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Ivanov GS, Tribulovich VG, Pestov NB, David TI, Amoah AS, Korneenko TV, Barlev NA. Artificial genetic polymers against human pathologies. Biol Direct 2022; 17:39. [PMID: 36474260 PMCID: PMC9727881 DOI: 10.1186/s13062-022-00353-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.
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Affiliation(s)
- Gleb S Ivanov
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Vyacheslav G Tribulovich
- St. Petersburg State Technological Institute (Technical University), Saint Petersburg, Russia, 190013
| | - Nikolay B Pestov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia, 108819
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б
| | - Temitope I David
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Abdul-Saleem Amoah
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141701
| | - Tatyana V Korneenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, 117997
| | - Nikolai A Barlev
- Institute of Cytology, Tikhoretsky Ave 4, Saint Petersburg, Russia, 194064.
- Institute of Biomedical Chemistry, Moscow, Russia, 119121б.
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan.
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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3
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Finotti A, Gasparello J, Casnati A, Corradini R, Gambari R, Sansone F. Delivery of Peptide Nucleic Acids Using an Argininocalix[4]arene as Vector. Methods Mol Biol 2021; 2211:123-143. [PMID: 33336275 DOI: 10.1007/978-1-0716-0943-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The importance of peptide nucleic acids (PNAs) for alteration of gene expression is nowadays firmly established. PNAs are characterized by a pseudo-peptide backbone composed of N-(2-aminoethyl)glycine units and have been found to be excellent candidates for antisense and antigene therapies. Recently, PNAs have been demonstrated to alter the action of microRNAs and thus can be considered very important tools for miRNA therapeutics. In fact, the pharmacological modulation of microRNA activity appears to be a very interesting approach in the development of new types of drugs. Among the limits of PNAs in applied molecular biology, the delivery to target cells and tissues is of key importance. The aim of this chapter is to describe methods for the efficient delivery of unmodified PNAs designed to target microRNAs involved in cancer, using as model system miR-221-3p and human glioma cells as in vitro experimental cellular system. The methods employed to deliver PNAs targeting miR-221-3p here presented are based on a macrocyclic multivalent tetraargininocalix[4]arene used as non-covalent vector for anti-miR-221-3p PNAs. High delivery efficiency, low cytotoxicity, maintenance of the PNA biological activity, and easy preparation makes this vector a candidate for a universal delivery system for this class of nucleic acid analogs.
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Affiliation(s)
- Alessia Finotti
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy.
| | - Jessica Gasparello
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy
| | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy
| | - Roberto Gambari
- Section of Biochemistry and Molecular Biology, Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy.,Interuniversity Consortium for Biotechnology, Trieste University, Trieste, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parma University, Parma, Italy.
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Abstract
The involvement of microRNAs in human pathologies is firmly established. Accordingly, the pharmacological modulation of microRNA activity appears to be a very interesting approach in the development of new types of drugs (miRNA therapeutics). One important research area is the possible development of miRNA therapeutics in the field of rare diseases. In this respect, appealing molecules are based on peptide nucleic acids (PNAs), displaying, in their first description, a pseudo-peptide backbone composed of N-(2-aminoethyl)glycine units, and found to be excellent candidates for antisense and antigene therapies. The aim of the present article is to describe methods for determining the activity of PNAs designed to target microRNAs involved in cystic fibrosis, using as model system miR-145-5p and its target cystic fibrosis transmembrane conductance regulator (CFTR) mRNA. The methods employed to study the effects of PNAs targeting miR-145-5p are presented here by discussing data obtained using as cellular model system the human lung epithelial Calu-3 cell line.
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5
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Avitabile C, Accardo A, Ringhieri P, Morelli G, Saviano M, Montagner G, Fabbri E, Gallerani E, Gambari R, Romanelli A. Incorporation of Naked Peptide Nucleic Acids into Liposomes Leads to Fast and Efficient Delivery. Bioconjug Chem 2015; 26:1533-41. [PMID: 26176882 DOI: 10.1021/acs.bioconjchem.5b00156] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The delivery of peptide nucleic acids (PNAs) to cells is a very challenging task. We report here that a liposomal formulation composed of egg PC/cholesterol/DSPE-PEG2000 can be loaded, according to different encapsulation techniques, with PNA or fluorescent PNA oligomers. PNA loaded liposomes efficiently and quickly promote the uptake of a PNA targeting the microRNA miR-210 in human erythroleukemic K562 cells. By using this innovative delivery system for PNA, down-regulation of miR-210 is achieved at a low PNA concentration.
