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Molecules
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Chemistry of Nucleosides and Nucleotides and Their Analogues
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Chemistry of Nucleosides and Nucleotides and Their Analogues

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 5860

Special Issue Editors

Dr. Stefano D’Errico

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Guest Editor
Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
Interests: nucleosides; nucleotides and analogues; chemistry and biological/biotechnological applications; oligonucleotides; platinum complexes in cancer therapy
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Nicola Borbone

E-Mail Website
Guest Editor
Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
Interests: nucleic acid chemistry and biology; DNA quadruplexes formed by telomers, aptamers, and synthetic G-rich oligonucleotides; chemical-physical characterization of soft interfaces; hybrid interfaces; therapeutics; diagnostics
Special Issues, Collections and Topics in MDPI journals
Dr. Andrea Patrizia Falanga

E-Mail Website
Guest Editor
Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
Interests: peptide nucleic acid; G-quadruplex; delivery; solid-phase synthesis; small molecule-DNA interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The importance of nucleosides and nucleotides in medicinal chemistry is widely recognized. In recent years, there has been a growing interest in the synthesis of modified compounds and analogues, particularly considering the COVID-19 pandemic. Besides their role as antimetabolites, these compounds serve as essential building blocks for constructing oligonucleotides (ODNs), which have applications as bio-probes and in the development of new materials. Precise modifications of heterocyclic bases and/or sugar-phosphate backbones can yield cutting-edge scaffolds that offer insights into unknown molecular mechanisms and enhance our understanding of the properties of ODNs. The aim of this Special Issue is to explore the key aspects related to the design and synthesis of novel nucleosides, nucleotides, and analogues, along with their potential applications in relevant fields. We welcome original research and reviews focusing on these topics.

Dr. Stefano D’Errico
Prof. Dr. Nicola Borbone
Dr. Andrea Patrizia Falanga
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • nucleosides, nucleotides, and nucleic acids
  • modified nucleosides and nucleotides
  • nucleoside and nucleotide analogues
  • antimetabolites
  • oligonucleotides
  • organic synthesis
  • bioorganic chemistry
  • medicinal chemistry

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Published Papers (2 papers)

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Review

29 pages, 5564 KiB  
Review
Synthesis and Properties of α-Phosphate-Modified Nucleoside Triphosphates
by Alina I. Novgorodtseva, Alexander A. Lomzov and Svetlana V. Vasilyeva
Molecules 2024, 29(17), 4121; https://doi.org/10.3390/molecules29174121 - 30 Aug 2024
Viewed by 1964
Abstract
This review article is focused on the progress made in the synthesis of 5′-α-P-modified nucleoside triphosphates (α-phosphate mimetics). A variety of α-P-modified nucleoside triphosphates (NTPαXYs, Y = O, S; X = S, Se, BH3, alkyl, amine, N-alkyl, imido, or others) have [...] Read more.
This review article is focused on the progress made in the synthesis of 5′-α-P-modified nucleoside triphosphates (α-phosphate mimetics). A variety of α-P-modified nucleoside triphosphates (NTPαXYs, Y = O, S; X = S, Se, BH3, alkyl, amine, N-alkyl, imido, or others) have been developed. There is a unique class of nucleoside triphosphate analogs with different properties. The main chemical approaches to the synthesis of NTPαXYs are analyzed and systematized here. Using the data presented here on the diversity of NTPαXYs and their synthesis protocols, it is possible to select an appropriate method for obtaining a desired α-phosphate mimetic. Triphosphates’ substrate properties toward nucleic acid metabolism enzymes are highlighted too. We reviewed some of the most prominent applications of NTPαXYs including the use of modified dNTPs in studies on mechanisms of action of polymerases or in systematic evolution of ligands by exponential enrichment (SELEX). The presence of heteroatoms such as sulfur, selenium, or boron in α-phosphate makes modified triphosphates nuclease resistant. The most distinctive feature of NTPαXYs is that they can be recognized by polymerases. As a result, S-, Se-, or BH3-modified phosphate residues can be incorporated into DNA or RNA. This property has made NTPαXYs a multifunctional tool in molecular biology. This review will be of interest to synthetic chemists, biochemists, biotechnologists, or biologists engaged in basic or applied research. Full article
(This article belongs to the Special Issue Chemistry of Nucleosides and Nucleotides and Their Analogues)
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21 pages, 2548 KiB  
Review
A Visual Compendium of Principal Modifications within the Nucleic Acid Sugar Phosphate Backbone
by Daria Novikova, Aleksandra Sagaidak, Svetlana Vorona and Vyacheslav Tribulovich
Molecules 2024, 29(13), 3025; https://doi.org/10.3390/molecules29133025 - 26 Jun 2024
Cited by 3 | Viewed by 3253
Abstract
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of [...] Read more.
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics. Full article
(This article belongs to the Special Issue Chemistry of Nucleosides and Nucleotides and Their Analogues)
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