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Pals MJ, Lindberg A, Velema WA. Chemical strategies for antisense antibiotics. Chem Soc Rev 2024; 53:11303-11320. [PMID: 39436264 PMCID: PMC11495246 DOI: 10.1039/d4cs00238e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Indexed: 10/23/2024]
Abstract
Antibacterial resistance is a severe threat to modern medicine and human health. To stay ahead of constantly-evolving bacteria we need to expand our arsenal of effective antibiotics. As such, antisense therapy is an attractive approach. The programmability allows to in principle target any RNA sequence within bacteria, enabling tremendous selectivity. In this Tutorial Review we provide guidelines for devising effective antibacterial antisense agents and offer a concise perspective for future research. We will review the chemical architectures of antibacterial antisense agents with a special focus on the delivery and target selection for successful antisense design. This Tutorial Review will strive to serve as an essential guide for antibacterial antisense technology development.
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Affiliation(s)
- Mathijs J Pals
- Institute for Molecules and Materials, Radboud University Nijmegen, the Netherlands. Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Alexander Lindberg
- Institute for Molecules and Materials, Radboud University Nijmegen, the Netherlands. Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, the Netherlands. Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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2
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Brück M, Köbel TS, Dittmar S, Ramírez Rojas AA, Georg J, Berghoff BA, Schindler D. A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. iScience 2024; 27:110774. [PMID: 39280619 PMCID: PMC11402225 DOI: 10.1016/j.isci.2024.110774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/14/2024] [Accepted: 08/15/2024] [Indexed: 09/18/2024] Open
Abstract
All organisms must respond to environmental changes. In bacteria, small RNAs (sRNAs) are an important aspect of the regulation network underlying the adaptation to such changes. sRNAs base-pair with their target mRNAs, allowing rapid modulation of the proteome. This post-transcriptional regulation is usually facilitated by RNA chaperones, such as Hfq. sRNAs have a potential as synthetic regulators that can be modulated by rational design. In this study, we use a library-based approach and oxacillin susceptibility assays to investigate the importance of the seed region length for synthetic sRNAs based on RybB and SgrS scaffolds in Escherichia coli. In the presence of Hfq we show that 12 nucleotides are sufficient for regulation. Furthermore, we observe a scaffold-specific Hfq-dependency and processing by RNase E. Our results provide information for design considerations of synthetic sRNAs in basic and applied research.
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Affiliation(s)
- Michel Brück
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Tania S Köbel
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Sophie Dittmar
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Adán A Ramírez Rojas
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Jens Georg
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Daniel Schindler
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35032 Marburg, Germany
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Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J. A comparative analysis of peptide-delivered antisense antibiotics using diverse nucleotide mimics. RNA (NEW YORK, N.Y.) 2024; 30:624-643. [PMID: 38413166 PMCID: PMC11098465 DOI: 10.1261/rna.079969.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically distinct 10mer ASOs, all designed to target the essential gene acpP upon delivery with a KFF-peptide carrier into Salmonella. Our systematic analysis of PNA, PMO, phosphorothioate (PTO)-modified DNA, 2'-methylated RNA (RNA-OMe), 2'-methoxyethylated RNA (RNA-MOE), 2'-fluorinated RNA (RNA-F), and 2'-4'-locked RNA (LNA) is based on a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and inhibition of bacterial growth. Our data show that only PNA and PMO are efficiently delivered by the KFF peptide into Salmonella to inhibit bacterial growth. Nevertheless, the strong target binding affinity and in vitro translational repression activity of LNA and RNA-MOE make them promising modalities for antisense antibiotics that will require the identification of an effective carrier.
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Affiliation(s)
- Chandradhish Ghosh
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
| | - V Dhamodharan
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Julia Dietzsch
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Cluster for Nucleic Acid Therapeutics Munich (CNATM), Munich, Germany
- Faculty of Medicine, University of Würzburg, 97080, Würzburg, Germany
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El-Fateh M, Chatterjee A, Zhao X. A systematic review of peptide nucleic acids (PNAs) with antibacterial activities: Efficacy, potential and challenges. Int J Antimicrob Agents 2024; 63:107083. [PMID: 38185398 DOI: 10.1016/j.ijantimicag.2024.107083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Peptide nucleic acids (PNAs) are synthetic molecules that are like DNA/RNA, but with different building blocks. PNAs target and bind to mRNAs and disrupt the function of a targeted gene, hence they have been studied as potential antibacterials. The aim of this systematic review was to provide an in-depth analysis of the current status of PNAs as antibacterial agents, define the characteristics of the effective PNA constructs, and address the gap in advancing PNAs to become clinically competent agents. Following the PRISMA model, four electronic databases were searched: Web of Science, PubMed, SciFinder and Scopus. A total of 627 articles published between 1994 and 2023 were found. After screening and a rigorous selection process using explicit inclusion and exclusion criteria, 65 scientific articles were selected, containing 656 minimum inhibitory concentration (MIC) data. The antibacterial activity of PNAs was assessed against 20 bacterial species. The most studied Gram-negative and Gram-positive bacteria were Escherichia coli (n=266) and Staphylococcus aureus (n=53), respectively. In addition, the effect of PNA design, including construct length, binding location, and carrier agents, on antibacterial activity was shown. Finally, antibacterial test models to assess the inhibitory effects of PNAs were examined, emphasising gaps and prospects. This systematic review provides a comprehensive assessment of the potential of PNAs as antibacterial agents and offers valuable insights for researchers and clinicians seeking novel therapeutic strategies in the context of increasing rates of antibiotic-resistant bacteria.
