1
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Sangsuwan W, Taweesablamlert A, Boonkerd A, Isarangkool Na Ayutthaya C, Yoo S, Javid B, Faikhruea K, Vilaivan T, Aonbangkhen C, Chuawong P. A quest for novel antimicrobial targets: Inhibition of Asp-tRNA Asn/Glu-tRNA Gln amidotransferase (GatCAB) by synthetic analogs of aminoacyl-adenosine in vitro and live bacteria. Bioorg Chem 2024; 150:107530. [PMID: 38852310 DOI: 10.1016/j.bioorg.2024.107530] [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: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
The Asp-tRNAAsn/Glu-tRNAGln amidotransferase (GatCAB) has been proposed as a novel antibacterial drug target due to its indispensability in prominent human pathogens. While several inhibitors with in vitro activity have been identified, none have been demonstrated to have potent activity against live bacteria. In this work, seven non-hydrolyzable transition state mimics of GatCAB were synthesized and tested as the transamidase inhibitors against GatCAB from the human pathogen Helicobacter pylori. Notably, the methyl sulfone analog of glutamyl-adenosine significantly reduced GatCAB's transamination rate. Additionally, four lipid-conjugates of these mimics displayed antibacterial activity against Bacillus subtilis, likely due to enhanced cell permeability. Inhibitory activity against GatCAB in live bacteria was confirmed using a sensitive gain-of-function dual luciferase reporter in Mycobacterium bovis-BCG. Only the lipid-conjugated methyl sulfone analog exhibited a significant increase in mistranslation rate, highlighting its cell permeability and inhibitory potential. This study provides insights for developing urgently needed novel antibacterial agents amidst emerging antimicrobial drug resistance.
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Affiliation(s)
- Withsakorn Sangsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Amata Taweesablamlert
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Anon Boonkerd
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Chawarat Isarangkool Na Ayutthaya
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Sion Yoo
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Babak Javid
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand; Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Pitak Chuawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand.
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2
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Chen Y, Zhang J, Weng Y, Xu Y, Lu W, Liu W, Liu M, Hua T, Song G. Cryo-EM structure of the human adenosine A 2B receptor-G s signaling complex. SCIENCE ADVANCES 2022; 8:eadd3709. [PMID: 36563137 PMCID: PMC9788782 DOI: 10.1126/sciadv.add3709] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/22/2022] [Indexed: 06/03/2023]
Abstract
The human adenosine A2B receptor (A2BR) is a class A G protein-coupled receptor that is involved in several major physiological and pathological processes throughout the body. A2BR recognizes its ligands adenosine and NECA with relatively low affinity, but the detailed mechanism for its ligand recognition and signaling is still elusive. Here, we present two structures determined by cryo-electron microscopy of A2BR bound to its agonists NECA and BAY60-6583, each coupled to an engineered Gs protein. The structures reveal conserved orthosteric binding pockets with subtle differences, whereas the selectivity or specificity can mainly be attributed to regions extended from the orthosteric pocket. We also found that BAY60-6583 occupies a secondary pocket, where residues V2506.51 and N2737.36 were two key determinants for its selectivity against A2BR. This study offers a better understanding of ligand selectivity for the adenosine receptor family and provides a structural template for further development of A2BR ligands for related diseases.
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Affiliation(s)
- Ying Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jinyi Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuan Weng
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yueming Xu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiqiang Lu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gaojie Song
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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3
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Deganutti G, Barkan K, Preti B, Leuenberger M, Wall M, Frenguelli BG, Lochner M, Ladds G, Reynolds CA. Deciphering the Agonist Binding Mechanism to the Adenosine A1 Receptor. ACS Pharmacol Transl Sci 2021; 4:314-326. [PMID: 33615181 PMCID: PMC7887845 DOI: 10.1021/acsptsci.0c00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 12/21/2022]
Abstract
Despite being among the most characterized G protein-coupled receptors (GPCRs), adenosine receptors (ARs) have always been a difficult target in drug design. To date, no agonist other than the natural effector and the diagnostic regadenoson has been approved for human use. Recently, the structure of the adenosine A1 receptor (A1R) was determined in the active, Gi protein complexed state; this has important repercussions for structure-based drug design. Here, we employed supervised molecular dynamics simulations and mutagenesis experiments to extend the structural knowledge of the binding of selective agonists to A1R. Our results identify new residues involved in the association and dissociation pathway, they suggest the binding mode of N6-cyclopentyladenosine (CPA) related ligands, and they highlight the dramatic effect that chemical modifications can have on the overall binding mechanism, paving the way for the rational development of a structure-kinetics relationship of A1R agonists.
