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Novotná B, Vaneková L, Zavřel M, Buděšínský M, Dejmek M, Smola M, Gutten O, Tehrani ZA, Pimková Polidarová M, Brázdová A, Liboska R, Štěpánek I, Vavřina Z, Jandušík T, Nencka R, Rulíšek L, Bouřa E, Brynda J, Páv O, Birkuš G. Enzymatic Preparation of 2'-5',3'-5'-Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations. J Med Chem 2019; 62:10676-10690. [PMID: 31715099 DOI: 10.1021/acs.jmedchem.9b01062] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cyclic dinucleotides are second messengers in the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, which plays an important role in recognizing tumor cells and viral or bacterial infections. They bind to the STING adaptor protein and trigger expression of cytokines via TANK binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) and inhibitor of nuclear factor-κB (IκB) kinase (IKK)/nuclear factor-κB (NFκB) signaling cascades. In this work, we describe an enzymatic preparation of 2'-5',3'-5'-cyclic dinucleotides (2'3'CDNs) with use of cyclic GMP-AMP synthases (cGAS) from human, mouse, and chicken. We profile substrate specificity of these enzymes by employing a small library of nucleotide-5'-triphosphate (NTP) analogues and use them to prepare 33 2'3'CDNs. We also determine affinity of these CDNs to five different STING haplotypes in cell-based and biochemical assays and describe properties needed for their optimal activity toward all STING haplotypes. Next, we study their effect on cytokine and chemokine induction by human peripheral blood mononuclear cells (PBMCs) and evaluate their cytotoxic effect on monocytes. Additionally, we report X-ray crystal structures of two new CDNs bound to STING protein and discuss structure-activity relationship by using quantum and molecular mechanical (QM/MM) computational modeling.
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Affiliation(s)
- Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Lenka Vaneková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Zahra Aliakbar Tehrani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Markéta Pimková Polidarová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Andrea Brázdová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ivan Štěpánek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Food and Biochemical Technology , University of Chemistry and Technology , Prague 166 28 , Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
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Šimák O, Pachl P, Fábry M, Buděšínský M, Jandušík T, Hnízda A, Skleničková R, Petrová M, Veverka V, Řezáčová P, Brynda J, Rosenberg I. Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-nucleotidases. Org Biomol Chem 2014; 12:7971-82. [DOI: 10.1039/c4ob01332h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-deoxynucleotidases.
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Affiliation(s)
- Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
- 14220 Prague 4, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Department of Chemistry of Natural Compounds
- Institute of Chemical Technology
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Radka Skleničková
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
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