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Salmaso V, Persico M, Da Ros T, Spalluto G, Kachler S, Klotz KN, Moro S, Federico S. Pyrazolo-triazolo-pyrimidine Scaffold as a Molecular Passepartout for the Pan-Recognition of Human Adenosine Receptors. Biomolecules 2023; 13:1610. [PMID: 38002292 PMCID: PMC10669182 DOI: 10.3390/biom13111610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Adenosine receptors are largely distributed in our organism and are promising therapeutic targets for the treatment of many pathologies. In this perspective, investigating the structural features of the ligands leading to affinity and/or selectivity is of great interest. In this work, we have focused on a small series of pyrazolo-triazolo-pyrimidine antagonists substituted in positions 2, 5, and N8, where bulky acyl moieties at the N5 position and small alkyl groups at the N8 position are associated with affinity and selectivity at the A3 adenosine receptor even if a good affinity toward the A2B adenosine receptor has also been observed. Conversely, a free amino function at the 5 position induces high affinity at the A2A and A1 receptors with selectivity vs. the A3 subtype. A molecular modeling study suggests that differences in affinity toward A1, A2A, and A3 receptors could be ascribed to two residues: one in the EL2, E168 in human A2A/E172 in human A1, that is occupied by the hydrophobic residue V169 in the human A3 receptor; and the other in TM6, occupied by H250/H251 in human A2A and A1 receptors and by a less bulky S247 in the A3 receptor. In the end, these findings could help to design new subtype-selective adenosine receptor ligands.
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Affiliation(s)
- Veronica Salmaso
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, I-35131 Padova, Italy;
| | - Margherita Persico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
| | - Tatiana Da Ros
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
| | - Sonja Kachler
- Institut für Pharmakologie, Universität of Würzburg, Versbacher Str. 9, D-97078 Würzburg, Germany; (S.K.); (K.-N.K.)
| | - Karl-Norbert Klotz
- Institut für Pharmakologie, Universität of Würzburg, Versbacher Str. 9, D-97078 Würzburg, Germany; (S.K.); (K.-N.K.)
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, I-35131 Padova, Italy;
| | - Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
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2
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Bassani D, Pavan M, Sturlese M, Moro S. Sodium or Not Sodium: Should Its Presence Affect the Accuracy of Pose Prediction in Docking GPCR Antagonists? Pharmaceuticals (Basel) 2022; 15:ph15030346. [PMID: 35337144 PMCID: PMC8950631 DOI: 10.3390/ph15030346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
The function of the allosteric sodium ion in stabilizing the inactive form of GPCRs has been extensively described in the past decades. Its presence has been reported to be essential for the binding of antagonist molecules in the orthosteric site of these very important therapeutical targets. Among the GPCR–antagonist crystal structures available, in most cases, the sodium ion could not be experimentally resolved, obliging computational scientists using GPCRs as targets for virtual screening to ask: “Should the sodium ion affect the accuracy of pose prediction in docking GPCR antagonists?” In the present study, we examined the performance of three orthogonal docking programs in the self-docking of GPCR antagonists to try to answer this question. The results of the present work highlight that if the sodium ion is resolved in the crystal structure used as the target, it should also be taken into account during the docking calculations. If the crystallographic studies were not able to resolve the sodium ion then no advantage would be obtained if this is manually inserted in the virtual target. The outcomes of the present analysis are useful for researchers exploiting molecular docking-based virtual screening to efficiently identify novel GPCR antagonists.