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Affiliation(s)
- Concetta Avitabile
- †Institute of Biostructure and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Antonella Accardo
- ‡Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy.,§Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy
| | - Paola Ringhieri
- ‡Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy
| | - Giancarlo Morelli
- ‡Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy.,§Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy
| | - Michele Saviano
- §Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy.,∥Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, Italy
| | - Giulia Montagner
- ⊥Department of Life Sciences and Biotechnologies, University of Ferrara, via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Enrica Fabbri
- ⊥Department of Life Sciences and Biotechnologies, University of Ferrara, via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Eleonora Gallerani
- ⊥Department of Life Sciences and Biotechnologies, University of Ferrara, via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Roberto Gambari
- ⊥Department of Life Sciences and Biotechnologies, University of Ferrara, via Fossato di Mortara 74, 44121 Ferrara, Italy
| | - Alessandra Romanelli
- ‡Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134 Napoli, Italy.,§Interuniversity Research Centre on Bioactive Peptides (CIRPeB), via Mezzocannone 16, 80134 Napoli, Italy
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6
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Marzaro G, Lampronti I, Borgatti M, Manzini P, Gambari R, Chilin A. Psoralen derivatives as inhibitors of NF-κB interaction: the critical role of the furan ring. Mol Divers 2015; 19:551-61. [PMID: 25869956 DOI: 10.1007/s11030-015-9586-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 03/21/2015] [Indexed: 12/26/2022]
Abstract
Simplified analogues of previously reported NF-κB interaction inhibitors, lacking the furan moiety, were synthesized and evaluated by performing experiments based on electrophoretic mobility shift assay (EMSA). The synthetic modifications led to simpler coumarin derivatives with lower activity allowing to better understand the minimal structural requirement for the binding to NF-κB.
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Affiliation(s)
- Giovanni Marzaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
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Rad SMAH, Langroudi L, Kouhkan F, Yazdani L, Koupaee AN, Asgharpour S, Shojaei Z, Bamdad T, Arefian E. Transcription factor decoy: a pre-transcriptional approach for gene downregulation purpose in cancer. Tumour Biol 2015; 36:4871-81. [PMID: 25835969 DOI: 10.1007/s13277-015-3344-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/15/2015] [Indexed: 12/13/2022] Open
Abstract
Gene therapy as a therapeutic approach has been the dream for many scientists around the globe. Many strategies have been proposed and applied for this purpose, yet the void for a functional safe method is still apparent. Since most of the diseases are caused by undesirable upregulation (oncogenes) or downregulation (tumor suppressor genes) of genes, major gene therapy's techniques affect gene expression. Most of the methods are used in post-transcriptional level such as RNA inhibitory (RNAi) and splice-switching oligonucleotides (SSOs). RNAi blocks messenger RNA (mRNA) translation by mRNA degradation or interruption between attachments of mRNA with ribosomes' subunits. However, one of the novel methods is the usage of transcription factor targeted decoys. DNA decoys are the new generation of functional gene downregulatory oligonucleotides which compete with specific binding sites of transcription factors. Considering the exponential growth of this technique in both in vitro and in vivo studies, in this paper, we aim to line out the description, design, and application of decoys in research and therapy.
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Muresan XM, Cervellati F, Sticozzi C, Belmonte G, Chui CH, Lampronti I, Borgatti M, Gambari R, Valacchi G. The loss of cellular junctions in epithelial lung cells induced by cigarette smoke is attenuated by corilagin. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:631758. [PMID: 25802682 PMCID: PMC4354730 DOI: 10.1155/2015/631758] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/02/2015] [Accepted: 01/21/2015] [Indexed: 12/17/2022]
Abstract
Cigarette smoke (CS) contains over 4700 compounds, many of which can affect cellular redox balance through free radicals production or through the modulation of antioxidant enzymes. The respiratory tract is one of the organs directly exposed to CS and it is known that CS can damage the integrity of lung epithelium by affecting cell junctions and increasing epithelium permeability. In this study, we have used a human lung epithelial cell line, Calu-3, to evaluate the effect of CS on lung epithelial cell junctions levels, with special focus on the expression of two proteins involved in intercellular communication: connexins (Cx) 40 and 43. CS exposure increased Cx40 gene expression but not of Cx43. CS also induced NFκB activation and the formation of 4HNE-Cxs adducts. Since corilagin, a natural polyphenol, is able to inhibit NFκB activation, we have determined whether corilagin could counteract the effect of CS on Cxs expression. Corilagin was able to diminish CS induced Cx40 gene expression, 4HNE-Cx40 adducts formation, and NFκB activation. The results of this study demonstrated that CS induced the loss of cellular junctions in lung epithelium, possibly as a consequence of Cx-4HNE adducts formation, and corilagin seems to be able to abolish these CS induced alterations.
