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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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2
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Antiviral Peptide-Based Conjugates: State of the Art and Future Perspectives. Pharmaceutics 2023; 15:pharmaceutics15020357. [PMID: 36839679 PMCID: PMC9958607 DOI: 10.3390/pharmaceutics15020357] [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: 12/07/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Infectious diseases caused by microbial pathogens (bacteria, virus, fungi, parasites) claim millions of deaths per year worldwide and have become a serious challenge to global human health in our century. Viral infections are particularly notable in this regard, not only because humankind is facing some of the deadliest viral pandemics in recent history, but also because the arsenal of drugs to combat the high levels of mutation, and hence the antigenic variability of (mostly RNA) viruses, is disturbingly scarce. Therefore, the search for new antivirals able to successfully fight infection with minimal or no adverse effects on the host is a pressing task. Traditionally, antiviral therapies have relied on relatively small-sized drugs acting as proteases, polymerases, integrase inhibitors, etc. In recent decades, novel approaches involving targeted delivery such as that achieved by peptide-drug conjugates (PDCs) have gained attention as alternative (pro)drugs for tackling viral diseases. Antiviral PDC therapeutics typically involve one or more small drug molecules conjugated to a cell-penetrating peptide (CPP) carrier either directly or through a linker. Such integration of two bioactive elements into a single molecular entity is primarily aimed at achieving improved bioavailability in conditions where conventional drugs are challenged, but may also turn up novel unexpected functionalities and applications. Advances in peptide medicinal chemistry have eased the way to antiviral PDCs, but challenges remain on the way to therapeutic success. In this paper, we review current antiviral CPP-drug conjugates (antiviral PDCs), with emphasis on the types of CPP and antiviral cargo. We integrate the conjugate and the chemical approaches most often applied to combine both entities. Additionally, we comment on various obstacles faced in the design of antiviral PDCs and on the future outlooks for this class of antiviral therapeutics.
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3
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Economos NG, Quijano E, Carufe KEW, Perera J, Glazer P. Antispacer peptide nucleic acids for sequence-specific CRISPR-Cas9 modulation. Nucleic Acids Res 2022; 50:e59. [PMID: 35235944 PMCID: PMC9177974 DOI: 10.1093/nar/gkac095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022] Open
Abstract
Despite the rapid and broad implementation of CRISPR-Cas9-based technologies, convenient tools to modulate dose, timing, and precision remain limited. Building on methods using synthetic peptide nucleic acids (PNAs) to bind RNA with unusually high affinity, we describe guide RNA (gRNA) spacer-targeted, or 'antispacer', PNAs as a tool to modulate Cas9 binding and activity in cells in a sequence-specific manner. We demonstrate that PNAs rapidly and efficiently target complexed gRNA spacer sequences at low doses and without design restriction for sequence-selective Cas9 inhibition. We further show that short PAM-proximal antispacer PNAs achieve potent cleavage inhibition (over 2000-fold reduction) and that PAM-distal PNAs modify gRNA affinity to promote on-target specificity. Finally, we apply antispacer PNAs for temporal regulation of two dCas9-fusion systems. These results present a novel rational approach to nucleoprotein engineering and describe a rapidly implementable antisense platform for CRISPR-Cas9 modulation to improve spatiotemporal versatility and safety across applications.
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Affiliation(s)
- Nicholas G Economos
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Elias Quijano
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - J Dinithi R Perera
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520 USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
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4
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Introduction and History of the Chemistry of Nucleic Acids Therapeutics. Methods Mol Biol 2022; 2434:3-31. [PMID: 35213007 PMCID: PMC7612508 DOI: 10.1007/978-1-0716-2010-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This introduction charts the history of the development of the major chemical modifications that have influenced the development of nucleic acids therapeutics focusing in particular on antisense oligonucleotide analogues carrying modifications in the backbone and sugar. Brief mention is made of siRNA development and other applications that have by and large utilized the same modifications. We also point out the pitfalls of the use of nucleic acids as drugs, such as their unwanted interactions with pattern recognition receptors, which can be mitigated by chemical modification or used as immunotherapeutic agents.