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Affiliation(s)
- Giuseppe Deganutti
- Centre
for Sport, Exercise and Life Sciences, Faculty of Health and Life
Sciences, Coventry University, Alison Gingell Building, Coventry CV1 5FB, U.K.
| | - Kerry Barkan
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, U.K.
| | - Barbara Preti
- Institute
of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Michele Leuenberger
- Institute
of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Mark Wall
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Bruno G. Frenguelli
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - Martin Lochner
- Institute
of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland
| | - Graham Ladds
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, U.K.
| | - Christopher A. Reynolds
- Centre
for Sport, Exercise and Life Sciences, Faculty of Health and Life
Sciences, Coventry University, Alison Gingell Building, Coventry CV1 5FB, U.K.
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4
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Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors. Molecules 2017; 22:molecules22111945. [PMID: 29125553 PMCID: PMC6150288 DOI: 10.3390/molecules22111945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
The four receptors that signal for adenosine, A1, A2A, A2B and A3 ARs, belong to the superfamily of G protein-coupled receptors (GPCRs). They mediate a number of (patho)physiological functions and have attracted the interest of the biopharmaceutical sector for decades as potential drug targets. The many crystal structures of the A2A, and lately the A1 ARs, allow for the use of advanced computational, structure-based ligand design methodologies. Over the last decade, we have assessed the efficient synthesis of novel ligands specifically addressed to each of the four ARs. We herein review and update the results of this program with particular focus on molecular dynamics (MD) and free energy perturbation (FEP) protocols. The first in silico mutagenesis on the A1AR here reported allows understanding the specificity and high affinity of the xanthine-antagonist 8-Cyclopentyl-1,3-dipropylxanthine (DPCPX). On the A2AAR, we demonstrate how FEP simulations can distinguish the conformational selectivity of a recent series of partial agonists. These novel results are complemented with the revision of the first series of enantiospecific antagonists on the A2BAR, and the use of FEP as a tool for bioisosteric design on the A3AR.
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5
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Pharmacological targeting of adenosine receptor signaling. Mol Aspects Med 2017; 55:4-8. [PMID: 28088486 DOI: 10.1016/j.mam.2016.12.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/22/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022]
Abstract
Adenosine receptor signaling plays important roles in normal physiology, but is also known to modulate the development or progression of several different diseases. The design of new, efficient, and safe pharmacological approaches to target the adenosine system may have considerable therapeutic potential, but is also associated with many challenges. This review summarizes the main challenges of adenosine receptor targeted treatment including tolerance, disease stage, cell type-specific effects, caffeine intake, adenosine level assessment and receptor distribution in vivo. Moreover, we discuss several potential ways to overcome these obstacles (i.e., the use of partial agonists, indirect receptor targeting, allosteric enhancers, prodrugs, non-receptor-mediated effects, neoreceptors, conditional knockouts). It is important to address these concerns during development of new and successful therapeutic approaches targeting the adenosine system.
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Thimm D, Schiedel AC, Sherbiny FF, Hinz S, Hochheiser K, Bertarelli DCG, Maass A, Müller CE. Ligand-specific binding and activation of the human adenosine A(2B) receptor. Biochemistry 2013; 52:726-40. [PMID: 23286920 DOI: 10.1021/bi3012065] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Adenosine A(2B) receptors, which play a role in inflammation and cancer, are of considerable interest as novel drug targets. To gain deeper insights into ligand binding and receptor activation, we exchanged amino acids predicted to be close to the binding pocket. The alanine mutants were stably expressed in CHO cells and characterized by radioligand binding and cAMP assays using three structural classes of ligands: xanthine (antagonist), adenosine, and aminopyridine derivatives (agonists). Asn282(7.45) and His280(7.43) were found to stabilize the binding site by intramolecular hydrogen bond formation as in the related A(2A) receptor subtype. Trp247(6.48), Val250(6.51), and particularly Ser279(7.42) were shown to be important for binding of nucleosidic agonists. Leu81(3.28), Asn186(5.42), and Val250(6.51) were discovered to be crucial for binding of the xanthine-derived antagonist PSB-603. Leu81(3.28), which is not conserved among adenosine receptor subtypes, may be important for the high selectivity of PSB-603. The N186(5.42)A mutant resulted in an increased potency for agonists. The interactions of the non-nucleosidic agonist BAY60-6583 were different from those of the nucleosides: while BAY60-6583 appeared not to interact with Ser279(7.42), its interactions with Trp247(6.48) and Val250(6.51) were significantly weaker compared to those of NECA. Moreover, our results discount the hypothesis of Trp247(6.48) serving as a "toogle switch" because BAY60-6583 was able to activate the corresponding mutant. This study reveals distinct interactions of structurally diverse ligands with the human A(2B) receptor and differences between closely related receptor subtypes (A(2B) and A(2A)). It will contribute to the understanding of G protein-coupled receptor function and advance A(2B) receptor ligand design.
