Design, Synthesis, and Evaluation of Nucleobase, Nucleoside, and Nucleotide Analogues

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Biopharmaceuticals".

Deadline for manuscript submissions: closed (25 February 2025) | Viewed by 12756

Special Issue Editor

Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
Interests: Enzyme activity and inhibition; structural and chemical biology; computational chemistry; machine learning; medicinal chemistry

Special Issue Information

Dear Colleagues,

Since the initial approval of cytarabine, a cytidine analogue, in 1969 by US Food and Drug Administration to treat acute myeloid leukemia, numerous analogues and derivatives of nucleobases, nucleosides, and nucleotides have been developed as anticancer and antiviral agents. Notable examples include 5-fluorouracil, a uracil analogue, for the treatment of various cancers; tenofovir, an analogue of deoxyadenosine 5'-monophosphate, for the treatment of chronic hepatitis B; and most recently, molnupiravir, a cytidine analogue, for the treatment of COVID-19. Not only can such analogues and derivatives be incorporated into nucleic acids, but they can also act on enzymes such as polymerases, kinases, and other transferases thanks to their structural mimicry of the endogenous substrate, cofactor, and/or modulator, expanding their therapeutic potential beyond cancer and viral infections.  

However, the emergence of novel nucleot(s)ide-recognizing therapeutic targets in recent years requires new nucleot(s)ide-mimicking probes and/or drugs, while there are issues of drug resistance, toxicity, and oral bioavailability for many existing analogues of nucleobases, nucleosides, and nucleotides. Therefore, the development of new agents and the examination of their biological effects are needed. 

This Special Issue aims to collect research articles and reviews on the design, (bio)synthesis, and biological evaluation of analogues and derivatives of nucleobases, nucleosides, and nucleotides. Structural and functional investigations of endogenous nucleot(s)ides, including dinucleotides and oligonucleotides, are also welcome. In addition, contributions of computational studies on such analogues and derivatives are highly encouraged.

Dr. Yun Shi
Guest Editor

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Keywords

  • nucleobase
  • nucleoside
  • nucleotide
  • drug design
  • structural mimicry
  • enzyme inhibitors
  • anticancer agents
  • antivirals

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Published Papers (2 papers)

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Research

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14 pages, 2788 KiB  
Article
The Synergistic Effect of N2 and N7 Modifications on the Inhibitory Efficacy of mRNA Cap Analogues
by Karol Kurpiejewski, Karolina Piecyk, Maciej Lukaszewicz, Karol Kamel, Kazimierz Chmurski, Sebastian Kmiecik and Marzena Jankowska-Anyszka
Pharmaceuticals 2024, 17(5), 632; https://doi.org/10.3390/ph17050632 - 14 May 2024
Cited by 3 | Viewed by 1896
Abstract
In the fight against cancer, researchers have turned their attention to the eukaryotic initiation factor eIF4E, a protein whose increased level is strongly correlated with the development and progression of various types of cancer. Among the numerous strategies devised to tackle eIF4E overexpression, [...] Read more.
In the fight against cancer, researchers have turned their attention to the eukaryotic initiation factor eIF4E, a protein whose increased level is strongly correlated with the development and progression of various types of cancer. Among the numerous strategies devised to tackle eIF4E overexpression, the use of 5′ end mRNA cap analogues has emerged as a promising approach. Here, we present new candidates as potent m7GMP analogues for inhibiting translation and interfacing with eIF4E. By employing an appropriate strategy, we synthesized doubly modified mono- and dinucleotide cap analogues, introducing simultaneous substituents at both the N7 and N2 positions of the guanine ring. This approach was identified as an effective and promising combination. Our findings reveal that these dual modifications increase the potency of the dinucleotide analogue, marking a significant advancement in the development of cancer therapeutics targeting the eIF4E pathway. Full article
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Review

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20 pages, 2244 KiB  
Review
Application of Mammalian Nudix Enzymes to Capped RNA Analysis
by Maciej Lukaszewicz
Pharmaceuticals 2024, 17(9), 1195; https://doi.org/10.3390/ph17091195 - 11 Sep 2024
Viewed by 9933
Abstract
Following the success of mRNA vaccines against COVID-19, mRNA-based therapeutics have now become a great interest and potential. The development of this approach has been preceded by studies of modifications found on mRNA ribonucleotides that influence the stability, translation and immunogenicity of this [...] Read more.
Following the success of mRNA vaccines against COVID-19, mRNA-based therapeutics have now become a great interest and potential. The development of this approach has been preceded by studies of modifications found on mRNA ribonucleotides that influence the stability, translation and immunogenicity of this molecule. The 5′ cap of eukaryotic mRNA plays a critical role in these cellular functions and is thus the focus of intensive chemical modifications to affect the biological properties of in vitro-prepared mRNA. Enzymatic removal of the 5′ cap affects the stability of mRNA in vivo. The NUDIX hydrolase Dcp2 was identified as the first eukaryotic decapping enzyme and is routinely used to analyse the synthetic cap at the 5′ end of RNA. Here we highlight three additional NUDIX enzymes with known decapping activity, namely Nudt2, Nudt12 and Nudt16. These enzymes possess a different and some overlapping activity towards numerous 5′ RNA cap structures, including non-canonical and chemically modified ones. Therefore, they appear as potent tools for comprehensive in vitro characterisation of capped RNA transcripts, with special focus on synthetic RNAs with therapeutic activity. Full article
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