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5
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Zhao Y, Shu R, Liu J. The development and improvement of ribonucleic acid therapy strategies. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:997-1013. [PMID: 34540356 PMCID: PMC8437697 DOI: 10.1016/j.omtn.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The biological understanding of RNA has evolved since the discovery of catalytic RNAs in the early 1980s and the establishment of RNA interference (RNAi) in the 1990s. RNA is no longer seen as the simple mid-product between transcription and translation but as potential molecules to be developed as RNA therapeutic drugs. RNA-based therapeutic drugs have gained recognition because of their ability to regulate gene expression and perform cellular functions. Various nucleobase, backbone, and sugar-modified oligonucleotides have been synthesized, as natural oligonucleotides have some limitations such as poor low nuclease resistance, binding affinity, poor cellular uptake, and toxicity, which affect their use as RNA therapeutic drugs. In this review, we briefly discuss different RNA therapeutic drugs and their internal connections, including antisense oligonucleotides, small interfering RNAs (siRNAs) and microRNAs (miRNAs), aptamers, small activating RNAs (saRNAs), and RNA vaccines. We also discuss the important roles of RNA vaccines and their use in the fight against COVID-19. In addition, various chemical modifications and delivery systems used to improve the performance of RNA therapeutic drugs and overcome their limitations are discussed.
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Affiliation(s)
- Yuxi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Rui Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Corresponding author: Rui Shu, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Jiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Corresponding author: Jiang Liu, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
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6
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Campbell B, Hood T, Shank N. Synthesis of a new disulfide Fmoc monomer for creating biologically susceptible linkages in peptide nucleic acid oligomers. Bioorg Chem 2018; 84:394-398. [PMID: 30551065 DOI: 10.1016/j.bioorg.2018.11.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/28/2022]
Abstract
Peptide nucleic acids (PNA) are one of many synthetic mimics of DNA and RNA that have found applications as biological probes, as nano-scaffold components, and in diagnostics. In an effort to use PNA as constructs for cellular delivery we investigated the possibility of installing a biologically susceptible disulfide bond in the backbone of a PNA oligomer. Here we report the synthesis of a new abasic Fmoc monomer containing a disulfide bond that can be incorporated into a PNA oligomer (DS-PNA) using standard solid phase peptide synthesis. The disulfide bond survives cleavage from the resin and DS-PNA forms duplexes with complementary PNA oligomers. Initial studies aimed at determining if the disulfide bond is cleavable to reducing agents while in a duplex are explored using UV thermal analysis and HPLC.
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Affiliation(s)
- Brandon Campbell
- Department of Chemistry and Biochemistry, Georgia Southern University, Savannah, GA, USA
| | - Taylor Hood
- Department of Chemistry and Biochemistry, Georgia Southern University, Savannah, GA, USA
| | - Nathaniel Shank
- Department of Chemistry and Biochemistry, Georgia Southern University, Savannah, GA, USA.
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7
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Sun Y, Zhao Y, Zhao X, Lee RJ, Teng L, Zhou C. Enhancing the Therapeutic Delivery of Oligonucleotides by Chemical Modification and Nanoparticle Encapsulation. Molecules 2017; 22:E1724. [PMID: 29027965 PMCID: PMC6158866 DOI: 10.3390/molecules22101724] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 09/22/2017] [Accepted: 10/09/2017] [Indexed: 12/30/2022] Open
Abstract
Oligonucleotide (ON) drugs, including small interfering RNA (siRNA), microRNA (miRNA) and antisense oligonucleotides, are promising therapeutic agents. However, their low membrane permeability and sensitivity to nucleases present challenges to in vivo delivery. Chemical modifications of the ON offer a potential solution to improve the stability and efficacy of ON drugs. Combined with nanoparticle encapsulation, delivery at the site of action and gene silencing activity of chemically modified ON drugs can be further enhanced. In the present review, several types of ON drugs, selection of chemical modification, and nanoparticle-based delivery systems to deliver these ON drugs are discussed.
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Affiliation(s)
- Yating Sun
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Yarong Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Xiuting Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Robert J Lee
- School of Life Sciences, Jilin University, Changchun 130012, China.
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.
| | - Lesheng Teng
- School of Life Sciences, Jilin University, Changchun 130012, China.
