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Molecules
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Nucleosides – Nucleotides – Oligonucleotides
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Nucleosides – Nucleotides – Oligonucleotides

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 August 2020) | Viewed by 18665

Special Issue Editors

Prof. Dr. Luigi A. Agrofoglio

E-Mail Website
Guest Editor
ICOA UMR CNRS 7311, Universite d\'Orleans, Rue de Chartres, 45067 Orleans, CEDEX 2, France
Interests: nucleoside and nucleotide analogues; heterocycles; infectious diseases, oncolytic virus; drug delivery system; (asymmetric)-organic synthesis; medicinal chemistry; synthetic methodologies; enzyme inhibitors
Dr. Vincent Roy

E-Mail Website
Guest Editor
ICOA UMR CNRS 7311, Universite d'Orleans, Rue de Chartres, 45067 Orleans, CEDEX 2, France
Interests: nucleoside and nucleotide analogues; heterocycles; infectious diseases, oncolytic virus; organic synthesis; medicinal chemistry
Dr. Cyril Nicolas

E-Mail Website
Guest Editor
Institut de Chimie Organique et Analytique UMR 7311, Université d’Orléans et CNRS. Rue de Chartres, BP 6759, 45067 Orléans cedex 2, France
Interests: new methods; organic synthesis; organometallic chemistry; carbohydrates; glycomimetics; iminosugar-C-glycosides; asymmetric synthesis; catalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will publish the latest developments in innovation-driven nucleos(t)ide and oligonucleotide chemistry, which deals with the new challenges of our century. These compounds are used not only as building blocks in the genetic code, but also as biosynthetic intermediates, energy donors, metabolic regulators, and cofactors in enzymatic processes. Thanks to the broad spectrum of their biological functions, they are identified as lead pharmaceutical anticancer, antiviral and antibacterial compounds for the treatment of metabolic and genetic diseases. Several nucleotide analogs and methylated nucleosides are also suitable for epigenetic modification analysis. They possess strong potential as future drugs, and an improved synthetic approach is an important target of the current research. New elegant and innovative organic, organometallic, and bio-oriented reactions have recently been developed for the synthesis of these complex, biologically-active compounds. This includes asymmetric synthesis, modern catalysis, C-H functionalization, olefin metathesis, gold-catalyzed reactions, and phosphorus chemistry.

The scope of this Special Issue is to bring together reviews, original research articles and short communications covering all current aspects of the design, synthesis and characterization of both small molecules (nucleoside analogues) and oligomers from innovative synthesis to potential therapeutic applications, e.g. the discovery and development of anticancer and anti-infectious drugs, small molecule recognition of DNA and RNA, backbone-modified oligonucleotides and DNA repair, and fluorescent imaging agents.

Prof. Luigi A. Agrofoglio
Dr. Vincent Roy
Dr. Cyril Nicolas
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Nucleoside and nucleotide analogues
  • Nucleoside natural products
  • Nucleotide signaling molecules
  • Oligonucleotides for therapeutic applications and biotechnology
  • Carbasugars
  • Iminosugars
  • Innovation-driven chemistry

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Published Papers (4 papers)