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Affiliation(s)
- Ximena M. Muresan
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Franco Cervellati
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Claudia Sticozzi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Giuseppe Belmonte
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Chung Hin Chui
- Clinical Division, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ilaria Lampronti
- Biotechnology Center, University of Ferrara, 44121 Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Giuseppe Valacchi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
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9
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Montagner G, Gemmo C, Fabbri E, Manicardi A, Accardo I, Bianchi N, Finotti A, Breveglieri G, Salvatori F, Borgatti M, Lampronti I, Bresciani A, Altamura S, Corradini R, Gambari R. Peptide nucleic acids targeting β-globin mRNAs selectively inhibit hemoglobin production in murine erythroleukemia cells. Int J Mol Med 2014; 35:51-8. [PMID: 25405921 PMCID: PMC4249754 DOI: 10.3892/ijmm.2014.2005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/03/2014] [Indexed: 12/21/2022] Open
Abstract
In the treatment of hemoglobinopathies, amending altered hemoglobins and/or globins produced in excess is an important part of therapeutic strategies and the selective inhibition of globin production may be clinically beneficial. Therefore the development of drug-based methods for the selective inhibition of globin accumulation is required. In this study, we employed peptide nucleic acids (PNAs) to alter globin gene expression. The main conclusion of the present study was that PNAs designed to target adult murine β-globin mRNA inhibit hemoglobin accumulation and erythroid differentiation of murine erythroleukemia (MEL) cells with high efficiency and fair selectivity. No major effects were observed on cell proliferation. Our study supports the concept that PNAs may be used to target mRNAs that, similar to globin mRNAs, are expressed at very high levels in differentiating erythroid cells. Our data suggest that PNAs inhibit the excess production of globins involved in the pathophysiology of hemoglobinopathies.
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Affiliation(s)
- Giulia Montagner
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Chiara Gemmo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alex Manicardi
- Department of Chemistry, University of Parma, Parma, Italy
| | - Igea Accardo
- Department of Chemistry, University of Parma, Parma, Italy
| | - Nicoletta Bianchi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giulia Breveglieri
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesca Salvatori
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Ilaria Lampronti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | | | | | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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Brognara E, Fabbri E, Bianchi N, Finotti A, Corradini R, Gambari R. Molecular methods for validation of the biological activity of peptide nucleic acids targeting microRNAs. Methods Mol Biol 2014; 1095:165-76. [PMID: 24166312 DOI: 10.1007/978-1-62703-703-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The involvement of microRNAs in human pathologies is a firmly established fact. Accordingly, the pharmacological modulation of their activity appears to be a very appealing issue in the development of new types of drugs (miRNA therapeutics). One of the most interesting issues is the possible development of miRNA therapeutics for development of anti-cancer molecules. In this respect appealing molecules are based on peptide nucleic acids (PNAs), displaying a pseudo-peptide backbone composed of N-(2-aminoethyl)glycine units and found to be excellent candidates for antisense and antigene therapies. The major limit in the use of PNAs for alteration of gene expression is the low uptake by eukaryotic cells. The aim of this chapter is to describe methods for determining the activity of PNAs designed to target oncomiRNAs, using as model system miR-221 and its target p27(Kip1) mRNA. The effects of PNAs targeting miR-221 are here presented discussing data obtained using as model system the human breast cancer cell line MDA-MB-231, in which miR-221 is up-regulated and p27(Kip1) down-regulated.
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Affiliation(s)
- Eleonora Brognara
- Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
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11
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Cheng CJ, Saltzman WM, Slack FJ. Canonical and non-canonical barriers facing antimiR cancer therapeutics. Curr Med Chem 2014; 20:3582-93. [PMID: 23745563 DOI: 10.2174/0929867311320290004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 12/14/2022]
Abstract
Once considered genetic "oddities", microRNAs (miRNAs) are now recognized as key epigenetic regulators of numerous biological processes, including some with a causal link to the pathogenesis, maintenance, and treatment of cancer. The crux of small RNA-based therapeutics lies in the antagonism of potent cellular targets; the main shortcoming of the field in general, lies in ineffective delivery. Inhibition of oncogenic miRNAs is a relatively nascent therapeutic concept, but as with predecessor RNA-based therapies, success hinges on delivery efficacy. This review will describes the canonical (e.g. pharmacokinetics and clearance, cellular uptake, endosome escape, etc.) and non-canonical (e.g. spatial localization and accessibility of miRNA, technical limitations of miRNA inhibition, off-target impacts, etc.) challenges to the delivery of antisense-based anti-miRNA therapeutics (i.e. antimiRs) for the treatment of cancer. Emphasis will be placed on how the current leading antimiR platforms-ranging from naked chemically modified oligonucleotides to nanoscale delivery vehicles-are affected by and overcome these barriers. The perplexity of antimiR delivery presents both engineering and biological hurdles that must be overcome in order to capitalize on the extensive pharmacological benefits of antagonizing tumor-associated miRNAs.
