Engineering Antisense Oligonucleotides as Antibacterial Agents That Target FMN Riboswitches and Inhibit the Growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli

Traykovska, Martina; Penchovsky, Robert

doi:10.1021/acssynbio.2c00013

Cited by 21 publications

(33 citation statements)

References 19 publications

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“…ASO-1 is delivered into the bacterial cells by a non-toxic oligopeptide (pVEC) derived from the murine vascular endothelial-cadherin protein, which is degraded by peptidases after its entry into the cells. The ASO-1/FMN aptamer hybrid is recognized and cleaved by RNase H. Strikingly, ASO-1 at the same concentration showed a bacteriostatic effect against S. aureus , L. monocytogenes , and E. coli with MIC 80 700 nM and non-toxic effect in the lung cancer A549 cell line [ 62 ]. Antisense oligonucleotides seem to be promising antimicrobial agents due to their straightforward design, as well as their convenient cellular delivery.…”

Section: Fmn Riboswitchesmentioning

confidence: 99%

A Riboswitch-Driven Era of New Antibacterials

et al. 2022

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Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.

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Section: Fmn Riboswitchesmentioning

confidence: 99%

A Riboswitch-Driven Era of New Antibacterials

et al. 2022

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“…In vitro experiments in Penchovsky’s laboratory with antisense oligonucleotides, for the first time designed with cell-penetrating peptides and targeted to GlmS [ 44 ] and FMN riboswitches [ 45 ] in three different bacteria, demonstrated that our previous genome-wide bioinformatics results [ 8 ] were proved true and could be used as a milestone for the antisense technology for antibacterial drug development.…”

Section: Resultsmentioning

confidence: 99%

“…Following the logic of our previous research for the genome-wide analyses of the riboswitches TPP, FMN, GlmS, lysine, cobalamin, SAM, SAH, adenine, and guanine, we grouped the riboswitches into four categories based on their suitability as antibacterial drug targets [ 8 , 44 , 45 , 50 ]. The ‘Most suitable riboswitches’ group controls the unique, essential biosynthetic pathway and the ‘Very suitable riboswitches control the essential biosynthetic pathway and protein transporter for the key metabolites.…”

Section: Resultsmentioning

confidence: 99%

“…Two of them are the GlmS and FMN riboswitches, which have been targeted with an antisense oligonucleotide. The results of the experimental work have been published [ 44 , 45 ].…”

Section: Discussionmentioning

confidence: 99%

“…Recently, new chimeric antisense oligonucleotides targeted to glmS riboswitches have been shown to block the synthesis of glucosamine-6-phosphate to inhibit the growth of Staphylococcus aureus and bacterial growth [ 44 ]. Other ASOs have been engineered to target flavin mononucleotide riboswitches in Escherichia coli , Listeria monocytogenes , and Staphylococcus aureus [ 45 ]. The two mentioned types of research confirm that antisense oligonucleotides are suitable molecules for antibacterial drug discovery.…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets

Pavlova

Penchovsky

2022

Antibiotics

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Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.

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Catechol‐Siderophore Mimics Convey Nucleic Acid Therapeutics into Bacteria

Pals,

Wijnberg,

Yildiz

et al. 2024

Angewandte Chemie

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Antibacterial resistance is a major threat for human health. There is a need for new antibacterials to stay ahead of constantly‐evolving resistant bacteria. Nucleic acid therapeutics hold promise as powerful antibiotics, but issues with their delivery hamper their applicability. Here, we exploit the siderophore‐mediated iron uptake pathway to efficiently transport antisense oligomers into bacteria. We appended a synthetic siderophore to antisense oligomers targeting the essential acpP gene in Escherichia coli. Siderophore‐conjugated PNA and PMO antisense oligomers displayed potent antibacterial properties. Conjugates bearing a minimal siderophore consisting of a mono‐catechol group showed equally effective. Targeting the lacZ transcript resulted in dose‐dependent decreased β‐galactosidase production, demonstrating selective protein downregulation. Applying this concept to Acinetobacter baumannii, also showed concentration dependent growth inhibition. Whole‐genome sequencing of resistant mutants and competition experiments with the endogenous siderophore verified selective uptake through the siderophore‐mediated iron uptake pathway. Lastly, no toxicity towards mammalian cells was found. Collectively, we demonstrate for the first time that large nucleic acid therapeutics can be efficiently transported into bacteria using synthetic siderophore mimics.

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Engineering Antisense Oligonucleotides as Antibacterial Agents That Target FMN Riboswitches and Inhibit the Growth of Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli

Cited by 21 publications

References 19 publications

A Riboswitch-Driven Era of New Antibacterials

A Riboswitch-Driven Era of New Antibacterials

Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets

Catechol‐Siderophore Mimics Convey Nucleic Acid Therapeutics into Bacteria

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