Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Targeting RNA Molecules
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Targeting RNA Molecules

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 October 2025 | Viewed by 6378

Special Issue Editor

Prof. Dr. Constantinos Stathopoulos

E-Mail Website
Guest Editor
Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
Interests: protein synthesis inhibitors; antibiotic resistance; novel antibiotics; riboswitch inhibitors; RNA inhibitors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Riboswitches are important regulators of bacterial metabolism and control the transcription or translation of essential genes through elaborate structures of their 5′UTR. Due to their dynamic characteristics and pivotal regulatory function within bacterial metabolism, riboswitches have become a focal point for developing advanced RNA-targeting antibacterials to tackle drug resistance issues. In recent years, exploring various riboswitch structures across a spectrum of bacterial strains, including prominent human pathogens, has underscored their suitability as targets for novel compounds capable of disrupting their structure and function, with a decreased likelihood of resistance emerging. Particularly noteworthy is the effectiveness of mainstream antibiotics, which target the ribosome, in modulating the regulatory behavior and potential of numerous riboswitches, both in laboratory settings and within living organisms, highlighting the necessity for the further comprehensive investigation and biological assessment of new antibiotic candidates.

Prof. Dr. Constantinos Stathopoulos
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • riboswitch
  • noncoding RNA
  • antibiotics
  • resistance
  • bacteria
  • antimicrobial resistance

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Review

36 pages, 2247 KiB  
Review
RNA Structure: Past, Future, and Gene Therapy Applications
by William A. Haseltine, Kim Hazel and Roberto Patarca
Int. J. Mol. Sci. 2025, 26(1), 110; https://doi.org/10.3390/ijms26010110 - 26 Dec 2024
Viewed by 3435
Abstract
First believed to be a simple intermediary between the information encoded in deoxyribonucleic acid and that functionally displayed in proteins, ribonucleic acid (RNA) is now known to have many functions through its abundance and intricate, ubiquitous, diverse, and dynamic structure. About 70–90% of [...] Read more.
First believed to be a simple intermediary between the information encoded in deoxyribonucleic acid and that functionally displayed in proteins, ribonucleic acid (RNA) is now known to have many functions through its abundance and intricate, ubiquitous, diverse, and dynamic structure. About 70–90% of the human genome is transcribed into protein-coding and noncoding RNAs as main determinants along with regulatory sequences of cellular to populational biological diversity. From the nucleotide sequence or primary structure, through Watson–Crick pairing self-folding or secondary structure, to compaction via longer distance Watson–Crick and non-Watson–Crick interactions or tertiary structure, and interactions with RNA or other biopolymers or quaternary structure, or with metabolites and biomolecules or quinary structure, RNA structure plays a critical role in RNA’s lifecycle from transcription to decay and many cellular processes. In contrast to the success of 3-dimensional protein structure prediction using AlphaFold, RNA tertiary and beyond structures prediction remains challenging. However, approaches involving machine learning and artificial intelligence, sequencing of RNA and its modifications, and structural analyses at the single-cell and intact tissue levels, among others, provide an optimistic outlook for the continued development and refinement of RNA-based applications. Here, we highlight those in gene therapy. Full article
(This article belongs to the Special Issue Targeting RNA Molecules)
►▼ Show Figures

Figure 1

24 pages, 4362 KiB  
Review
Opportunities for Riboswitch Inhibition by Targeting Co-Transcriptional RNA Folding Events
by Christine Stephen, Danea Palmer and Tatiana V. Mishanina
Int. J. Mol. Sci. 2024, 25(19), 10495; https://doi.org/10.3390/ijms251910495 - 29 Sep 2024
Viewed by 2354
Abstract
Antibiotic resistance is a critical global health concern, causing millions of prolonged bacterial infections every year and straining our healthcare systems. Novel antibiotic strategies are essential to combating this health crisis and bacterial non-coding RNAs are promising targets for new antibiotics. In particular, [...] Read more.
Antibiotic resistance is a critical global health concern, causing millions of prolonged bacterial infections every year and straining our healthcare systems. Novel antibiotic strategies are essential to combating this health crisis and bacterial non-coding RNAs are promising targets for new antibiotics. In particular, a class of bacterial non-coding RNAs called riboswitches has attracted significant interest as antibiotic targets. Riboswitches reside in the 5′-untranslated region of an mRNA transcript and tune gene expression levels in cis by binding to a small-molecule ligand. Riboswitches often control expression of essential genes for bacterial survival, making riboswitch inhibitors an exciting prospect for new antibacterials. Synthetic ligand mimics have predominated the search for new riboswitch inhibitors, which are designed based on static structures of a riboswitch’s ligand-sensing aptamer domain or identified by screening a small-molecule library. However, many small-molecule inhibitors that bind an isolated riboswitch aptamer domain with high affinity in vitro lack potency in vivo. Importantly, riboswitches fold and respond to the ligand during active transcription in vivo. This co-transcriptional folding is often not considered during inhibitor design, and may explain the discrepancy between a low Kd in vitro and poor inhibition in vivo. In this review, we cover advances in riboswitch co-transcriptional folding and illustrate how intermediate structures can be targeted by antisense oligonucleotides—an exciting new strategy for riboswitch inhibitor design. Full article
(This article belongs to the Special Issue Targeting RNA Molecules)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop