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Deganutti G, Moro S, Reynolds CA. A Supervised Molecular Dynamics Approach to Unbiased Ligand–Protein Unbinding. J Chem Inf Model 2020; 60:1804-1817. [DOI: 10.1021/acs.jcim.9b01094] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Giuseppe Deganutti
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Christopher A. Reynolds
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
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2
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Federico S, Margiotta E, Salmaso V, Pastorin G, Kachler S, Klotz KN, Moro S, Spalluto G. [1,2,4]Triazolo[1,5-c]pyrimidines as adenosine receptor antagonists: Modifications at the 8 position to reach selectivity towards A3 adenosine receptor subtype. Eur J Med Chem 2018; 157:837-851. [DOI: 10.1016/j.ejmech.2018.08.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 12/27/2022]
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3
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Pandya AN, Baraiya AB, Jalani HB, Pandya D, Kaila JC, Kachler S, Salmaso V, Moro S, Klotz KN, Vasu KK. Discovery of 2-aminoimidazole and 2-amino imidazolyl-thiazoles as non-xanthine human adenosine A 3 receptor antagonists: SAR and molecular modeling studies. MEDCHEMCOMM 2018; 9:676-684. [PMID: 30108958 DOI: 10.1039/c7md00643h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/27/2018] [Indexed: 01/07/2023]
Abstract
A small-molecule combinatorial library of 24 compounds with 2-aminoimidazole and 2-aminoimidazolyl-thiazole derivatives was synthesized using a 2-chloro trityl resin. The generated compound library was tested against all the human adenosine receptors subtypes. The 2-aminoimidazole derivatives (6a-6l) showed weak to moderate affinity towards the human adenosine receptors. Further modification to 2-aminoimidazolyl-thiazole derivatives (12a-12l) resulted in an improvement of affinity at adenosine A1, A2A and A3 receptor subtypes. Compound 12b was the most potent and selective non-xanthine human adenosine A3 receptor antagonist of this series. A receptor-based modeling study was performed to explore the possible binding mode of these novel 2-aminoimidazole and 2-aminoimidazolyl-thiazole derivatives into human adenosine A1, A2A and A3 receptor subtypes.
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Affiliation(s)
- Amit N Pandya
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Arshi B Baraiya
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Hitesh B Jalani
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Dhaivat Pandya
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Jitendra C Kaila
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Sonja Kachler
- Institut für Pharmakologie und Toxikologie , Julius-Maximilians-Universität Würzburg , Germany
| | - Veronica Salmaso
- Molecular Modeling Section (MMS) , Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS) , Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxikologie , Julius-Maximilians-Universität Würzburg , Germany
| | - Kamala K Vasu
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
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Squarcialupi L, Betti M, Catarzi D, Varano F, Falsini M, Ravani A, Pasquini S, Vincenzi F, Salmaso V, Sturlese M, Varani K, Moro S, Colotta V. The role of 5-arylalkylamino- and 5-piperazino- moieties on the 7-aminopyrazolo[4,3-d]pyrimidine core in affecting adenosine A 1 and A 2A receptor affinity and selectivity profiles. J Enzyme Inhib Med Chem 2017; 32:248-263. [PMID: 28114825 PMCID: PMC6009979 DOI: 10.1080/14756366.2016.1247060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
New 7-amino-2-phenylpyrazolo[4,3-d]pyrimidine derivatives, substituted at the 5-position with aryl(alkyl)amino- and 4-substituted-piperazin-1-yl- moieties, were synthesized with the aim of targeting human (h) adenosine A1 and/or A2A receptor subtypes. On the whole, the novel derivatives 1–24 shared scarce or no affinities for the off-target hA2B and hA3 ARs. The 5-(4-hydroxyphenethylamino)- derivative 12 showed both good affinity (Ki = 150 nM) and the best selectivity for the hA2A AR while the 5-benzylamino-substituted 5 displayed the best combined hA2A (Ki = 123 nM) and A1 AR affinity (Ki = 25 nM). The 5-phenethylamino moiety (compound 6) achieved nanomolar affinity (Ki = 11 nM) and good selectivity for the hA1 AR. The 5-(N4-substituted-piperazin-1-yl) derivatives 15–24 bind the hA1 AR subtype with affinities falling in the high nanomolar range. A structure-based molecular modeling study was conducted to rationalize the experimental binding data from a molecular point of view using both molecular docking studies and Interaction Energy Fingerprints (IEFs) analysis.