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Affiliation(s)
- Christopher J Cheng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
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Guerrini A, Mancini I, Maietti S, Rossi D, Poli F, Sacchetti G, Gambari R, Borgatti M. Expression of Pro-inflammatory Interleukin-8 is Reduced by Ayurvedic Decoctions. Phytother Res 2014; 28:1173-81. [DOI: 10.1002/ptr.5109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 01/13/2023]
Affiliation(s)
| | - Irene Mancini
- Department of Life Sciences and Biotechnology; University of Ferrara; Italy
| | - Silvia Maietti
- Department of Life Sciences and Biotechnology; University of Ferrara; Italy
| | - Damiano Rossi
- Department of Life Sciences and Biotechnology; University of Ferrara; Italy
| | - Ferruccio Poli
- Department of Pharmacy and Biotechnology; University of Bologna; Italy
| | - Gianni Sacchetti
- Department of Life Sciences and Biotechnology; University of Ferrara; Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology; University of Ferrara; Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology; University of Ferrara; Italy
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Gambari R. Peptide nucleic acids: a review on recent patents and technology transfer. Expert Opin Ther Pat 2014; 24:267-94. [PMID: 24405414 DOI: 10.1517/13543776.2014.863874] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION DNA/RNA-based drugs are considered of major interest in molecular diagnosis and nonviral gene therapy. In this field, peptide nucleic acids (PNAs, DNA analogs in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units or similar building blocks) have been demonstrated to be excellent candidates as diagnostic reagents and biodrugs. AREAS COVERED Recent (2002 - 2013) patents based on studies on development of PNA analogs, delivery systems for PNAs, applications of PNAs in molecular diagnosis, and use of PNA for innovative therapeutic protocols. EXPERT OPINION PNAs are unique reagents in molecular diagnosis and have been proven to be very active and specific for alteration of gene expression, despite the fact that solubility and uptake by target cells can be limiting factors. Accordingly, patents on PNAs have taken in great consideration delivery strategies. PNAs have been proven stable and effective in vivo, despite the fact that possible long-term toxicity should be considered. For possible clinical applications, the use of PNA molecules in combination with drugs already employed in therapy has been suggested. Considering the patents available and the results on in vivo testing on animal models, we expect in the near future relevant PNA-based clinical trials.
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Affiliation(s)
- Roberto Gambari
- University of Ferrara, Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section , Via Fossato di Mortara n.74, 44100 Ferrara , Italy +39 532 974443 ; +39 532 974500 ;
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14
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Brognara E, Fabbri E, Aimi F, Manicardi A, Bianchi N, Finotti A, Breveglieri G, Borgatti M, Corradini R, Marchelli R, Gambari R. Peptide nucleic acids targeting miR-221 modulate p27Kip1 expression in breast cancer MDA-MB-231 cells. Int J Oncol 2012; 41:2119-27. [PMID: 22992757 DOI: 10.3892/ijo.2012.1632] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/08/2012] [Indexed: 01/02/2023] Open
Abstract
The activity of a peptide nucleic acid (PNA) targeting cancer-associated microRNA-221 is described. PNAs against miR-221 were designed in order to bind very efficiently to the target RNA strand and to undergo efficient uptake in the cells. A polyarginine-PNA conjugate targeted against miR-221 (Rpep-PNA-a221) showed both very high affinity for RNA and efficient cellular uptake without the addition of transfection reagents. Unmodified PNA with the same sequence displayed RNA binding, but cellular uptake was very poor. Consistently, only Rpep-PNA-a221 strongly inhibited miR-221. Targeting miR-221 by PNA resulted in i) lowering of the hybridization levels of miR-221 measured by RT-qPCR, ii) upregulation of p27Kip1 gene expression, measured by RT-qPCR and western blot analysis. The major conclusion of this study is that efficient delivery of anti‑miR PNA through a suitable peptide carrier (Rpep‑PNA-a221) leads to inhibition of miR-221 activity, altering the expression of miR-221-regulated functions in breast cancer cells.
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Affiliation(s)
- Eleonora Brognara
- BioPharmaNet, Department of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
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Regulation of neural stem cell differentiation by transcription factors HNF4-1 and MAZ-1. Mol Neurobiol 2012; 47:228-40. [PMID: 22944911 DOI: 10.1007/s12035-012-8335-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/16/2012] [Indexed: 10/27/2022]
Abstract
Neural stem cells (NSCs) are promising candidates for a variety of neurological diseases due to their ability to differentiate into neurons, astrocytes, and oligodentrocytes. During this process, Rho GTPases are heavily involved in neuritogenesis, axon formation and dendritic development, due to their effects on the cytoskeleton through downstream effectors. The activities of Rho GTPases are controlled by Rho-GDP dissociation inhibitors (Rho-GDIs). As shown in our previous study, these are also involved in the differentiation of NSCs; however, little is known about the underlying regulatory mechanism. Here, we describe how the transcription factors hepatic nuclear factor (HNF4-1) and myc-associated zinc finger protein (MAZ-1) regulate the expression of Rho-GDIγ in the stimulation of NSC differentiation. Using a transfection of cis-element double-stranded oligodeoxynucleotides (ODNs) strategy, referred to as "decoy" ODNs, we examined the effects of HNF4-1 and MAZ-1 on NSC differentiation in the NSC line C17.2. Our results show that HNF4-1 and MAZ-1 decoy ODNs significantly knock down Rho-GDIγ gene transcription, leading to NSC differentiation towards neurons. We observed that HNF4-1 and MAZ-1 decoy ODNs are able enter to the cell nucleolus and specifically bind to their target transcription factors. Furthermore, the expression of Rho-GDIγ-mediated genes was identified, suggesting that the regulatory mechanism for the differentiation of NSCs is triggered by the transcription factors MAZ-1 and HNF4-1. These findings indicate that HNF4-1 and MAZ-1 regulate the expression of Rho-GDIγ and contribute to the differentiation of NSCs. Our findings provide a new perspective within regulatory mechanism research during differentiation of NSCs, especially the clinical application of transcription factor decoys in vivo, suggesting potential therapeutic strategies for neurodegenerative disease.