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8
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Obstruction of BRAF V600E transcription by complementary PNA oligomers as a means to inhibit BRAF-mutant melanoma growth. Cancer Gene Ther 2017; 24:401-408. [PMID: 28937091 DOI: 10.1038/cgt.2017.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/05/2017] [Indexed: 11/08/2022]
Abstract
Peptide nucleic acid (PNA) oligomers are DNA mimics, which are capable of binding gene sequences 1000-fold more avidly than complementary native DNA by strand invasion and effectively obstruct transcription. Irreversibly obstructing the transcription or replication of a gene sequence, such as BRAFV600E, offers a potential route to specifically target the cancer cell itself. We have employed PNA oligomers to target BRAFV600E in a sequence-specific complementary manner. These PNAs have been modified by appending configurationally stabilizing cationic peptides in order to improve their cellular delivery and target avidity. Our results indicate that exposure of the melanoma cell lines to a modified PNA-peptide conjugate complementary to BRAFV600E mutation sequence results in a concentration-dependent and time-dependent inhibition of cell growth that is specific for the BRAFV600E-mutant melanoma cell lines with inhibition of mRNA and protein expression. Xenograft mouse trials show increased tumor growth delay and necrosis with the BRAFV600E-complementary PNA-peptide conjugates as compared with the saline and scrambled PNA sequence controls. Similarly, quantitative measurement shows a 2.5-fold decrease in Ki67 and a 3-fold increase in terminal deoxynucleotidyl transferase dUTP nick end labeling expression with this approach. PNA-delivery peptide conjugates represent a novel way to target BRAFV600E and represent a new approach in targeting selective oncogenes that induce tumor growth.
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9
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Gupta A, Bahal R, Gupta M, Glazer PM, Saltzman WM. Nanotechnology for delivery of peptide nucleic acids (PNAs). J Control Release 2016; 240:302-311. [PMID: 26776051 DOI: 10.1016/j.jconrel.2016.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/10/2015] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Over the past three decades, peptide nucleic acids have been employed in numerous chemical and biological applications. Peptide nucleic acids possess enormous potential because of their superior biophysical properties, compared to other oligonucleotide chemistries. However, for therapeutic applications, intracellular delivery of peptide nucleic acids remains a challenge. In this review, we summarize the progress that has been made in delivering peptide nucleic acids to intracellular targets. In addition, we emphasize recent nanoparticle-based strategies for efficient delivery of conventional and chemically-modified peptides nucleic acids.
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Affiliation(s)
- Anisha Gupta
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Meera Gupta
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Chemical Engineering, Indian Institute of Technology-Delhi, New Delhi, India
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA; Department of Genetics, Yale University, New Haven, CT, USA.
| | - W Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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10
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Boisguérin P, Deshayes S, Gait MJ, O'Donovan L, Godfrey C, Betts CA, Wood MJA, Lebleu B. Delivery of therapeutic oligonucleotides with cell penetrating peptides. Adv Drug Deliv Rev 2015; 87:52-67. [PMID: 25747758 PMCID: PMC7102600 DOI: 10.1016/j.addr.2015.02.008] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 12/15/2022]
Abstract
Oligonucleotide-based drugs have received considerable attention for their capacity to modulate gene expression very specifically and as a consequence they have found applications in the treatment of many human acquired or genetic diseases. Clinical translation has been often hampered by poor biodistribution, however. Cell-penetrating peptides (CPPs) appear as a possibility to increase the cellular delivery of non-permeant biomolecules such as nucleic acids. This review focuses on CPP-delivery of several classes of oligonucleotides (ONs), namely antisense oligonucleotides, splice switching oligonucleotides (SSOs) and siRNAs. Two main strategies have been used to transport ONs with CPPs: covalent conjugation (which is more appropriate for charge-neutral ON analogues) and non-covalent complexation (which has been used for siRNA delivery essentially). Chemical synthesis, mechanisms of cellular internalization and various applications will be reviewed. A comprehensive coverage of the enormous amount of published data was not possible. Instead, emphasis has been put on strategies that have proven to be effective in animal models of important human diseases and on examples taken from the authors' own expertise.
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Affiliation(s)
- Prisca Boisguérin
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, 1919 Route de Mende, 34293 Montpellier, France.
