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Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
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Affiliation(s)
- 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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Ping L, Ruxian J, Mengping Z, Pei J, Zhuoya L, Guosheng L, Zhenyu W, Hailei W. Whole-cell biosynthesis of cytarabine by an unnecessary protein-reduced Escherichia coli that coexpresses purine and uracil phosphorylase. Biotechnol Bioeng 2022; 119:1768-1780. [PMID: 35383880 DOI: 10.1002/bit.28098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/10/2022]
Abstract
Currently, whole-cell catalysts face challenges due to the complexity of reaction systems, although they have a cost advantage over pure enzymes. In this work, cytarabine was synthesized by purified purine phosphorylase 1 (PNP1) and uracil phosphorylase (UP), and the conversion of cytarabine from adenine arabinoside reached 72.3±4.3%. However, the synthesis was unsuccessful by whole-cell catalysis due to interference from unnecessary proteins (UNPs) in cells. Thus, we carried out a large-scale gene editing involving 377 genes in the genome of Escherichia coli to reduce the negative effect of UNPs on substrate conversion and cytarabine production. Finally, the PNP1 and UP activities of the obtained mutant were increased significantly compared with the parental strain, and more importantly, the conversion rate of cytarabine by whole-cell catalysis reached 67.4±2.5%. The lack of 148 proteins and down-regulation of 783 proteins caused by gene editing were equivalent to partial purification of the enzymes within cells, and thus, we provided inspiration to solve the problem caused by UNP interference, which is ubiquitous in the field of whole-cell catalysis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Li Ping
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Jing Ruxian
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Zhou Mengping
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Jia Pei
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Li Zhuoya
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Liu Guosheng
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Wang Zhenyu
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China
| | - Wang Hailei
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes,College of Life Science, Henan Normal University, Xinxiang, 453007, China.,Advanced Environmental Biotechnology Center, Nanyang Technological University, Singapore, 637141, Singapore
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Ludford P, Yang S, Bucardo MS, Tor Y. A New Variant of Emissive RNA Alphabets. Chemistry 2022; 28:e202104472. [PMID: 35018663 PMCID: PMC8891053 DOI: 10.1002/chem.202104472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 12/15/2022]
Abstract
A new fluorescent ribonucleoside alphabet (mth N) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (th N) and isothiazole[4,3-d]pyrimidine (tz N) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding mth N/mth NTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the mth N alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.
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Affiliation(s)
- Paul Ludford
- University of California San Diego, Chemistry and Biochemistry, UNITED STATES
| | - Shenghua Yang
- University of California San Diego, Chemistry and Biochemistry, UNITED STATES
| | - Marcela S Bucardo
- University of California San Diego, Chemistry and Biochemistry, UNITED STATES
| | - Yitzhak Tor
- University of California, San Diego, Department of Chemistry and Biochemistry, 9500 Gilman Drive, MC 0358, 92093-0358, La Jolla, UNITED STATES
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Ludford PT, Li Y, Yang S, Tor Y. Cytidine deaminase can deaminate fused pyrimidine ribonucleosides. Org Biomol Chem 2021; 19:6237-6243. [PMID: 34019616 PMCID: PMC8295196 DOI: 10.1039/d1ob00705j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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] [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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Stachelska-Wierzchowska A, Wierzchowski J. Non-typical nucleoside analogs as fluorescent and fluorogenic indicators of purine-nucleoside phosphorylase activity in biological samples. Anal Chim Acta 2020; 1139:119-128. [PMID: 33190694 DOI: 10.1016/j.aca.2020.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Affiliation(s)
- A Stachelska-Wierzchowska
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 4 Oczapowskiego St., PL-10-710, Olsztyn, Poland.
| | - J Wierzchowski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 4 Oczapowskiego St., PL-10-710, Olsztyn, Poland.
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Adamek RN, Ludford P, Duggan SM, Tor Y, Cohen SM. Identification of Adenosine Deaminase Inhibitors by Metal-binding Pharmacophore Screening. ChemMedChem 2020; 15:2151-2156. [PMID: 32729197 DOI: 10.1002/cmdc.202000271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Adenosine deaminase (ADA) is a human mononuclear Zn2+ metalloenzyme that converts adenosine to inosine. ADA is a validated drug target for cancer, but there has been little recent work on the development of new therapeutics against this enzyme. The lack of new advancements can be partially attributed to an absence of suitable assays for high-throughput screening (HTS) against ADA. To facilitate more rapid drug discovery efforts for this target, an in vitro assay was developed that utilizes the enzymatic conversion of a visibly emitting adenosine analogue to the corresponding fluorescent inosine analogue by ADA, which can be monitored via fluorescence intensity changes. Utilizing this assay, a library of ∼350 small molecules containing metal-binding pharmacophores (MBPs) was screened in an HTS format to identify new inhibitor scaffolds against ADA. This approach yielded a new metal-binding scaffold with a Ki value of 26±1 μM.
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Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Paul Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Stephanie M Duggan
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego La Jolla, CA 92093, USA
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Ludford PT, Tor Y. Ascertaining the activity and inhibition of adenosine deaminase via fluorescence-based assays. Methods Enzymol 2020; 639:71-90. [PMID: 32475413 DOI: 10.1016/bs.mie.2020.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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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