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Avitabile C, Moggio L, Malgieri G, Capasso D, Di Gaetano S, Saviano M, Pedone C, Romanelli A. γ Sulphate PNA (PNA S): highly selective DNA binding molecule showing promising antigene activity. PLoS One 2012; 7:e35774. [PMID: 22586450 PMCID: PMC3346730 DOI: 10.1371/journal.pone.0035774] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/21/2012] [Indexed: 11/18/2022] Open
Abstract
Peptide Nucleic Acids (PNAs), nucleic acid analogues showing high stability to enzyme degradation and strong affinity and specificity of binding toward DNA and RNA are widely investigated as tools to interfere in gene expression. Several studies have been focused on PNA analogues with modifications on the backbone and bases in the attempt to overcome solubility, uptake and aggregation issues. γ PNAs, PNA derivatives having a substituent in the γ position of the backbone show interesting properties in terms of secondary structure and affinity of binding toward complementary nucleic acids. In this paper we illustrate our results obtained on new analogues, bearing a sulphate in the γ position of the backbone, developed to be more DNA-like in terms of polarity and charge. The synthesis of monomers and oligomers is described. NMR studies on the conformational properties of monomers and studies on the secondary structure of single strands and triplexes are reported. Furthermore the hybrid stability and the effect of mismatches on the stability have also been investigated. Finally, the ability of the new analogue to work as antigene, interfering with the transcription of the ErbB2 gene on a human cell line overexpressing ErbB2 (SKBR3), assessed by FACS and qPCR, is described.
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Affiliation(s)
- Concetta Avitabile
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Loredana Moggio
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze Ambientali, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Domenica Capasso
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
| | | | | | - Carlo Pedone
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
- Istituto di Biostrutture e Bioimmagini (CNR), Napoli, Italy
| | - Alessandra Romanelli
- Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Università di Napoli “Federico II”, Napoli, Italy
- Istituto di Biostrutture e Bioimmagini (CNR), Napoli, Italy
- * E-mail:
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Corilagin is a potent inhibitor of NF-kappaB activity and downregulates TNF-alpha induced expression of IL-8 gene in cystic fibrosis IB3-1 cells. Int Immunopharmacol 2012; 13:308-15. [PMID: 22561123 DOI: 10.1016/j.intimp.2012.04.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 04/04/2012] [Accepted: 04/18/2012] [Indexed: 01/21/2023]
Abstract
Corilagin (beta-1-O-galloyl-3,6-(R)-hexahydroxydiphenoyl-d-glucose), a gallotannin identified in several plants, including Phyllanthus urinaria, has been shown to exhibit versatile medicinal activities. As far as possible anti-inflammatory effects of corilagin, only few reports are available, and the potential use of corilagin as possible therapeutic molecule for cystic fibrosis has not been evaluated. In the present paper we report experiments aimed at determining the activity of corilagin on nuclear factor kappaB (NF-kappaB) binding to DNA target and on the expression of the major pro-inflammatory gene involved in cystic fibrosis, interleukin-8 (IL-8). Both IL-8 mRNA content and IL-8 protein secretion were analyzed in cystic fibrosis bronchial IB3-1 cells stimulated by tumor necrosis factor-alpha (TNF-alpha), one of the most potent pro-inflammatory agents. The data obtained demonstrate that corilagin binds to NF-kappaB, inhibits NF-kappaB/DNA interactions and affects IL-8 gene expression in TNF-alpha treated IB3-1 cells. In addition, corilagin inhibits TNF-alpha induced secretion of MCP-1 and RANTES, exhibiting low or no effect on the release of G-CSF, IL-6 and VEGF. Therefore, corilagin might be of interest for experimental anti-inflammatory therapy of cystic fibrosis.
