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Tosh D, Pavan M, Cronin C, Pottie E, Wan TC, Chen E, Lewicki SA, Campbell RG, Gao ZG, Auchampach JA, Stove CP, Liang BT, Jacobson KA. 2-Substituted (N)-Methanocarba A 3 Adenosine Receptor Agonists: In Silico, In Vitro, and In Vivo Characterization. ACS Pharmacol Transl Sci 2024; 7:2154-2173. [PMID: 39022354 PMCID: PMC11249627 DOI: 10.1021/acsptsci.4c00223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
2-Arylethynyl (N)-methanocarba adenosine 5'-methylamides are selective A3 adenosine receptor (AR) agonists containing a preestablished receptor-preferred pseudoribose conformation. Here, we compare analogues having bulky 2-substitution, either containing or lacking an ethynyl spacer between adenine and a cyclic group. 2-Aryl compounds 9-11, 13, 14, 19, 22, 23, 27, 29, 31, and 34, lacking a spacer, had human (h) A3AR K i values of 2-30 nM, and others displayed lower affinity. Mouse (m) A3AR affinity varied, with 2-arylethynyl having a higher affinity than 2-aryl analogues (7, 8 > 3c, 3d > 3b). However, 2-aryl-4'-truncated derivatives had greatly reduced hA3AR affinity, even containing affinity-enhancing N 6-dopamine-derived substituents. Molecular modeling, including molecular dynamics simulation, predicted stable poses in the canonical A3AR agonist binding site, but 2-aryl (ECL2 interactions) and 2-arylethynyl (TM2 interactions) substituents have different conformations and environments. In a hA3AR miniGαi recruitment assay, 31 (MRS8062) was (slightly) more potent compared to a β-arrestin2 recruitment assay, both in engineered HEK293T cells, and its maximal efficacy (E max) was much higher (165%) than reference agonist NECA's. Thus, in the 2-aryl series, A3AR affinity and selectivity were variable and generally reduced compared to the 2-arylethynyl series, with a greater dependence on the specific aryl group present. Selected compounds were studied in vivo in an ischemic model of peripheral artery disease (PAD). Rigidified 2-arylethynyl analogues 3a-3c were protective in this model of skeletal muscle ischemia-reperfusion injury/claudication, as previously shown only for moderately A3AR-selective ribosides or (N)-methanocarba derivatives. Thus, we have expanded the A3AR agonist SAR for (N)-methanocarba adenosines.
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Affiliation(s)
- Dilip
K. Tosh
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Matteo Pavan
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Chunxia Cronin
- Pat
and Jim Calhoun Cardiology Center, University
of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Eline Pottie
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg
460, B-9000 Ghent, Belgium
| | - Tina C. Wan
- Department
of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Eric Chen
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Sarah A. Lewicki
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Ryan G. Campbell
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - John A. Auchampach
- Department
of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Christophe P. Stove
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg
460, B-9000 Ghent, Belgium
| | - Bruce T. Liang
- Pat
and Jim Calhoun Cardiology Center, University
of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes and Digestive and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
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Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin. Biomolecules 2022; 12:biom12040584. [PMID: 35454173 PMCID: PMC9031165 DOI: 10.3390/biom12040584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and (S)-GTP, respectively. With dynamin as a model system, we examined the effects of (N)-GTP and (S)-GTP on dynamin-mediated membrane constriction, an activity essential for endocytosis. Dynamin membrane constriction and fission activity are dependent on GTP binding and hydrolysis, but the effect of the conformational state of the GTP nucleotide on dynamin activity is not known. After reconstituting dynamin-mediated lipid tubulation and membrane constriction in vitro, we observed via cryo-electron microscopy (cryo-EM) that (N)-GTP, but not (S)-GTP, enables the constriction of dynamin-decorated lipid tubules. These findings suggest that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, a survey of nucleotide ribose conformations associated with dynamin structures in nature shows almost exclusively the (S)-conformation. The explanation for this mismatch of (N) vs. (S) required for GTP analogues in a dynamin-mediated process will be addressed in future studies.
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Scortichini M, Idris RM, Moschütz S, Keim A, Salmaso V, Dobelmann C, Oliva P, Losenkova K, Irjala H, Vaittinen S, Sandholm J, Yegutkin GG, Sträter N, Junker A, Müller CE, Jacobson KA. Structure-Activity Relationship of 3-Methylcytidine-5'-α,β-methylenediphosphates as CD73 Inhibitors. J Med Chem 2022; 65:2409-2433. [PMID: 35080883 PMCID: PMC8865918 DOI: 10.1021/acs.jmedchem.1c01852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We recently reported N4-substituted 3-methylcytidine-5'-α,β-methylenediphosphates as CD73 inhibitors, potentially useful in cancer immunotherapy. We now expand the structure-activity relationship of pyrimidine nucleotides as human CD73 inhibitors. 4-Chloro (MRS4598 16; Ki = 0.673 nM) and 4-iodo (MRS4620 18; Ki = 0.436 nM) substitution of the N4-benzyloxy group decreased Ki by ∼20-fold. Primary alkylamine derivatives coupled through a p-amido group with a varying methylene chain length (24 and 25) were functionalized congeners, for subsequent conjugation to carrier or reporter moieties. X-ray structures of hCD73 with two inhibitors indicated a ribose ring conformational adaptation, and the benzyloxyimino group (E configuration) binds to the same region (between the C-terminal and N-terminal domains) as N4-benzyl groups in adenine inhibitors. Molecular dynamics identified stabilizing interactions and predicted conformational diversity. Thus, by N4-benzyloxy substitution, we have greatly enhanced the inhibitory potency and added functionality enabling molecular probes. Their potential as anticancer drugs was confirmed by blocking CD73 activity in tumor tissues in situ.