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Research

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21 pages, 8323 KiB  
Article
Design and Synthesis of Various 5′-Deoxy-5′-(4-Substituted-1,2,3-Triazol-1-yl)-Uridine Analogues as Inhibitors of Mycobacterium tuberculosis Mur Ligases
by Vincent Hervin, Ritu Arora, Jyoti Rani, Srinivasan Ramchandran, Urmi Bajpai, Luigi A. Agrofoglio and Vincent Roy
Molecules 2020, 25(21), 4953; https://doi.org/10.3390/molecules25214953 - 26 Oct 2020
Cited by 10 | Viewed by 2687
Abstract
The synthesis of hitherto unknown 5′-deoxy-5′-(4-substituted-1,2,3-triazol-1-yl)-uridine and its evaluation, through an one-pot screening assay, against MurA-F enzymes involved in Mycobacterium tuberculosis (Mtb), are described. Starting from UDP-N-acetylmuramic acid (UDP-MurNAc), the natural substrate involved in the peptidoglycan biosynthesis, our strategy was to [...] Read more.
The synthesis of hitherto unknown 5′-deoxy-5′-(4-substituted-1,2,3-triazol-1-yl)-uridine and its evaluation, through an one-pot screening assay, against MurA-F enzymes involved in Mycobacterium tuberculosis (Mtb), are described. Starting from UDP-N-acetylmuramic acid (UDP-MurNAc), the natural substrate involved in the peptidoglycan biosynthesis, our strategy was to substitute the diphosphate group of UDP-MurNAc by a 1,2,3-triazolo spacer under copper-catalyzed azide-alkyne cycloaddition conditions. The structure-activity relationship was discussed and among the 23 novel compounds developed, N-acetylglucosamine analogues 11c and 11e emerged as the best inhibitors against the Mtb MurA-F enzymes reconstruction pathway with an inhibitory effect of 56% and 50%, respectively, at 100 μM. Both compounds are selective inhibitors of Mtb MurE, the molecular docking and molecular dynamic simulation suggesting that 11c and 11e are occupying the active site of Mtb MurE ligase. Full article
(This article belongs to the Special Issue Nucleosides – Nucleotides – Oligonucleotides)
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18 pages, 3324 KiB  
Article
Tri-Cyclic Nucleobase Analogs and Their Ribosides as Substrates of Purine-Nucleoside Phosphorylases. II Guanine and Isoguanine Derivatives
by Alicja Stachelska-Wierzchowska, Jacek Wierzchowski, Michał Górka, Agnieszka Bzowska and Beata Wielgus-Kutrowska
Molecules 2019, 24(8), 1493; https://doi.org/10.3390/molecules24081493 - 16 Apr 2019
Cited by 12 | Viewed by 3386
Abstract
Etheno-derivatives of guanine, O6-methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,N2-etheno-guanine and [...] Read more.
Etheno-derivatives of guanine, O6-methylguanine, and isoguanine were prepared and purified using standard methods. The title compounds were examined as potential substrates of purine-nucleoside phosphorylases from various sources in the reverse (synthetic) pathway. It was found that 1,N2-etheno-guanine and 1,N6-etheno-isoguanine are excellent substrates for purine-nucleoside phosphorylase (PNP) from E. coli, while O6-methyl-N2,3-etheno-guanine exhibited moderate activity vs. this enzyme. The latter two compounds displayed intense fluorescence in neutral aqueous medium, and so did the corresponding ribosylation products. By contrast, PNP from calf spleens exhibited only modest activity towards 1,N6-etheno-isoguanine; the remaining compounds were not ribosylated by this enzyme. The enzymatic ribosylation of 1,N6-etheno-isoguanine using two forms of calf PNP (wild type and N243D) and E. coli PNP (wild type and D204N) gave three different products, which were identified on the basis of NMR analysis and comparison with the product of the isoguanosine reaction with chloroacetic aldehyde, which gave an essentially single compound, identified unequivocally as N9-riboside. With the wild-type E. coli enzyme as a catalyst, N9-β-d- and N7-β-d-ribosides are obtained in proportion ~1:3, while calf PNP produced another riboside, tentatively identified as N6-β-d-riboside. The potential application of various forms of PNP for synthesis of the tri-cyclic nucleoside analogs is discussed. Full article
(This article belongs to the Special Issue Nucleosides – Nucleotides – Oligonucleotides)
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Review

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23 pages, 3498 KiB  
Review
Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides
by Steven Ochoa and Valeria T. Milam
Molecules 2020, 25(20), 4659; https://doi.org/10.3390/molecules25204659 - 13 Oct 2020
Cited by 67 | Viewed by 6537
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome [...] Read more.
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides. Full article
(This article belongs to the Special Issue Nucleosides – Nucleotides – Oligonucleotides)
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24 pages, 1308 KiB  
Review
Therapeutic Perspectives of Adenosine Deaminase Inhibition in Cardiovascular Diseases
by Barbara Kutryb-Zajac, Paulina Mierzejewska, Ewa M. Slominska and Ryszard T. Smolenski
Molecules 2020, 25(20), 4652; https://doi.org/10.3390/molecules25204652 - 12 Oct 2020
Cited by 37 | Viewed by 5458
Abstract
Adenosine deaminase (ADA) is an enzyme of purine metabolism that irreversibly converts adenosine to inosine or 2′deoxyadenosine to 2′deoxyinosine. ADA is active both inside the cell and on the cell surface where it was found to interact with membrane proteins, such as CD26 [...] Read more.
Adenosine deaminase (ADA) is an enzyme of purine metabolism that irreversibly converts adenosine to inosine or 2′deoxyadenosine to 2′deoxyinosine. ADA is active both inside the cell and on the cell surface where it was found to interact with membrane proteins, such as CD26 and adenosine receptors, forming ecto-ADA (eADA). In addition to adenosine uptake, the activity of eADA is an essential mechanism that terminates adenosine signaling. This is particularly important in cardiovascular system, where adenosine protects against endothelial dysfunction, vascular inflammation, or thrombosis. Besides enzymatic function, ADA protein mediates cell-to-cell interactions involved in lymphocyte co-stimulation or endothelial activation. Furthermore, alteration in ADA activity was demonstrated in many cardiovascular pathologies such as atherosclerosis, myocardial ischemia-reperfusion injury, hypertension, thrombosis, or diabetes. Modulation of ADA activity could be an important therapeutic target. This work provides a systematic review of ADA activity and anchoring inhibitors as well as summarizes the perspectives of their therapeutic use in cardiovascular pathologies associated with increased activity of ADA. Full article
(This article belongs to the Special Issue Nucleosides – Nucleotides – Oligonucleotides)
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