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18
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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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19
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Finotti A, Borgatti M, Bezzerri V, Nicolis E, Lampronti I, Dechecchi M, Mancini I, Cabrini G, Saviano M, Avitabile C, Romanelli A, Gambari R. Effects of decoy molecules targeting NF-kappaB transcription factors in Cystic fibrosis IB3-1 cells: recruitment of NF-kappaB to the IL-8 gene promoter and transcription of the IL-8 gene. ARTIFICIAL DNA, PNA & XNA 2012; 3:97-296. [PMID: 22772035 PMCID: PMC3429536 DOI: 10.4161/adna.21061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
One of the clinical features of cystic fibrosis (CF) is a deep inflammatory process, which is characterized by production and release of cytokines and chemokines, among which interleukin 8 (IL-8) represents one of the most important. Accordingly, there is a growing interest in developing therapies against CF to reduce the excessive inflammatory response in the airways of CF patients. Since transcription factor NF-kappaB plays a critical role in IL-8 expression, the transcription factor decoy (TFD) strategy might be of interest. In order to demonstrate that TFD against NF-kappaB interferes with the NF-kappaB pathway we proved, by chromatin immunoprecipitation (ChIP) that treatment with TFD oligodeoxyribonucleotides of cystic fibrosis IB3–1 cells infected with Pseudomonas aeruginosa leads to a decrease occupancy of the Il-8 gene promoter by NF-kappaB factors. In order to develop more stable therapeutic molecules, peptide nucleic acids (PNAs) based agents were considered. In this respect PNA-DNA-PNA (PDP) chimeras are molecules of great interest from several points of view: (1) they can be complexed with liposomes and microspheres; (2) they are resistant to DNases, serum and cytoplasmic extracts; (3) they are potent decoy molecules. By using electrophoretic mobility shift assay and RT-PCR analysis we have demonstrated that (1) the effects of PDP/PDP NF-kappaB decoy chimera on accumulation of pro-inflammatory mRNAs in P.aeruginosa infected IB3–1 cells reproduce that of decoy oligonucleotides; in particular (2) the PDP/PDP chimera is a strong inhibitor of IL-8 gene expression; (3) the effect of PDP/PDP chimeras, unlike those of ODN-based decoys, are observed even in the absence of protection with lipofectamine. These informations are of great impact, in our opinion, for the development of stable molecules to be used in non-viral gene therapy of cystic fibrosis.
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Affiliation(s)
- Alessia Finotti
- ER-GenTech and BioPharmaNet, Department of Biochemistry and Molecular Biology, Università di Ferrara, Ferrara, Italy
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Gambari R. Recent patents on therapeutic applications of the transcription factor decoy approach. Expert Opin Ther Pat 2012; 21:1755-71. [PMID: 22017413 DOI: 10.1517/13543776.2011.629605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Transcription is considered as an important target of drugs employed in biomedicine. Therefore, novel strategies to inhibit the biological effects of transcription factors (TFs) are of interest, such as targeting promoters with triple-helix-forming oligonucleotides and antisense targeting of mRNAs coding for TFs. AREAS COVERED The objective of this review is to describe studies considering inhibition of TF functions with molecules mimicking TF binding sites (transcription factor decoy approach, TFD) and to summarize the patents on possible clinical applications of this approach. EXPERT OPINION Treatment of cells with TFD molecules leads to inhibition (or activation) of genes regulated by the target transcription factors. The studies and patents on this specific issue have taken in great consideration the delivery strategy, which is a very important parameter. The TFD strategy has been proven effective in vivo. The stability of the TFD molecules in vivo should be carefully considered, as well as the possible toxicity and/or possible effects on innate and adaptive immune response. In order to improve clinical parameters, many patents suggest the use of the TFD molecules in combination with drugs already employed in therapy. We are expecting in the near future relevant clinical trials based on the TFD strategy.
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Affiliation(s)
- Roberto Gambari
- University of Ferrara, Interdisciplinary Center for the Study of Inflammation, ER-GenTech and BioPharmaNet, Department of Biochemistry and Molecular Biology, Ferrara, Italy.
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21
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Fabbri E, Manicardi A, Tedeschi T, Sforza S, Bianchi N, Brognara E, Finotti A, Breveglieri G, Borgatti M, Corradini R, Marchelli R, Gambari R. Modulation of the biological activity of microRNA-210 with peptide nucleic acids (PNAs). ChemMedChem 2011; 6:2192-202. [PMID: 22012891 DOI: 10.1002/cmdc.201100270] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 09/28/2011] [Indexed: 12/13/2022]
Abstract
Herein we describe the activity of a peptide nucleic acid (PNA) that targets microRNA-210 (miR-210), which is associated with hypoxia and is modulated during erythroid differentiation. PNAs directed against miR-210 were designed to bind with high affinity to the target RNA strand and to undergo efficient uptake in target cells. A polyarginine-PNA conjugate directed against miR-210 (Rpep-PNA-a210) showed both very high affinity for RNA and efficient uptake into target cells without the need for transfection reagents. An unmodified PNA of the same sequence displayed the ability to bind RNA, but cellular uptake was very poor. Consistent with this, only Rpep-PNA-a210 strongly inhibited miR-210 activity, as evaluated by assays on undifferentiated K562 cells and on cells treated with mithramycin, which was found to induce erythroid differentiation and miR-210 overexpression. Targeting miR-210 by Rpep-PNA-a210 resulted in: 1) a decrease in miR-210 levels as measured by RT-PCR, 2) up-regulation of raptor mRNA, 3) a decrease in γ-globin mRNA, and 4) decreased expression of differentiated functions (i.e., proportion of benzidine-positive cells, content of embryo-fetal hemoglobins). The efficient delivery of anti-miR PNAs through a suitable peptide carrier (Rpep-PNA-a210) leads to the inhibition of miR-210 activity, altering the expression of miR-210-regulated erythroid functions.
