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Cong D, Li Y, Ludford PT, Tor Y. Isomorphic Fluorescent Nucleosides Facilitate Real‐Time Monitoring of RNA Depurination by Ribosome Inactivating Proteins. Chemistry 2022; 28:e202200994. [DOI: 10.1002/chem.202200994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 12/20/2022]
Affiliation(s)
- Deyuan Cong
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Yao Li
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Paul T. Ludford
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Abstract
The tolerance of cytidine deaminase (CDA) to expanded heterocycles is explored via three fluorescent cytidine analogues, where the pyrimidine core is fused to three distinct five-membered heterocycles at the 5/6 positions. The reaction between CDA and each analogue is followed by absorption and emission spectroscopy, revealing shorter reaction times for all analogues than the native substrate. Pseudo-first order and Michaelis-Menten kinetic analyses provide insight into the enzymatic deamination reactions and assist in drawing comparison to established structure activity relationships. Finally, inhibitor screening modalities are created for each analogue and validated with zebularine and tetrahydrouridine, two known CDA inhibitors.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | - Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | - Shenghua Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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Bucardo MS, Wu Y, Ludford PT, Li Y, Fin A, Tor Y. Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog. ACS Chem Biol 2021; 16:1208-1214. [PMID: 34190533 DOI: 10.1021/acschembio.1c00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Guanine deaminase (GDA) deaminates guanine to xanthine. Despite its significance, the study of human GDA remains limited compared to other metabolic deaminases. As a result, its substrate and inhibitor repertoire are limited, and effective real-time activity, inhibitory, and discovery assays are missing. Herein, we explore two emissive heterocyclic cores, based on thieno[3,4-d]pyrimidine (thN) and isothiazole[4,3-d]pyrimidine (tzN), as surrogate GDA substrates. We demonstrate that, unlike the thieno analog, thGN, the isothiazolo guanine surrogate, tzGN, does undergo effective enzymatic deamination by GDA and yields the spectroscopically distinct xanthine analog, tzXN. Further, we showcase the potential of this fluorescent nucleobase surrogate to provide a visible spectral window for a real-time study of GDA and its inhibition.
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Affiliation(s)
- Marcela S. Bucardo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - You Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul T. Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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Abstract
Bacterial cyclic dinucleotides (CDNs) play important roles in regulating biofilm formation, motility and virulence. In eukaryotic cells, theses bacterial CDNs are recognized as pathogen-associated molecular patterns (PAMPs) and trigger an innate immune response. We report the photophysical analyses of a novel group of enzymatically synthesized emissive CDN analogues comprised of two families of isomorphic ribonucleotides. The highly favorable photophysical features of the CDN analogues, when compared to their non-emissive natural counterparts, are used to monitor in real time the dinucleotide cyclase-mediated synthesis and phosphodiesterase (PDE)-mediated hydrolysis of homodimeric and mixed CDNs, providing effective means to probe the activities of two classes of bacterial enzymes and insight into their biomolecular recognition and catalytic features.
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Affiliation(s)
- Yao Li
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Paul T Ludford
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
- Dipartimento di Scienza e Tecnologia del Farmaco, University of Turin, Via P. Giuria 9, 10125, Turin, Italy
| | - Alexander R Rovira
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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Abstract
A fluorescence-based assay for adenosine deaminase (ADA) activity and inhibition, which may also be formatted as an inhibitor discovery assay, is described. It relies on differences in fluorescence between an isothiazolo-based adenosine analogs (tzA) and its deaminated product, the corresponding inosine derivative (tzI), which facilitates a real-time monitoring of enzymatic activity. Inhibitors are added to the enzyme-substrate reaction mixture at various concentrations and the fluorescence signal is recorded over 10min. The percent inhibition is calculated from the signal change at 10min relative to the uninhibited reaction. The percent inhibition is plotted against inhibitor concentration and fitted to a Hill curve. IC50 values are then calculated.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States.
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Beck KM, Krogh MB, Hornum M, Ludford PT, Tor Y, Nielsen P. Double-headed nucleotides as xeno nucleic acids: information storage and polymerase recognition. Org Biomol Chem 2020; 18:7213-7223. [PMID: 32909574 DOI: 10.1039/d0ob01426e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Xeno nucleic acids (XNAs) are artificial genetic systems based on sugar-modified nucleotides. Herein, we investigate double-headed nucleotides as a new XNA. A new monomer, AT, is presented, and together with previous double-headed nucleotide monomers, new nucleic acid motifs consisting of up to five consecutive A·T base pairs have been obtained. Sections composed entirely of double-headed nucleotides are well-tolerated within a DNA duplex and can condense the genetic information. For instance, a 13-mer duplex is condensed to an 11-mer modified duplex containing four double-headed nucleotides while simultaneously improving duplex thermal stability with +14.0 °C. Also, the transfer of information from double-headed to natural nucleotides by DNA polymerases has been examined. The first double-headed nucleoside triphosphate was prepared but could not be recognized and incorporated by the tested DNA polymerases. On the other hand, it proved possible for Therminator DNA polymerase to transfer the information of a double-headed nucleotide in a template sequence to natural DNA under controlled conditions.
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Affiliation(s)
- Kasper M Beck
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Marie B Krogh
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Mick Hornum
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
| | - Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Poul Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark.
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Ludford PT, Rovira AR, Fin A, Tor Y. Front Cover: Fluorescing Isofunctional Ribonucleosides: Assessing Adenosine Deaminase Activity and Inhibition (ChemBioChem 5/2019). Chembiochem 2019. [DOI: 10.1002/cbic.201900080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Paul T. Ludford
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Alexander R. Rovira
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Ludford PT, Rovira AR, Fin A, Tor Y. Fluorescing Isofunctional Ribonucleosides: Assessing Adenosine Deaminase Activity and Inhibition. Chembiochem 2019; 20:718-726. [PMID: 30566279 DOI: 10.1002/cbic.201800665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/12/2022]
Abstract
The enzymatic conversion of isothiazolo[4,3-d]pyrimidine-based adenosine (tz A) and 2-aminoadenosine (tz 2-AA) analogues to the corresponding isothiazolo[4,3-d]pyrimidine-based inosine (tz I) and guanosine (tz G) derivatives is evaluated and compared to the conversion of native adenosine to inosine. Henri-Michaelis-Menten analyses provides the foundation for a high-throughput screening assay, and the efficacy of the assay is showcased by fluorescence-based analysis of tz A conversion to tz I in the presence of known and newly synthesized inhibitors.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Alexander R Rovira
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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