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Affiliation(s)
- Mirko Scortichini
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Riham Mohammed Idris
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Susanne Moschütz
- Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Antje Keim
- Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Clemens Dobelmann
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstrasse 15, D-48149 Münster, Germany
| | - Paola Oliva
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | | | - Heikki Irjala
- Department of Otorhinolaryngology-Head and Neck Surgery, Turku University Hospital and Turku University, 20520 Turku, Finland
| | - Samuli Vaittinen
- Department of Pathology, Turku University Hospital and Turku University, 20520 Turku, Finland
| | - Jouko Sandholm
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | | | - Norbert Sträter
- Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Anna Junker
- European Institute for Molecular Imaging (EIMI), University of Münster, Waldeyerstrasse 15, D-48149 Münster, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - 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, United States
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Jacobson KA, Salmaso V, Suresh RR, Tosh DK. Expanding the repertoire of methanocarba nucleosides from purinergic signaling to diverse targets. RSC Med Chem 2021; 12:1808-1825. [PMID: 34825182 PMCID: PMC8597424 DOI: 10.1039/d1md00167a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
Nucleoside derivatives are well represented as pharmaceuticals due to their druglike physicochemical properties, and some nucleoside drugs are designed to act on receptors. The purinergic signaling pathways for extracellular nucleosides and nucleotides, consisting of adenosine receptors, P2Y/P2X receptors for nucleotides, and enzymes such as adenosine (ribo)kinase, have been extensively studied. A general modification, i.e. a constrained, bicyclic ring system (bicyclo[3.1.0]hexane, also called methanocarba) substituted in place of a furanose ring, can increase nucleoside/nucleotide potency and/or selectivity at purinergic and antiviral targets and in interactions at diverse and unconventional targets. Compared to other common drug discovery scaffolds containing planar rings, methanocarba nucleosides display greater sp3 character (i.e. more favorable as drug-like molecules) and can manifest as sterically-constrained North (N) or South (S) conformations. Initially weak, off-target interactions of (N)-methanocarba adenosine derivatives were detected as leads that were structurally optimized to enhance activity and selectivity toward target proteins that normally do not recognize nucleosides. By this approach, novel modulators for 5HT2 serotonin and κ-opioid receptors, dopamine (DAT) and ATP-binding cassette (ABC) transporters were found, and previously undetected antiviral activities were revealed. Thus, through methanocarba nucleoside synthesis, structure-activity relationships, and multi-target pharmacology, a robust purinergic receptor scaffold has been repurposed to satisfy the pharmacophoric requirements of various GPCRs, enzymes and transporters.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
| | - Dilip K Tosh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health Bethesda MD 20892-0810 USA +301 480 8422 +301 496 9024
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Salmaso V, Jacobson KA. Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design. ChemMedChem 2020; 15:1958-1973. [PMID: 32803849 PMCID: PMC8276773 DOI: 10.1002/cmdc.202000465] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 12/16/2022]
Abstract
The purinergic signaling system includes membrane-bound receptors for extracellular purines and pyrimidines, and enzymes/transporters that regulate receptor activation by endogenous agonists. Receptors include: adenosine (A1 , A2A , A2B, and A3 ) and P2Y (P2Y1 , P2Y2 , P2Y4 , P2Y6 , P2Y11 , P2Y12 , P2Y13 , and P2Y14 ) receptors (all GPCRs), as well as P2X receptors (ion channels). Receptor activation, especially accompanying physiological stress or damage, creates a temporal sequence of signaling to counteract this stress and either mobilize (P2Rs) or suppress (ARs) immune responses. Thus, modulation of this large signaling family has broad potential for treating chronic diseases. Experimentally determined structures represent each of the three receptor families. We focus on selective purinergic agonists (A1 , A3 ), antagonists (A3 , P2Y14 ), and allosteric modulators (P2Y1 , A3 ). Examples of applying structure-based design, including the rational modification of known ligands, are presented for antithrombotic P2Y1 R antagonists and anti-inflammatory P2Y14 R antagonists and A3 AR agonists. A3 AR agonists are a potential, nonaddictive treatment for chronic neuropathic pain.
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Affiliation(s)
- Veronica Salmaso
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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