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Affiliation(s)
- Enrica Fabbri
- BioPharmaNet, Department of Biochemistry and Molecular Biology, University of Ferrara, Via Fossato di Mortara n.74, 44121 Ferrara, Italy.
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22
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Borgatti M, Chilin A, Piccagli L, Lampronti I, Bianchi N, Mancini I, Marzaro G, Francesco dall’Acqua, Guiotto A, Gambari R. Development of a novel furocoumarin derivative inhibiting NF-κB dependent biological functions: Design, synthesis and biological effects. Eur J Med Chem 2011; 46:4870-7. [DOI: 10.1016/j.ejmech.2011.07.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 07/13/2011] [Accepted: 07/18/2011] [Indexed: 12/15/2022]
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23
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Gambari R, Fabbri E, Borgatti M, Lampronti I, Finotti A, Brognara E, Bianchi N, Manicardi A, Marchelli R, Corradini R. Targeting microRNAs involved in human diseases: a novel approach for modification of gene expression and drug development. Biochem Pharmacol 2011; 82:1416-29. [PMID: 21864506 DOI: 10.1016/j.bcp.2011.08.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/30/2022]
Abstract
The identification of all epigenetic modifications (i.e. DNA methylation, histone modifications and expression of noncoding RNAs such as microRNAs) involved in gene regulation is one of the major steps forward for understanding human biology in both normal and pathological conditions and for development of novel drugs. In this context, microRNAs play a pivotal role. This review article focuses on the involvement of microRNAs in the regulation of gene expression, on the possible role of microRNAs in the onset and development of human pathologies, and on the pharmacological alteration of the biological activity of microRNAs. RNA and DNA analogs, which can selectively target microRNAs using Watson-Crick base pairing schemes, provide a rational and efficient way to modulate gene expression. These compounds, termed antago-miR or anti-miR have been described in many examples in the recent literature and have proved to be able to perform regulatory as well as therapeutic functions. Among these, a still not fully exploited class is that of peptide nucleic acids (PNAs), promising tools for the inhibition of miRNA activity, with important applications in gene therapy and in drug development. PNAs targeting miR-122, miR-155 and miR-210 have already been developed and their biological effects studied both in vitro and in vivo.
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Affiliation(s)
- Roberto Gambari
- Laboratory for Development of Pharmacological and Pharmacogenomic Therapy of Thalassaemia, Biotechnology Center, University of Ferrara, Ferrara, Italy.
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Tamanini A, Borgatti M, Finotti A, Piccagli L, Bezzerri V, Favia M, Guerra L, Lampronti I, Bianchi N, Dall'Acqua F, Vedaldi D, Salvador A, Fabbri E, Mancini I, Nicolis E, Casavola V, Cabrini G, Gambari R. Trimethylangelicin reduces IL-8 transcription and potentiates CFTR function. Am J Physiol Lung Cell Mol Physiol 2011; 300:L380-90. [DOI: 10.1152/ajplung.00129.2010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chronic inflammatory response in the airway tract of patients affected by cystic fibrosis is characterized by an excessive recruitment of neutrophils to the bronchial lumina, driven by the chemokine interleukin (IL)-8. We previously found that 5-methoxypsoralen reduces Pseudomonas aeruginosa -dependent IL-8 transcription in bronchial epithelial cell lines, with an IC50 of 10 μM (Nicolis E, Lampronti I, Dechecchi MC, Borgatti M, Tamanini A, Bezzerri V, Bianchi N, Mazzon M, Mancini I, Giri MG, Rizzotti P, Gambari R, Cabrini G. Int Immunopharmacol 9: 1411–1422, 2009). Here, we extended the investigation to analogs of 5-methoxypsoralen, and we found that the most potent effect is obtained with 4,6,4′-trimethylangelicin (TMA), which inhibits P. aeruginosa -dependent IL-8 transcription at nanomolar concentration in IB3–1, CuFi-1, CFBE41o−, and Calu-3 bronchial epithelial cell lines. Analysis of phosphoproteins involved in proinflammatory transmembrane signaling evidenced that TMA reduces the phosphorylation of ribosomal S6 kinase-1 and AKT2/3, which we found indeed involved in P. aeruginosa -dependent activation of IL-8 gene transcription by testing the effect of pharmacological inhibitors. In addition, we found a docking site of TMA into NF-κB by in silico analysis, whereas inhibition of the NF-κB/DNA interactions in vitro by EMSA was observed at high concentrations (10 mM TMA). To further understand whether NF-κB pathway should be considered a target of TMA, chromatin immunoprecipitation was performed, and we observed that TMA (100 nM) preincubated in whole living cells reduced the interaction of NF-κB with the promoter of IL-8 gene. These results suggest that TMA could inhibit IL-8 gene transcription mainly by intervening on driving the recruitment of activated transcription factors on IL-8 gene promoter, as demonstrated here for NF-κB. Although the complete understanding of the mechanism of action of TMA deserves further investigation, an activity of TMA on phosphorylating pathways was already demonstrated by our study. Finally, since psoralens have been shown to potentiate cystic fibrosis transmembrane conductance regulator (CFTR)-mediated chloride transport, TMA was tested and found to potentiate CFTR-dependent chloride efflux. In conclusion, TMA is a dual-acting compound reducing excessive IL-8 expression and potentiating CFTR function.