| | - Sébastien Deshayes
- Centre de Recherche de Biochimie Macromoléculaire, UMR 5237 CNRS, 1919 Route de Mende, 34293 Montpellier, France
| | - Michael J Gait
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Liz O'Donovan
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Caroline Godfrey
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Corinne A Betts
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Matthew J A Wood
- University of Oxford, Department of Physiology, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK
| | - Bernard Lebleu
- UMR 5235 CNRS, Université Montpellier 2, Place Eugene Bataillon, Montpellier 34095, France
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11
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Vigorito E, Kohlhaas S, Lu D, Leyland R. miR-155: an ancient regulator of the immune system. Immunol Rev 2013; 253:146-57. [PMID: 23550644 DOI: 10.1111/imr.12057] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are a newly recognized class of regulatory genes which repress the expression of protein-coding genes. Numerous studies have uncovered a complex role for miRNAs regulating many aspects of a variety of cellular processes including cell growth, differentiation, and lineage commitment. In the immune system, miR-155 is unique in its ability to shape the transcriptome of activated myeloid and lymphoid cells controlling diverse biological functions ranging from inflammation to immunological memory. Not surprisingly, a tight control of miR-155 expression is required to avoid malignant transformation, as evidenced by miR-155 overexpression in many cancers of B-cell origin. In this review, we discuss the potential of miR-155 as a molecular target for therapeutic intervention and discuss the function of miR-155 in the context of protective immunity. We first look back into the emergence of miR-155 in evolution, which is coincidental with the emergence of the ancestors of the antigen receptors. We then summarize what we have learned about the role of miR-155 in the regulation of lymphoid subsets at the cellular and molecular level in the context of recent progress in this field.
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Affiliation(s)
- Elena Vigorito
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK.
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12
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Järver P, Coursindel T, Andaloussi SEL, Godfrey C, Wood MJA, Gait MJ. Peptide-mediated Cell and In Vivo Delivery of Antisense Oligonucleotides and siRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e27. [PMID: 23344079 PMCID: PMC3390225 DOI: 10.1038/mtna.2012.18] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/26/2012] [Accepted: 04/26/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Peter Järver
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Samir EL Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
- Department of Laboratory Medicine, Karolinska Institute, Hudidnge, Sweden
| | - Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Matthew JA Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Michael J Gait
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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13
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Fabbri E, Brognara E, Borgatti M, Lampronti I, Finotti A, Bianchi N, Sforza S, Tedeschi T, Manicardi A, Marchelli R, Corradini R, Gambari R. miRNA therapeutics: delivery and biological activity of peptide nucleic acids targeting miRNAs. Epigenomics 2012; 3:733-45. [PMID: 22126292 DOI: 10.2217/epi.11.90] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Peptide nucleic acids (PNAs) are DNA/RNA mimics extensively used for pharmacological regulation of gene expression in a variety of cellular and molecular systems, and they have been described as excellent candidates for antisense and antigene therapies. At present, very few data are available on the use of PNAs as molecules targeting miRNAs. miRNAs are a family of small nc RNAs that regulate gene expression by sequence-selective targeting of mRNAs, leading to a translational repression or mRNA degradation to the control of highly regulated biological functions, such as differentiation, cell cycle and apoptosis. The aim of this article is to present the state-of-the-art concerning the possible use of PNAs to target miRNAs and modify their biological metabolism within the cells. The results present in the literature allow to propose PNA-based molecules as very promising reagents to modulate the biological activity of miRNAs. In consideration of the involvement of miRNAs in human pathologies, PNA-mediated targeting of miRNAs has been proposed as a potential novel therapeutic approach.
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Affiliation(s)
- Enrica Fabbri
- Department of Biochemistry & Molecular Biology, University of Ferrara, Ferrara, Italy
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14
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Design of embedded chimeric peptide nucleic acids that efficiently enter and accurately reactivate gene expression in vivo. Proc Natl Acad Sci U S A 2010; 107:16846-51. [PMID: 20837550 DOI: 10.1073/pnas.0912896107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pharmacological treatments designed to reactivate fetal γ-globin can lead to an effective and successful clinical outcome in patients with hemoglobinopathies. However, new approaches remain highly desired because such treatments are not equally effective for all patients, and toxicity issues remain. We have taken a systematic approach to develop an embedded chimeric peptide nucleic acid (PNA) that effectively enters the cell and the nucleus, binds to its target site at the human fetal γ-globin promoter, and reactivates this transcript in adult transgenic mouse bone marrow and human primary peripheral blood cells. In vitro and in vivo DNA-binding assays in conjunction with live-cell imaging have been used to establish and optimize chimeric PNA design parameters that lead to successful gene activation. Our final molecule contains a specific γ-promoter-binding PNA sequence embedded within two amino acid motifs: one leads to efficient cell/nuclear entry, and the other generates transcriptional reactivation of the target. These embedded PNAs overcome previous limitations and are generally applicable to the design of in vivo transcriptional activation reagents that can be directed to any promoter region of interest and are of direct relevance to clinical applications that would benefit from such a need.