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Thomas BN, Parrill AL, Baker DL. Self-docking and cross-docking simulations of G protein-coupled receptor-ligand complexes: Impact of ligand type and receptor activation state. J Mol Graph Model 2021; 112:108119. [PMID: 34979368 DOI: 10.1016/j.jmgm.2021.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/05/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022]
Abstract
G protein-coupled receptors (GPCR) are the largest family of cell surface receptors in vertebrates. Their abundance and role in nearly all physiological systems make GPCR the largest protein family targeted for development of pharmaceuticals. Ligand discovery aimed at identification of chemical tools and drug leads is aided by molecular docking simulations that allow critical analysis of the potential interactions between small molecules and proteins in resulting complexes. However, blind assessments of ligand pose quality and affinity prediction have thus far not provided broadly generalizable performance expectations for docking into experimentally-characterized GPCR targets. Likewise, the relative importance of receptor activation state and ligand function differences have also not been systematically assessed. This study compares performance when docking ligands of varied function into varied GPCR activation states in the absence of extensive resampling of the input GPCR structure, and only limited sidechain flexibility after ligand placement. Simulations were performed using 37 experimental structures of 11 Class A GPCR crystallized in multiple activation states (giving rise to 37 self-docking and 68 cross docking simulations). Our results show that one specific subset of cross-docking simulations gave results of similar quality to self-docking. Median ligand RMSD values for top-scored poses were 1.2 Å and 2.0 Å for self-docking and StateMatch/FunctionMatch cross-docking, respectively. The distributions of ligand RMSD values were not statistically different for these two conditions, according to a Kolmogorov-Smirnov test. Therefore, docking performance against GPCR targets can be estimated in advance based on docking target structure activation states, with higher accuracy expected when docking agonists into active state structures and inverse agonists or antagonists into inactive state structures. Receptor conformational sampling in advance of docking or receptor conformational adjustment after docking are more likely to produce substantial improvements for other pairings of receptor activation state and ligand function.
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Affiliation(s)
- Brittany N Thomas
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA
| | - Abby L Parrill
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA
| | - Daniel L Baker
- The University of Memphis, Department of Chemistry and Computational Research on Materials Institute (CROMIUM), USA.
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4
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Tiss A, Ben Boubaker R, Henrion D, Guissouma H, Chabbert M. Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom. Methods Mol Biol 2021; 2315:73-97. [PMID: 34302671 DOI: 10.1007/978-1-0716-1468-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With 700 members, G protein-coupled receptors (GPCRs) of the rhodopsin family (class A) form the largest membrane receptor family in humans and are the target of about 30% of presently available pharmaceutical drugs. The recent boom in GPCR structures led to the structural resolution of 57 unique receptors in different states (39 receptors in inactive state only, 2 receptors in active state only and 16 receptors in different activation states). In spite of these tremendous advances, most computational studies on GPCRs, including molecular dynamics simulations, virtual screening and drug design, rely on GPCR models obtained by homology modeling. In this protocol, we detail the different steps of homology modeling with the MODELLER software, from template selection to model evaluation. The present structure boom provides closely related templates for most receptors. If, in these templates, some of the loops are not resolved, in most cases, the numerous available structures enable to find loop templates with similar length for equivalent loops. However, simultaneously, the large number of putative templates leads to model ambiguities that may require additional information based on multiple sequence alignments or molecular dynamics simulations to be resolved. Using the modeling of the human bradykinin receptor B1 as a case study, we show how several templates are managed by MODELLER, and how the choice of template(s) and of template fragments can improve the quality of the models. We also give examples of how additional information and tools help the user to resolve ambiguities in GPCR modeling.
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Affiliation(s)
- Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.,Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
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5
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Federico S, Margiotta E, Moro S, Kozma E, Gao ZG, Jacobson KA, Spalluto G. Conjugable A 3 adenosine receptor antagonists for the development of functionalized ligands and their use in fluorescent probes. Eur J Med Chem 2019; 186:111886. [PMID: 31787357 DOI: 10.1016/j.ejmech.2019.111886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
Abstract
Compounds able to simultaneously bind a biological target and be conjugated to a second specific moiety are attractive tools for the development of multi-purpose ligands useful as multi-target ligands, receptor probes or drug delivery systems, with both therapeutic and diagnostic applications. The human A3 adenosine receptor is a G protein-coupled receptor involved in many physio-pathological conditions, e.g. cancer and inflammation, thus representing a promising research target. In this work, two series of conjugable hA3AR antagonists, based on the pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine nucleus, were developed. The introduction of an aromatic ring at the 5 position of the scaffold, before (phenylacetamido moiety) or after (1,2,3-triazole obtained by click chemistry) the conjugation is aimed to increase affinity and selectivity towards the hA3AR receptor. As expected, conjugable compounds showed good affinity towards the hA3AR. In order to prove their potential in the development of hA3AR ligands for different purposes, compounds were also functionalized with fluorescent probes. Unfortunately, conjugation decreased affinity and selectivity for the target as compared to the hA2AAR. Computational studies identified specific non-conserved residues of the extracellular loops which constitute a structural barrier able to discriminate between ligands, giving insights into the rational development of new highly selective ligands.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via Licio Giorgeri 1, 34127, Trieste, Italy.