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Affiliation(s)
- Dominik Thimm
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, 53121 Bonn, Germany
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7
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Abstract
The adenosine receptors (ARs) provide an example of how to accurately predict ligand recognition, even prior to the availability of a crystallographic structure. Homology modeling has been used to gain structural insight, in conjunction with site-directed mutagenesis, and structure-activity relationships of small molecular ligands. Recent X-ray structures greatly improved the accuracy of knowledge of AR ligand recognition and furthermore characterized conformational changes induced by receptor activation. Now, homology modeling extends these structural insights to related GPCRs and suggests new ligand structures. This strategy is also being applied to the eight subtypes of P2Y receptors for extracellular nucleotides, which lack X-ray structures and are best modeled by homology to the CXCR4 (peptide) receptor. Neoceptors, as studied for three of the four AR subtypes, create a molecular complementarity between a mutant receptor and a chemically tailored agonist ligand to selectively enhance affinity, implying direct physical contact and thus validating docking hypotheses.
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Affiliation(s)
- Kenneth A Jacobson
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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8
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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9
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Ivanov AA, Barak D, Jacobson KA. Evaluation of homology modeling of G-protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure. J Med Chem 2009; 52:3284-92. [PMID: 19402631 PMCID: PMC2720635 DOI: 10.1021/jm801533x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Homology modeling of the human A(2A) adenosine receptor (AR) based on bovine rhodopsin predicted a protein structure that was very similar to the recently determined crystallographic structure. The discrepancy between the experimentally observed orientation of the antagonist and those obtained by previous antagonist docking is related to the loop structure of rhodopsin being carried over to the model of the A(2A) AR and was rectified when the beta(2)-adrenergic receptor was used as a template for homology modeling. Docking of the triazolotriazine antagonist ligand ZM241385 1 was greatly improved by including water molecules of the X-ray structure or by using a constraint from mutagenesis. Automatic agonists docking to both a new homology modeled receptor and the A(2A) AR crystallographic structure produced similar results. Heterocyclic nitrogen atoms closely corresponded when the docked adenine moiety of agonists and 1 were overlaid. The cumulative mutagenesis data, which support the proposed mode of agonist docking, can be reexamined in light of the crystallographic structure. Thus, homology modeling of GPCRs remains a useful technique in probing the structure of the protein and predicting modes of ligand docking.
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Affiliation(s)
- Andrei A Ivanov
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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10
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Franchetti P, Cappellacci L, Vita P, Petrelli R, Lavecchia A, Kachler S, Klotz KN, Marabese I, Luongo L, Maione S, Grifantini M. N6-Cycloalkyl- and N6-Bicycloalkyl-C5′(C2′)-modified Adenosine Derivatives as High-Affinity and Selective Agonists at the Human A1 Adenosine Receptor with Antinociceptive Effects in Mice. J Med Chem 2009; 52:2393-406. [DOI: 10.1021/jm801456g] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Palmarisa Franchetti
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Loredana Cappellacci
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Patrizia Vita
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Riccardo Petrelli
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Antonio Lavecchia
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Sonja Kachler
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Karl-Norbert Klotz
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Ida Marabese
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Livio Luongo
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Sabatino Maione
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
| | - Mario Grifantini
- Department of Chemical Sciences, University of Camerino, 62032 Camerino, Italy, Department of Pharmaceutical and Toxicological Chemistry, University of Naples “Federico II”, 80131 Naples, Italy, Institut für Pharmakologie and Toxikologie, Universität Würzburg, D-97078 Würzburg, Germany, and Department of Experimental Medicine, Section of Pharmacology L. Donatelli, Second University of Naples, 80138 Naples, Italy
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11
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Ivanov AA, Jacobson KA. Molecular modeling of a PAMAM-CGS21680 dendrimer bound to an A2A adenosine receptor homodimer. Bioorg Med Chem Lett 2008; 18:4312-5. [PMID: 18639453 DOI: 10.1016/j.bmcl.2008.06.087] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 06/20/2008] [Accepted: 06/25/2008] [Indexed: 01/19/2023]
Abstract
The theoretical possibility of bivalent binding of a dendrimer, covalently appended with multiple copies of a small ligand, to a homodimer of a G protein-coupled receptor was investigated with a molecular modeling approach. A molecular model was constructed of a third generation (G3) poly(amidoamine) (PAMAM) dendrimer condensed with multiple copies of the potent A(2A) adenosine receptor agonist CGS21680. The dendrimer was bound to an A(2A) adenosine receptor homodimer. Two units of the nucleoside CGS21680 could occupy the A(2A) receptor homodimer simultaneously. The binding mode of CGS21680 moieties linked to the PAMAM dendrimer and docked to the A(2A) receptor was found to be similar to the binding mode of a monomeric CGS21680 ligand.