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15
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Fraternale A, Paoletti MF, Casabianca A, Orlandi C, Millo E, Balestra E, Damonte G, Perno CF, Magnani M. Erythrocytes as carriers of antisense PNA addressed against HIV-1 gag-pol transframe domain. J Drug Target 2010; 17:278-85. [PMID: 19255894 DOI: 10.1080/10611860902737474] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PNA(PR2) is a peptide nucleic acid (PNA) complementary to a sequence of the viral protease-encoding gene, effective in blocking HIV release, when used at high doses. Erythrocytes (RBC) were used to target PNA(PR2) to the macrophage compartment. The antiviral activity was assessed in human HIV-infected macrophages both as inhibition of p24 production and reduction of HIV DNA content. PNA(PR2), either added to the medium at a concentration of 100 microM or loaded into RBC at about 40 microM, inhibited p24 production approximately 80% compared with infected samples and reduced HIV DNA content by 83% and 90%, respectively. The results show that (1) a stronger anti-HIV effect is achievable with higher doses of PNA(PR2), both when given free and encapsulated into RBC; (2) the antiviral effect obtained by free PNA(PR2) at a concentration of 100 microM is achievable by encapsulating it into RBC at a concentration of 40 microM, suggesting that RBC can be used as a delivery system to increase the antisense effect of PNA(PR2).
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Affiliation(s)
- Alessandra Fraternale
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy.
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16
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Affiliation(s)
- Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, DK-2200, Copenhagen.
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17
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Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KGC, Enright AJ, Gait MJ, Vigorito E. Efficient inhibition of miR-155 function in vivo by peptide nucleic acids. Nucleic Acids Res 2010; 38:4466-75. [PMID: 20223773 PMCID: PMC2910044 DOI: 10.1093/nar/gkq160] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/24/2010] [Accepted: 02/24/2010] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in diverse physiological processes and are potential therapeutic agents. Synthetic oligonucleotides (ONs) of different chemistries have proven successful for blocking miRNA expression. However, their specificity and efficiency have not been fully evaluated. Here, we show that peptide nucleic acids (PNAs) efficiently block a key inducible miRNA expressed in the haematopoietic system, miR-155, in cultured B cells as well as in mice. Remarkably, miR-155 inhibition by PNA in primary B cells was achieved in the absence of any transfection agent. In mice, the high efficiency of the treatment was demonstrated by a strong overlap in global gene expression between B cells isolated from anti-miR-155 PNA-treated and miR-155-deficient mice. Interestingly, PNA also induced additional changes in gene expression. Our analysis provides a useful platform to aid the design of efficient and specific anti-miRNA ONs for in vivo use.
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Affiliation(s)
- Martin M. Fabani
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Cei Abreu-Goodger
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Donna Williams
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Paul A. Lyons
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Adrian G. Torres
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kenneth G. C. Smith
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Anton J. Enright
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J. Gait
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Elena Vigorito
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY and Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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18
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Delcroix M, Riley LW. Cell-Penetrating Peptides for Antiviral Drug Development. Pharmaceuticals (Basel) 2010; 3:448-470. [PMID: 27713263 PMCID: PMC4033964 DOI: 10.3390/ph3030448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 02/06/2010] [Accepted: 03/01/2010] [Indexed: 11/18/2022] Open
Abstract
Viral diseases affect hundreds of millions of people worldwide, and the few available drugs to treat these diseases often come with limitations. The key obstacle to the development of new antiviral agents is their delivery into infected cells in vivo. Cell-penetrating peptides (CPPs) are short peptides that can cross the cellular lipid bilayer with the remarkable capability to shuttle conjugated cargoes into cells. CPPs have been successfully utilized to enhance the cellular uptake and intracellular trafficking of antiviral molecules, and thereby increase the inhibitory activity of potential antiviral proteins and oligonucleotide analogues, both in cultured cells and in animal models. This review will address the notable findings of these studies, highlighting some promising results and discussing the challenges CPP technology has to overcome for further clinical applications.
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Affiliation(s)
- Melaine Delcroix
- School of Public Health, University of California, Berkeley, CA 94720, USA.
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, CA 94720, USA.
