In-silico study of antisense oligonucleotide antibiotics

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Abstract
  • Background: The rapid emergence of antibiotic-resistant bacteria directly contributes to a wave of untreatable i infections. The lack of new drug development is an important driver of this crisis. Most antibiotics today are small molecules that block vital processes in bacteria. To optimize such effects, the three-dimensional structure of targeted bacterial proteins is imperative, although such a task is time-consuming and tedious, impeding the development of antibiotics. The development of RNA-based therapeutics has catalyzed a new platform of antibiotics—antisense oligonucleotides (ASOs). These molecules hybridize with their target mRNAs with high specificity, knocking down or interfering with protein translation. This study aims to develop a bioinformatics pipeline to identify potent ASO targets in essential bacterial genes.
    Methods: Three bacterial species (P. gingivalis, H. influenzae, and S. aureus) were used to demonstrate the utility of the pipeline. Open reading frames of bacterial essential genes were downloaded from the Database of Essential Genes (DEG). After filtering for specificity and accessibility, ASO candidates were ranked based on their self-hybridization score, predicted melting temperature, and the position on the gene in an operon. Enrichment analysis was conducted on genes associated with putative potent ASOs.
    Results: A total of 45,628 ASOs were generated from 348 unique essential genes in P. gingivalis. A total of 1,117 of them were considered putative. A total of 27,273 ASOs were generated from 191 unique essential genes in H. influenzae. A total of 847 of them were considered putative. A total of 175,606 ASOs were generated from 346
    essential genes in S. aureus. A total of 7,061 of them were considered putative. Critical biological processes associated with these genes include translation, regulation of cell shape, cell division, and peptidoglycan biosynthetic process. Putative ASO targets generated for each bacterial species are publicly available here: https://github.com/
    EricSHo/AOA. The results demonstrate that our bioinformatics pipeline is useful in identifying unique and accessible ASO targets in bacterial species that post major public health issues.
TitleIn-silico study of antisense oligonucleotide antibiotics
CreatorHo, Eric S.
Chen, E. S.
PublisherPeerJ
Academic DepartmentBiology
DivisionNatural Sciences
OrganizationLafayette College
Date IssuedNovember 15, 2023
Date Available2023-11-22
TypeArticle
LanguageEnglish
KeywordAntibiotic resistance
Microbiology
Bioinformatics
Antisense oligonucleotide
Antibiotic
Pharmacology
Drugs and Devices
Bibliographic CitationChen, E. S. and E. S. Ho (2023 Nov 15) "In-silico study of antisense oligonucleotide antibiotics." PeerJ 11: e16343.
Standard IdentifierDOI 10.7717/peerj.16343
Handle 10385/73666574r
Permalinkhttp://hdl.handle.net/10385/73666574r
Rights Statement Creative Commons - Attribution Creative Commons - Attribution
Rights HoldersChen, E. S.
Ho, Eric S.
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File Ho-PeerJ-vol11-2023.pdf Uploaded 2023-11-22 Public Download
File Ho-PeerJ-vol11-2023.pdf Uploaded 2023-11-22 Public Download

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