Identification of Adenosine Deaminase Inhibitors by Metal‐binding Pharmacophore Screening

Adamek, Rebecca N.; Ludford, Paul T.; Duggan, Stephanie M; Tor, Yitzhak; Cohen, Seth M.

doi:10.1002/cmdc.202000271

Cited by 9 publications

(6 citation statements)

References 38 publications

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“…The fenugreek QUE acts as a non-competitive inhibitor with a K i value of 55.5 mM. Moreover, the K i result is novel because there is no evidence in the literatures to compare the results with however, some studies are not consistent with our results (Singh and Sharma 2000 ; Adamek et al 2020 ; Kumar and Sharanya 2020 ; Kutryb-Zajac et al 2020 ). Thus, our results indicated that Egyptian Fenugreek QUE may act as a natural inhibitor of ADA which is a key inflammatory enzyme.…”

Section: Discussioncontrasting

confidence: 54%

Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats

El-Said

Atta

Mobasher

et al. 2022

Mol Med

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Rheumatoid arthritis (RA) is a chronic inflammatory joint disease characterized by synovial proliferation and bone destruction. Adenosine deaminase (ADA) is a key inflammatory enzyme that increases joint stiffness and pain in RA. In this study, we evaluated the in-silico, and in vivo inhibitory effect of quercetin isolated from Egyptian Fenugreek on ADA enzyme activity. We also determined the combinatorial effect of quercetin on methotrexate mediated anti-inflammatory efficacy and toxicity. In-silico molecular docking was conducted and confirmed in an in vivo RA rat model. The results showed that the inhibition constant of quercetin on joint ADA by docking and in-vitro was 61.9 and 55.5 mM, respectively. Therefore, quercetin exhibits anti-inflammatory effect in a rat RA model as evidenced by reducing the specific activity of ADA in joint tissues, lower jaw volume, enhance body weight, downregulate ADA gene expression, reduce levels of RA cytokines interleukin-1β, interleukin-6, tumor necrosis factor-α, also, rheumatoid factor, C-reactive protein, and anti-cyclic citrullinated peptide RA biomarker levels. These findings demonstrate that the purified quercetin has a promising anti-inflammatory effect against RA disease through its inhibitory effects on the ADA enzyme. Furthermore, isolated quercetin improved the anti-inflammatory efficacy of methotrexate, reduced its toxic effects by increasing antioxidant enzymes and reducing oxidative stress.

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Section: Discussioncontrasting

confidence: 54%

Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats

El-Said

Atta

Mobasher

et al. 2022

Mol Med

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“…The preparation of multiple emissive ADA substrates (Figure ), displaying distinct MM kinetics and photophysical parameters, facilitated the fabrication of a high-throughput assay for discovering inhibitors for this zinc enzyme . In collaboration with Seth Cohen’s laboratory, Paul Ludford had screened >300 metal-binding pharmacophores, identifying novel inhibitory motifs . In addition to metabolic A to I deamination, mRNA editing and tRNA maturation via adenosine deaminases acting on RNAs (ADARs) and adenosine deaminases acting on tRNAs (ADATs) involve similar transformations in distinct oligomeric contexts.…”

Section: Emissive Rna Alphabetsmentioning

confidence: 99%

“… 57 In collaboration with Seth Cohen’s laboratory, Paul Ludford had screened >300 metal-binding pharmacophores, identifying novel inhibitory motifs. 58 In addition to metabolic A to I deamination, mRNA editing and tRNA maturation via adenosine deaminases acting on RNAs (ADARs) and adenosine deaminases acting on tRNAs (ADATs) involve similar transformations in distinct oligomeric contexts. With Peter Beal, we evaluated the reactivity of ADAR2 with the th A-modified GluR B mRNA R/G editing site.…”

Section: Emissive Rna Alphabetsmentioning

confidence: 99%

Isomorphic Fluorescent Nucleosides

Tor

2024

Acc. Chem. Res.

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Conspectus 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 transf...

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“…We have advanced two emissive RNA alphabets, based on thieno[3,4- d ]pyrimidine (1st generation; th N ) and isothiazole[4,3- d ]pyrimidine (2nd generation; tz N ) heterocyclic cores (Figure a). The emissive adenosine analogs have been successfully used to advance real-time activity and inhibition assays of adenosine deaminase, exploiting the distinct emission profiles of the substrates ( th A and tz A ), and their corresponding deamination products ( th I and tz I , respectively), with the latter ( tz A ) being essentially isofunctional (Figure b). , The red-shifted absorption and visible-range emission of such fluorescent substrate surrogates opens a spectral window not accessible by other means, which facilitates the real-time monitoring of these reactions even in the presence of potentially interfering chromophores …”

Section: Introductionmentioning

confidence: 99%

“…32,33 The red-shifted absorption and visible-range emission of such fluorescent substrate surrogates opens a spectral window not accessible by other means, which facilitates the real-time monitoring of these reactions even in the presence of potentially interfering chromophores. 34 Applying such approaches to nucleobase-processing enzymes such as human GDA represents, however, a minimally explored territory, as highly emissive nucleobase analogs have not been broadly tested and scrutinized as substrates. 6,13 The lack of the rather large and contact forming D-ribose residue presents the challenge of altering guanine without disturbing contacts at the active site of such a potentially fastidious nucleobase-processing enzyme.…”

Section: ■ Introductionmentioning

confidence: 99%

Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog

Bucardo

Ludford

et al. 2021

ACS Chem. Biol.

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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, thG N , the isothiazolo guanine surrogate, tzG N , does undergo effective enzymatic deamination by GDA and yields the spectroscopically distinct xanthine analog, tzX N . 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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Identification of Adenosine Deaminase Inhibitors by Metal‐binding Pharmacophore Screening

Cited by 9 publications

References 38 publications

Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats

Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats

Isomorphic Fluorescent Nucleosides

Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog

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