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Appella DH. Non-natural nucleic acids for synthetic biology. Curr Opin Chem Biol 2009; 13:687-96. [PMID: 19879178 PMCID: PMC3152792 DOI: 10.1016/j.cbpa.2009.09.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 11/29/2022]
Abstract
Genetic manipulation is an important facet of synthetic biology but can be complicated by undesired nuclease degradation. Incorporating non-natural nucleic acids into a gene could convey resistance to nucleases and promote expression. The compatibility of non-natural nucleosides with polymerases is reviewed with a focus on results from the past two years. Details are provided about how the different systems could be useful in synthetic biology.
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Affiliation(s)
- Daniel H Appella
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.
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20
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Pandey VN, Upadhyay A, Chaubey B. Prospects for antisense peptide nucleic acid (PNA) therapies for HIV. Expert Opin Biol Ther 2009; 9:975-89. [PMID: 19534584 DOI: 10.1517/14712590903052877] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Since the discovery and synthesis of a novel DNA mimic, peptide nucleic acid (PNA) in 1991, PNAs have attracted tremendous interest and have shown great promise as potential antisense drugs. They have been used extensively as tools for specific modulation of gene expression by targeting translation or transcription processes. This review discusses the present and future therapeutic potential of this class of compound as anti-HIV-1 drugs.
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Affiliation(s)
- Virendra N Pandey
- University of Medicine and Dentistry, New Jersey-New Jersey Medical School, Department of Biochemistry and Molecular Biology, Newark, NJ 07103, USA.
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21
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Wang D, Iera J, Baker H, Hogan P, Ptak R, Yang L, Hartman T, Buckheit RW, Desjardins A, Yang A, Legault P, Yedavalli V, Jeang KT, Appella DH. Multivalent binding oligomers inhibit HIV Tat-TAR interaction critical for viral replication. Bioorg Med Chem Lett 2009; 19:6893-7. [PMID: 19896372 DOI: 10.1016/j.bmcl.2009.10.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 10/19/2009] [Indexed: 12/11/2022]
Abstract
We describe the development of a new type of scaffold to target RNA structures. Multivalent binding oligomers (MBOs) are molecules in which multiple sidechains extend from a polyamine backbone such that favorable RNA binding occurs. We have used this strategy to develop MBO-based inhibitors to prevent the association of a protein-RNA complex, Tat-TAR, that is essential for HIV replication. In vitro binding assays combined with model cell-based assays demonstrate that the optimal MBOs inhibit Tat-TAR binding at low micromolar concentrations. Antiviral studies are also consistent with the in vitro and cell-based assays. MBOs provide a framework for the development of future RNA-targeting molecules.
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Affiliation(s)
- Deyun Wang
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, DHHS, Bethesda, MD 20892, USA.
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22
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Ganguly S, Chaubey B, Tripathi S, Upadhyay A, Neti PVSV, Howell RW, Pandey VN. Pharmacokinetic analysis of polyamide nucleic-acid-cell penetrating peptide conjugates targeted against HIV-1 transactivation response element. Oligonucleotides 2009; 18:277-86. [PMID: 18729823 DOI: 10.1089/oli.2008.0140] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have demonstrated that polyamide nucleic acids complementary to the transactivation response (TAR) element of HIV-1 LTR inhibit HIV-1 production when transfected in HIV-1 infected cells. We have further shown that anti-TAR PNA (PNA(TAR)) conjugated with cell-penetrating peptide (CPP) is rapidly taken up by cells and exhibits strong antiviral and anti-HIV-1 virucidal activities. Here, we pharmacokinetically analyzed (125)I-labeled PNA(TAR) conjugated with two CPPs: a 16-mer penetratin derived from antennapedia and a 13-mer Tat peptide derived from HIV-1 Tat. We administered the (125)I-labeled PNA(TAR)-CPP conjugates to male Balb/C mice through intraperitoneal or gavage routes. The naked (125)I-labeled PNA(TAR) was used as a control. Following a single administration of the labeled compounds, their distribution and retention in various organs were monitored at various time points. Regardless of the administration route, a significant accumulation of each PNA(TAR)-CPP conjugate was found in different mouse organs and tissues. The clearance profile of the accumulated radioactivity from different organs displayed a biphasic exponential pathway whereby part of the radioactivity cleared rapidly, but a significant portion of it was slowly released over a prolonged period. The kinetics of clearance of individual PNA(TAR)-CPP conjugates slightly varied in different organs, while the overall biphasic clearance pattern remained unaltered regardless of the administration route. Surprisingly, unconjugated naked PNA(TAR) displayed a similar distribution and clearance profile in most organs studied although extent of its uptake was lower than the PNA(TAR)-CPP conjugates.