| | - Enrico Margiotta
- Molecular Modeling Section (MMS), Dipartimento di Scienze Del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze Del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Eszter Kozma
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via Licio Giorgeri 1, 34127, Trieste, Italy
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6
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Bissaro M, Bolcato G, Deganutti G, Sturlese M, Moro S. Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A 2A Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations. Molecules 2019; 24:E2752. [PMID: 31362426 PMCID: PMC6695830 DOI: 10.3390/molecules24152752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
One of the most intriguing findings highlighted from G protein-coupled receptor (GPCR) crystallography is the presence, in many members of class A, of a partially hydrated sodium ion in the middle of the seven transmembrane helices (7TM) bundle. In particular, the human adenosine A2A receptor (A2A AR) is the first GPCR in which a monovalent sodium ion was crystallized in a distal site from the canonical orthosteric one, corroborating, from a structural point of view, its role as a negative allosteric modulator. However, the molecular mechanism by which the sodium ion influences the recognition of the A2A AR agonists is not yet fully understood. In this study, the supervised molecular dynamics (SuMD) technique was exploited to analyse the sodium ion recognition mechanism and how its presence influences the binding of the endogenous agonist adenosine. Due to a higher degree of flexibility of the receptor extracellular (EC) vestibule, we propose the sodium-bound A2A AR as less efficient in stabilizing the adenosine during the different steps of binding.
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Affiliation(s)
- Maicol Bissaro
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giovanni Bolcato
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Giuseppe Deganutti
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Mattia Sturlese
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Department of Pharmaceutical and Pharmacological Sciences, Molecular Modeling Section (MMS), University of Padova, via Marzolo 5, 35131 Padova, Italy.
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7
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Federico S, Margiotta E, Paoletta S, Kachler S, Klotz KN, Jacobson KA, Pastorin G, Moro S, Spalluto G. Pyrazolo[4,3- e][1,2,4]triazolo[1,5- c]pyrimidines to develop functionalized ligands to target adenosine receptors: fluorescent ligands as an example. MEDCHEMCOMM 2019; 10:1094-1108. [PMID: 31391881 PMCID: PMC6644567 DOI: 10.1039/c9md00014c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/16/2019] [Indexed: 01/07/2023]
Abstract
A series of adenosine receptor antagonists bearing a reactive linker was developed. Functionalization of these derivatives is useful to easily obtain multi-target ligands, receptor probes, drug delivery systems, and diagnostic or theranostic systems. The pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine scaffold was chosen as a pharmacophore for the adenosine receptors. It was substituted at the 5 position with reactive linkers of different lengths. Then, these compounds were used to synthesise probes for the adenosine receptors by functionalization with a fluorescent moiety. Both series of compounds were evaluated for their binding at the four adenosine receptor subtypes. Different affinity and selectivity profiles were observed towards hA1, hA2A and hA3 adenosine receptors. In particular, fluorescent compounds behave as dual hA2A/hA3 ligands. Computational studies suggested different binding modes for developed compounds at the three receptors. Both molecular docking and supervised molecular dynamics (SuMD) simulations confirmed that the preferred binding mode at the single receptor was driven by the substitution present at the 5 position. Obtained results rationalized the compounds' binding profile at the adenosine receptors and pave the way for the development of more potent conjugable and conjugated ligands targeting these membrane receptors.
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Affiliation(s)
- Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , Via Licio Giorgeri 1 , 34127 Trieste , Italy .
| | - Enrico Margiotta
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Silvia Paoletta
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Sonja Kachler
- Institut für Pharmakologie und Toxicologie , Universität Würzburg , Versbacher Straße 9 , 97078 Würzburg , Germany
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxicologie , Universität Würzburg , Versbacher Straße 9 , 97078 Würzburg , Germany
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry , National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892-0810 , USA
| | - Giorgia Pastorin
- Department of Pharmacy , National University of Singapore , 3 Science Drive 3 , 117543 Singapore
| | - Stefano Moro
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , Via Licio Giorgeri 1 , 34127 Trieste , Italy .
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