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Affiliation(s)
- Mohamed El-Fateh
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada, H9X3V9; Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, 35516, El-Dakhelia, Egypt; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada, H9X3V9; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA.
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Chen ES, Ho ES. In-silico study of antisense oligonucleotide antibiotics. PeerJ 2023; 11:e16343. [PMID: 38025700 PMCID: PMC10656905 DOI: 10.7717/peerj.16343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
Background The rapid emergence of antibiotic-resistant bacteria directly contributes to a wave of untreatable 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.
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Affiliation(s)
- Erica S. Chen
- Biology, Lafayette College, Easton, PA, United States
| | - Eric S. Ho
- Biology, Lafayette College, Easton, PA, United States
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Nanayakkara AK, Moustafa DA, Pifer R, Goldberg JB, Greenberg DE. Sequence specificity defines the effectiveness of PPMOs targeting Pseudomonas aeruginosa. Antimicrob Agents Chemother 2023; 67:e0024523. [PMID: 37610213 PMCID: PMC10508178 DOI: 10.1128/aac.00245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/18/2023] [Indexed: 08/24/2023] Open
Abstract
Development of new therapeutics against antibiotic resistant pathogenic bacteria is recognized as a priority across the globe. We have reported using peptide-conjugated phosphorodiamidate morpholino oligomers (PPMOs) as species-specific antibiotics. The oligo sequences, 11 bases are designed to be complementary to specific essential genes near the Shine-Dalgarno site and inhibit translation. Here, we analyzed target specificity and the impact of genetic mutations on lead PPMOs targeting the rpsJ or acpP gene of Pseudomonas aeruginosa. Mutants in P. aeruginosa PAO1 were generated with four, two, or one base-pair mutations within the 11-base target sequence of the rpsJ gene. All mutants exhibited increased MICs compared to wild-type PAO1 when treated with the RpsJ PPMO, and the increase in the MICs was proportional to the number of base-pair mutations. Among single base-pair mutants, mutations in the middle of the sequence were more impactful than mutations in 5' or 3' end of the sequence. The increased MICs shown by the rpsJ mutants could be reversed by PPMOs designed to target the mutated rpsJ sequence. BALB/c mice infected intratracheally with mutants demonstrated increased lung burden when treated with RpsJ PPMO compared to wild-type PAO1-infected mice treated with RpsJ PPMO. Treating mice with a PPMOs designed to specifically target the mutant sequence was more effective against these mutant strains. These experiments confirm target specificity of two lead P. aeruginosa PPMOs and illustrate one potential mechanism of resistance that could emerge from an antisense approach.
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Affiliation(s)
- A. K. Nanayakkara
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - D. A. Moustafa
- Department of Pediatrics and Children’s Healthcare of Atlanta, Center for Cystic Fibrosis and Airway Diseases Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - R. Pifer
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - J. B. Goldberg
- Department of Pediatrics and Children’s Healthcare of Atlanta, Center for Cystic Fibrosis and Airway Diseases Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - D. E. Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Tekintaş Y, Temel A. Antisense oligonucleotides: a promising therapeutic option against infectious diseases. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:1-39. [PMID: 37395450 DOI: 10.1080/15257770.2023.2228841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
Infectious diseases have been one of the biggest health problems of humanity for centuries. Nucleic acid-based therapeutics have received attention in recent years with their effectiveness in the treatment of various infectious diseases and vaccine development studies. This review aims to provide a comprehensive understanding of the basic properties underlying the mechanism of antisense oligonucleotides (ASOs), their applications, and their challenges. The efficient delivery of ASOs is the greatest challenge for their therapeutic success, but this problem is overcome with new-generation antisense molecules developed with chemical modifications. The types, carrier molecules, and gene regions targeted by sequences have been summarized in detail. Research and development of antisense therapy is still in its infancy; however, gene silencing therapies appear to have the potential for faster and longer-lasting activity than conventional treatment strategies. On the other hand, realizing the potential of antisense therapy will require a large initial economic investment to ascertain the pharmacological properties and learn how to optimize them. The ability of ASOs to be rapidly designed and synthesized to target different microbes can reduce drug discovery time from 6 years to 1 year. Since ASOs are not particularly affected by resistance mechanisms, they come to the fore in the fight against antimicrobial resistance. The design-based flexibility of ASOs has enabled it to be used for different types of microorganisms/genes and successful in vitro and in vivo results have been revealed. The current review summarized a comprehensive understanding of ASO therapy in combating bacterial and viral infections.
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Affiliation(s)
- Yamaç Tekintaş
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
| | - Aybala Temel
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
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