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Affiliation(s)
- Lucia Squarcialupi
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Marco Betti
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Daniela Catarzi
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Flavia Varano
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Matteo Falsini
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Annalisa Ravani
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Silvia Pasquini
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Fabrizio Vincenzi
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Veronica Salmaso
- c Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco , Università di Padova , Padova , Italy
| | - Mattia Sturlese
- c Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco , Università di Padova , Padova , Italy
| | - Katia Varani
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Stefano Moro
- c Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco , Università di Padova , Padova , Italy
| | - Vittoria Colotta
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
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Federico S, Ciancetta A, Porta N, Redenti S, Pastorin G, Cacciari B, Klotz KN, Moro S, Spalluto G. 5,7-Disubstituted-[1,2,4]triazolo[1,5-a][1,3,5]triazines as pharmacological tools to explore the antagonist selectivity profiles toward adenosine receptors. Eur J Med Chem 2015; 108:529-541. [PMID: 26717203 DOI: 10.1016/j.ejmech.2015.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/03/2015] [Accepted: 12/10/2015] [Indexed: 10/22/2022]
Abstract
The structure-activity relationship of new 5,7-disubstituted-[1,2,4]triazolo[1,5-a][1,3,5]triazines as adenosine receptors (ARs) antagonists has been explored. The introduction of a benzylamino group at C5 with a free amino group at C7 increases the affinity toward all the ARs subtypes (10: KihA1 = 94.6 nM; KihA2A = 1.11 nM; IC50hA2B = 2214 nM; KihA3 = 30.8 nM). Replacing the free amino group at C7 with a phenylureido moiety yields a potent and quite selective hA2A AR antagonist (14: hA2A AR Ki = 1.44 nM; hA1/hA2A = 216.0; hA3/hA2A = 20.6). This trend diverges from the analysis on the pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine series previously reported. With the help of an in silico receptor-driven approach, we have rationalized these observations and elucidated from a molecular point of view the role of the benzylamino group at C5 in determining affinity toward the hA2A AR.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Nicola Porta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Sara Redenti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Giorgia Pastorin
- Department of Pharmacy, National University of Singapore, 3 Science Drive 2, 117543 Singapore
| | - Barbara Cacciari
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17-19, 44100 Ferrara, Italy
| | - Karl Norbert Klotz
- Institut für Pharmakologie und Toxicologie, Universität of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, 35131 Padova, Italy.
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Piazzale Europa 1, 34127 Trieste, Italy.
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Advances in Computational Techniques to Study GPCR–Ligand Recognition. Trends Pharmacol Sci 2015; 36:878-890. [DOI: 10.1016/j.tips.2015.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 12/16/2022]
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Deganutti G, Cuzzolin A, Ciancetta A, Moro S. Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000. Bioorg Med Chem 2015; 23:4065-71. [DOI: 10.1016/j.bmc.2015.03.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 10/23/2022]
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Cavasotto CN, Palomba D. Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chem Commun (Camb) 2015; 51:13576-94. [DOI: 10.1039/c5cc05050b] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We show the key role of structural homology models in GPCR structure-based lead discovery and optimization, highlighting methodological aspects, recent progress and future directions.
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Affiliation(s)
- Claudio N. Cavasotto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
| | - Damián Palomba
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
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Costanzi S. G protein-coupled receptors: computer-aided ligand discovery and computational structural analyses in the 2010s. In Silico Pharmacol 2013; 1:20. [PMID: 25505664 PMCID: PMC4215811 DOI: 10.1186/2193-9616-1-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/07/2013] [Indexed: 01/02/2023] Open
Abstract
G protein-coupled receptors, or GPCRs, are a large superfamily of proteins found on the plasma membrane of cells. They are involved in most physiological and pathophysiological functions and constitute the target of the majority of marketed drugs. Although these receptors have been historically elusive to attempts of structural determination, GPCR crystallography is now in full blossom, opening the way to structure-based drug discovery and enabling homology modeling. This thematic issue of the journal In Silico Pharmacology, which illustrates how the expanding body of structural knowledge is fostering complex computational analyses of the structure-function relationships of the receptors and their interactions with their ligands, stems from the 31st Camerino-Cyprus-Noordwijkerhout Symposium held in Italy, in May 2013, at the University of Camerino. Specifically, it originates from a session of the symposium entitled “Structure-Based Discovery of Ligands of G Protein-Coupled Receptors: Finally a Reality”, and features a mix of research articles and reviews on the application of computational modeling to the analysis of the structure of GPCRs and the interactions of the receptors with their ligands.
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Affiliation(s)
- Stefano Costanzi
- Department of Chemistry and Center for Behavioral Neuroscience, American University, 4400 Massachusetts Ave, NW, 20016 Washington, DC USA
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