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Affiliation(s)
- Sabyasachi Ganguly
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, Newark, New Jersey, USA
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23
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Masotti A, Ortaggi G. Peptide nucleic acid-polyethylenimine conjugates promising multifunctional therapeutic tools for the future. Oligonucleotides 2009; 18:301-3. [PMID: 18752376 DOI: 10.1089/oli.2008.0147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andrea Masotti
- Chemistry Department, Sapienza Universita di Roma, Rome, Italy.
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24
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Upadhyay A, Ponzio NM, Pandey VN. Immunological response to peptide nucleic acid and its peptide conjugate targeted to transactivation response (TAR) region of HIV-1 RNA genome. Oligonucleotides 2009; 18:329-35. [PMID: 19006449 DOI: 10.1089/oli.2008.0152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Anti-human immunodeficiency virus-1 (HIV-1) polyamide (peptide) nucleic acids (PNAs) conjugated with cell-penetrating peptides (CPPs) targeted to the viral genome are potent virucidal and antiviral agents. Earlier, we have shown that the anti-HIV-1 PNA(TAR)-penetratin conjugate is rapidly taken up by cells and is nontoxic to mice when administered at repeat doses of as high as 100 mg/kg body weight. In the present studies we demonstrate that naked PNA(TAR) is immunologically inert as judged by the proliferation responses of splenocytes and lymph node cells from PNA(TAR)-immunized mice challenged with the immunizing antigen. In contrast, PNA(TAR)-penetratin conjugate is moderately immunogenic mainly due to its penetratin peptide component. Cytokine secretion profiles of the lymph node cells from the conjugate-immunized mice showed marginally elevated levels of proinflammatory cytokines, which are known to promote proliferation of T lymphocytes. Since the candidate compound, PNA(TAR)-penetratin conjugate displays potent virucidal and antiviral activities against HIV-1, the favorable immunological response together with negligible toxicity suggest a strong therapeutic potential for this class of compounds.
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Affiliation(s)
- Alok Upadhyay
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry, New Jersey Medical School, Newark, New Jersey 07103, USA
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25
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Veldhoen S, Laufer SD, Restle T. Recent developments in peptide-based nucleic acid delivery. Int J Mol Sci 2008; 9:1276-1320. [PMID: 19325804 PMCID: PMC2635728 DOI: 10.3390/ijms9071276] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 06/04/2008] [Accepted: 07/14/2008] [Indexed: 12/20/2022] Open
Abstract
Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cell-penetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10–30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisense-oligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls.
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Key Words
- CLSM, confocal laser scanning microscopy
- CPP, cell-penetrating peptide
- EIPA, ethylisopropylamiloride
- FCS, fetal calf serum
- GFP, green fluorescent protein
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HIV, human immunodeficiency virus
- IFN, interferon
- IL, interleukin
- LF, Lipofectamine™
- LF2000, Lipofectamine™ 2000
- MAP, model amphipathic peptide
- MEND, multifunctional envelope-type nano device
- NLS, nuclear localisation sequence
- OMe, O-methyl
- PAMAM, polyamidoamine
- PEG, polyethylene glycol
- PEI, polyethyleneimine
- PMO, phosphorodiamidate morpholino oligomer
- PNA, peptide nucleic acid
- PTD, protein transduction domains
- RNAi, RNA interference
- SAP, Sweet Arrow Peptide
- STR-R8, stearyl-R8
- TAR, transactivator responsive region
- TFO, triplex forming oligonucleotide
- TLR9, toll-like receptor 9
- TNF, tumour necrosis factor
- TP10, transportan 10
- bPrPp, bovine prion protein derived peptide
- cell-penetrating peptides
- endocytosis
- hCT, human calcitonin
- mPrPp, murine prion protein derived peptide
- miRNA, microRNA
- nucleic acid delivery
- nucleic acid drugs
- siRNA, small inhibitory RNA
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Affiliation(s)
- Sandra Veldhoen
- Department of Metabolomics, ISAS - Institute for Analytical Sciences, Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany
- Author to whom correspondence should be addressed; E-mail:
| | - Sandra D. Laufer
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Tobias Restle
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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