Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug Development Article Swipe
Samuel L. Neff
,
Thomas H. Hampton
,
Katja Koeppen
,
Sharanya Sarkar
,
Casey J. Latario
,
Benjamin D. Ross
,
Bruce A. Stanton
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.06.22.546111
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.06.22.546111
Developing software tools that leverage biological datasets to accelerate drug discovery is an important aspect of bioinformatics research. Here we present a novel example: a web application called Rocket-miR that applies an existing bioinformatics algorithm (IntaRNA) to predict cross-species miRNA-mRNA interactions and identify human miRNAs with potential antimicrobial activity against antibiotic resistant bacterial infections. Rocket-miR is the logical extension of our prior finding that human miRNA let-7b-5p impairs the ability of the ubiquitous opportunistic pathogen P. aeruginosa to form biofilms and resist the bactericidal effect of beta lactam antibiotics. Rocket-miR’s point and click interface enables researchers without programming expertise to predict additional human-miRNA-pathogen interactions. Identified miRNAs can be developed into novel antimicrobials effective against the 24 clinically relevant pathogens, implicated in diseases of the lung, gut and other organs, that are included in the application. The manuscript incorporates three case studies contributed by microbiologists that study human pathogens to demonstrate the usefulness and usability of the application. Rocket-miR is accessible at the following link: http://scangeo.dartmouth.edu/RocketmiR/ . Importance Antimicrobial resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE ( E nterococcus faecium, S taphylococcus aureus, K lebsiella pneumoniae, A cinetobacter baumannii, P seudomonas aeruginosa and E nterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The application’s target audience is microbiologists that have the laboratory resources to test the application’s predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including CF, COPD, urinary tract infections and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2023.06.22.546111
- https://www.biorxiv.org/content/biorxiv/early/2023/06/25/2023.06.22.546111.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 110
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4381949904
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4381949904Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2023.06.22.546111Digital Object Identifier
- Title
-
Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug DevelopmentWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2023Year of publication
- Publication date
-
2023-06-25Full publication date if available
- Authors
-
Samuel L. Neff, Thomas H. Hampton, Katja Koeppen, Sharanya Sarkar, Casey J. Latario, Benjamin D. Ross, Bruce A. StantonList of authors in order
- Landing page
-
https://doi.org/10.1101/2023.06.22.546111Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2023/06/25/2023.06.22.546111.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2023/06/25/2023.06.22.546111.full.pdfDirect OA link when available
- Concepts
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Antimicrobial, Antibiotics, Human pathogen, microRNA, Antibiotic resistance, Computational biology, Biology, Bioinformatics, Microbiology, Bacteria, Gene, GeneticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
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2024: 1Per-year citation counts (last 5 years)
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110Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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