinity adenosine A(2B) receptor antagonist is the xanthine analog, compound 16 (8-(1-(3-phenyl-1,2,4-oxadiazol-5-yl)methyl)-1H-pyrazol-4-yl)-1,3-dipropyl-1H-purine-2,6(3H,7H)-dione). The pyrrolopyrimidine analog OSIP339391 (73) is slightly less selective, 70-fold, but has a higher affinity 0.41 nM compared to 1 nM for compound 16. Other promising classes of compounds with selectivities ranging from 10- to 160-fold and affinities ranging from 3 to 112 nM include triazolo, aminothiazole, quinazoline, and pyrimidin-2-amine analogs. Progress has also been achieved concerning the development of selective high affinity agonists for the adenosine A(2B) receptor. For years the most potent, albeit non-selective adenosine A(2B) receptor agonist was (S)PHPNECA (88). Last year, a new class of non-ribose ligands was reported. Several compounds displayed selectivity with respect to adenosine A(2A) and A(3) receptors. In addition, full and partial agonists for the adenosine A(2B) receptor were identified with EC(50) values of 10 nM (LUF5835, 103) and 9 nM (LUF5845, 105), respectively.
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Affiliation(s)
- Margot W Beukers
- Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
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17
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Cacciari B, Bolcato C, Spalluto G, Klotz KN, Bacilieri M, Deflorian F, Moro S. Pyrazolo-triazolo-pyrimidines as adenosine receptor antagonists: A complete structure-activity profile. Purinergic Signal 2007; 3:183-93. [PMID: 18404432 PMCID: PMC2096643 DOI: 10.1007/s11302-006-9027-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 09/05/2006] [Accepted: 09/07/2006] [Indexed: 12/31/2022] Open
Abstract
In the last 5 years, many efforts have been conducted searching potent and selective human A(3) adenosine antagonists. In this field several different classes of compounds, possessing very good affinity (nM range) and with a broad range of selectivity, have been proposed. Recently, our group synthesized a new series of pyrazolo-triazolo-pyrimidines bearing different substitutions at the N(5) and N(8) positions, which have been described as highly potent and selective human A(3) adenosine receptor antagonists. The present review summarizes available data and provides an overview of the structure-activity relationships found for this class of human A(3) adenosine receptor antagonists.
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Affiliation(s)
- Barbara Cacciari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17–19, 44100 Ferrara, Italy
| | - Chiara Bolcato
- Dipartimento di Scienze Farmaceutiche, Università di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Giampiero Spalluto
- Dipartimento di Scienze Farmaceutiche, Università di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Karl-Norbet Klotz
- Institut für Pharmakologie und Toxikologie, Universität Würzburg, 97078 Würzburg, Germany
| | - Magdalena Bacilieri
- Molecular Modeling Section, Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Francesca Deflorian
- Molecular Modeling Section, Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section, Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, 35131 Padova, Italy
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18
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Moro S, Gao ZG, Jacobson KA, Spalluto G. Progress in the pursuit of therapeutic adenosine receptor antagonists. Med Res Rev 2006; 26:131-59. [PMID: 16380972 PMCID: PMC9194718 DOI: 10.1002/med.20048] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ever since the discovery of the hypotensive and bradycardiac effects of adenosine, adenosine receptors continue to represent promising drug targets. First, this is due to the fact that the receptors are expressed in a large variety of tissues. In particular, the actions of adenosine (or methylxanthine antagonists) in the central nervous system, in the circulation, on immune cells, and on other tissues can be beneficial in certain disorders. Second, there exists a large number of ligands, which have been generated by introducing several modifications in the structure of the lead compounds (adenosine and methylxanthine), some of them highly specific. Four adenosine receptor subtypes (A1, A2A, A2B, and A3) have been cloned and pharmacologically characterized, all of which are G protein-coupled receptors. Adenosine receptors can be distinguished according to their preferred mechanism of signal transduction: A1 and A3 receptors interact with pertussis toxin-sensitive G proteins of the Gi and Go family; the canonical signaling mechanism of the A2A and of the A2B receptors is stimulation of adenylyl cyclase via Gs proteins. In addition to the coupling to adenylyl cyclase, all four subtypes may positively couple to phospholipase C via different G protein subunits. The development of new ligands, in particular, potent and selective antagonists, for all subtypes of adenosine receptors has so far been directed by traditional medicinal chemistry. The availability of genetic information promises to facilitate understanding of the drug-receptor interaction leading to the rational design of a potentially therapeutically important class of drugs. Moreover, molecular modeling may further rationalize observed interactions between the receptors and their ligands. In this review, we will summarize the most relevant progress in developing new therapeutic adenosine receptor antagonists.
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Affiliation(s)
- Stefano Moro
- Molecular Modeling Section, Dipartimento di Scienze Farmaceutiche, Università di Padova, Via Marzolo 5, I-35131 Padova, Italy.
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19
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Baraldi PG, Tabrizi MA, Preti D, Bovero A, Romagnoli R, Fruttarolo F, Zaid NA, Moorman AR, Varani K, Gessi S, Merighi S, Borea PA. Design, synthesis, and biological evaluation of new 8-heterocyclic xanthine derivatives as highly potent and selective human A2B adenosine receptor antagonists. J Med Chem 2004; 47:1434-47. [PMID: 14998332 DOI: 10.1021/jm0309654] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we report the synthesis of 8-heterocycle-substituted xanthines as potent and selective A(2B) adenosine receptor antagonists. The structure-activity relationships (SAR) of the xanthines synthesized in binding to recombinant human A(2B) adenosine receptors (ARs) in HEK-293 cells (HEK-A(2B)) and at other AR subtypes were explored. The synthesized compounds showed A(2B) adenosine receptor affinity in the nanomolar range and good levels of selectivity evaluated in radioligand binding assays at human (h) A(1), A(2A), A(2B), and A(3) ARs. We introduced several heterocycles, such as pyrazole, isoxazole, pyridine, and pyridazine, at the 8-position of the xanthine nucleus and we have also investigated different spacers (substituted acetamide, oxyacetamide, and urea moieties) on the heterocycle introduced. Various groups at the 3- and 4-positions of phenylacetamide moiety were studied. This study allowed us to identify the derivatives 2-(3,4-dimethoxyphenyl)-N-[5-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-1-methyl-1H-pyrazol-3-yl]acetamide (29b, MRE2028F20) [K(i)(hA(2B)) = 38 nM, K(i)(hA(1),hA(2A),hA(3)) >1000 nM], N-benzo[1,3]dioxol-5-yl-2-[5-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-1-methyl-1H-pyrazol-3-yloxy]acetamide (62b, MRE2029F20) [K(i)(hA(2B)) = 5.5 nM, K(i)(hA(1),hA(2A),hA(3)) > 1000 nM], and N-(3,4-dimethoxyphenyl)-2-[5-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-1-methyl-1H-pyrazol-3-yloxy]acetamide (72b, MRE2030F20) [K(i)(hA(2B) = 12 nM, K(i)(hA(1),hA(2A), hA(3)) > 1000 nM], which showed high affinity at the A(2B) receptor subtype and very good selectivity vs the other ARs. Substitution of the acetamide with an urea moiety afforded bioisosteric xanthines with good affinity and selectivity comparable to the acetamide derivatives. Substitution at the para-position of a 4-benzyloxy group of the phenylacetamido chain enhanced affinity at the A(2B) receptor [compound 30b (K(i)(hA(2B)) = 13 nM) vs compound 21b (K(i)(hA(2B) = 56 nM)] but did not favor selectivity. The derivatives with higher affinity at human A(2B) AR proved to be antagonists, in the cyclic AMP assay, capable of inhibiting the stimulatory effect of NECA (100 nM) with IC(50) values in the nanomolar range, a trend similar to that observed in the binding assay (62b, IC(50) = 38 nM; 72b, IC(50) = 46 nM). In conclusion, the 8-pyrazolo-1,3-dipropyl-1H-purine-2,6-dione derivatives described herein represent a new family of selective antagonists for the adenosine A(2B) receptor.
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Affiliation(s)
- Pier Giovanni Baraldi
- Dipartimento di Scienze Farmaceutiche and Dipartimento di Medicina Clinica e Sperimentale-Sezione di Farmacologia, Università di Ferrara, 44100 Ferrara Italy.
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20
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Pastorin G, Da Ros T, Spalluto G, Deflorian F, Moro S, Cacciari B, Baraldi PG, Gessi S, Varani K, Borea PA. Pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine derivatives as adenosine receptor antagonists. Influence of the N5 substituent on the affinity at the human A 3 and A 2B adenosine receptor subtypes: a molecular modeling investigation. J Med Chem 2003; 46:4287-96. [PMID: 13678407 DOI: 10.1021/jm030852k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new series of pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidines bearing various substituents at both the N5-pyrimidinyl and N8-pyrazolyl positions have been synthesized, and their binding affinities at the four human adenosine receptor subtypes (hA(1), hA(2A), hA(2B), and hA(3)) have been evaluated. All the described compounds contain arylacetyl moieties at the N5 position and arylalkyl substituents at the N8 position. Surprisingly, all the compounds present their most potent affinities at the hA(2B) adenosine receptor with a range of selectivities against the other subtypes. When bulky groups are present simultaneously at the N5 and N8 positions (e.g., compound 9), the best selectivity for the hA(2B) receptor was observed (K(i)(hA(1)) = 1100 nM; K(i)(hA(2A)) = 800 nM; K(i)(hA(2B)) = 20 nM; K(i)(hA(3)) = 300 nM, K(i)(hA(1)/A(2B)) = 55, K(i)(hA(2A)/A(2B)) = 40, K(i)(hA(3)/hA(2B)) = 15). To understand the molecular significance of these results, we compared the putative TM (transmembrane) binding motif of compound 9 on both hA(2B) and hA(3) receptors. From our docking studies, compound 9 fits neatly inside the TM region of the hA(2B) receptor but not in the corresponding hA(3) region, illustrating significant differences between the two subtypes. The study herein presented permits an understanding of why the bioisosteric replacement of an -NH, present in previously reported hA(3) receptor antagonists, with a -CH(2) group at the N5 position induces such large differences in hA(2B)/hA(3) affinity. In the molecular structure of the hA(3) receptor, two residues, Ser243 (TM6) and Ser271 (TM7), create a hydrophilic region, which seems to permit a better accommodation of the phenylurea series into this putative hA(3) binding site than the phenylacetyl series.
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Affiliation(s)
- Giorgia Pastorin
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy
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