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Affiliation(s)
- Andrei A Ivanov
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Ko H, Carter RL, Cosyn L, Petrelli R, de Castro S, Besada P, Zhou Y, Cappellacci L, Franchetti P, Grifantini M, Van Calenbergh S, Harden TK, Jacobson KA. Synthesis and potency of novel uracil nucleotides and derivatives as P2Y2 and P2Y6 receptor agonists. Bioorg Med Chem 2008; 16:6319-32. [PMID: 18514530 PMCID: PMC2483329 DOI: 10.1016/j.bmc.2008.05.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/02/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
Abstract
The phosphate, uracil, and ribose moieties of uracil nucleotides were varied structurally for evaluation of agonist activity at the human P2Y(2), P2Y(4), and P2Y(6) receptors. The 2-thio modification, found previously to enhance P2Y(2) receptor potency, could be combined with other favorable modifications to produce novel molecules that exhibit high potencies and receptor selectivities. Phosphonomethylene bridges introduced for stability in analogues of UDP, UTP, and uracil dinucleotides markedly reduced potency. Truncation of dinucleotide agonists of the P2Y(2) receptor, in the form of Up(4)-sugars, indicated that a terminal uracil ring is not essential for moderate potency at this receptor and that specific SAR patterns are observed at this distal end of the molecule. Key compounds reported in this study include 9, alpha,beta-methylene-UDP, a P2Y(6) receptor agonist; 30, Up(4)-phenyl ester and 34, Up(4)-[1]glucose, selective P2Y(2) receptor agonists; dihalomethylene phosphonate analogues 16 and 41, selective P2Y(2) receptor agonists; 43, the 2-thio analogue of INS37217 (P(1)-(uridine-5')-P(4)-(2'-deoxycytidine-5')tetraphosphate), a potent and selective P2Y(2) receptor agonist.
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Affiliation(s)
- Hyojin Ko
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-0810, USA
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13
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Ivanov AA, Wang B, Klutz AM, Chen VL, Gao ZG, Jacobson KA. Probing distal regions of the A2B adenosine receptor by quantitative structure-activity relationship modeling of known and novel agonists. J Med Chem 2008; 51:2088-99. [PMID: 18321038 PMCID: PMC6540094 DOI: 10.1021/jm701442d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The binding modes at the A 2B adenosine receptor (AR) of 72 derivatives of adenosine and its 5'- N-methyluronamide with diverse substitutions at the 2 and N (6) positions were studied using a molecular modeling approach. The compounds in their receptor-docked conformations were used to build CoMFA and CoMSIA quantitative structure-activity relationship models. Various parameters, including different types of atomic charges, were examined. The best statistical parameters were obtained with a joint CoMFA and CoMSIA model: R (2) = 0.960, Q (2) = 0.676, SEE = 0.175, F = 158, and R (2) test = 0.782 for an independent test set containing 18 compounds. On the basis of the modeling results, four novel adenosine analogues, having elongated or bulky substitutions at N (6) position and/or 2 position, were synthesized and evaluated biologically. All of the proposed compounds were potent, full agonists at the A 2B AR in adenylate cyclase studies. Thus, in support of the modeling, bulky substitutions at both positions did not prevent A 2B AR activation, which predicts separate regions for docking of these moieties.
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Affiliation(s)
- Andrei A. Ivanov
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Ben Wang
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Athena M. Klutz
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Vincent L. Chen
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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