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Affiliation(s)
- Anna Tamanini
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Monica Borgatti
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Alessia Finotti
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Laura Piccagli
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Valentino Bezzerri
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Maria Favia
- Department of General and Environmental Physiology, University of Bari, Bari
| | - Lorenzo Guerra
- Department of General and Environmental Physiology, University of Bari, Bari
| | - Ilaria Lampronti
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Nicoletta Bianchi
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | | | - Daniela Vedaldi
- Department of Pharmaceutical Sciences, University of Padova, Padova; and
| | - Alessia Salvador
- Department of Pharmaceutical Sciences, University of Padova, Padova; and
| | - Enrica Fabbri
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Irene Mancini
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Elena Nicolis
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Valeria Casavola
- Department of General and Environmental Physiology, University of Bari, Bari
| | - Giulio Cabrini
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Roberto Gambari
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
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Virtual screening against nuclear factor κB (NF-κB) of a focus library: Identification of bioactive furocoumarin derivatives inhibiting NF-κB dependent biological functions involved in cystic fibrosis. Bioorg Med Chem 2010; 18:8341-9. [DOI: 10.1016/j.bmc.2010.09.063] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/22/2010] [Accepted: 09/24/2010] [Indexed: 11/23/2022]
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26
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Gambari R, Borgatti M, Bezzerri V, Nicolis E, Lampronti I, Dechecchi MC, Mancini I, Tamanini A, Cabrini G. Decoy oligodeoxyribonucleotides and peptide nucleic acids-DNA chimeras targeting nuclear factor kappa-B: inhibition of IL-8 gene expression in cystic fibrosis cells infected with Pseudomonas aeruginosa. Biochem Pharmacol 2010; 80:1887-94. [PMID: 20615393 DOI: 10.1016/j.bcp.2010.06.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 06/24/2010] [Accepted: 06/28/2010] [Indexed: 12/25/2022]
Abstract
Cystic fibrosis (CF) is characterized by a deep inflammatory process, with production and release of cytokines and chemokines, among which interleukin 8 (IL-8) represents one of the most important. Accordingly, there is a growing interest in developing therapies against IL-8, with the aim of reducing the excessive inflammatory response in the airways of CF patients. Since transcription factor NF-kappaB plays a critical role in IL-8 expression, the transcription factor decoy (TFD) strategy might be of interest. TFD is based on biomolecules mimicking the target sites of transcription factors (TFs) and able to interfere with TF activity when delivered to target cells. Here, we review the inhibitory effects of decoy oligodeoxyribonucleotides (ODNs) on expression of IL-8 gene and secretion of IL-8 by cystic fibrosis cells infected by Pseudomonas aeruginosa. In addition, the effects of decoy molecules based on peptide nucleic acids (PNAs) are discussed. In this respect PNA-DNA-PNA (PDP) chimeras are interesting: (a) unlike PNAs, they can be complexed with liposomes and microspheres; (b) unlike oligodeoxyribonucleotides (ODNs), they are resistant to DNAses, serum and cytoplasmic extracts; (c) unlike PNA/PNA and PNA/DNA hybrids, they are potent decoy molecules. Interestingly, PDP/PDP NF-kappaB decoy chimeras inhibit accumulation of pro-inflammatory mRNAs (including IL-8 mRNA) in P. aeruginosa infected IB3-1, cells reproducing the effects of decoy oligonucleotides. The effects of PDP/PDP chimeras, unlike ODN-based decoys, are observed even in absence of protection with lipofectamine. Since IL-8 is pivotal in pro-inflammatory processes affecting cystic fibrosis, inhibition of its functions might have a clinical relevance.
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Affiliation(s)
- Roberto Gambari
- ER-GenTech and BioPharmaNet, Department of Biochemistry and Molecular Biology, University of Ferrara, Italy.
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27
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Piccagli L, Fabbri E, Borgatti M, Bianchi N, Bezzerri V, Mancini I, Nicolis E, Dechecchi C, Lampronti I, Cabrini G, Gambari R. Virtual Screening against p50 NF-κB Transcription Factor for the Identification of Inhibitors of the NF-κB-DNA Interaction and Expression of NF-κB Upregulated Genes. ChemMedChem 2009; 4:2024-33. [DOI: 10.1002/cmdc.200900362] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Piccagli L, Fabbri E, Borgatti M, Bezzerri V, Mancini I, Nicolis E, Dechecchi MC, Lampronti I, Cabrini G, Gambari R. Docking of molecules identified in bioactive medicinal plants extracts into the p50 NF-kappaB transcription factor: correlation with inhibition of NF-kappaB/DNA interactions and inhibitory effects on IL-8 gene expression. BMC STRUCTURAL BIOLOGY 2008; 8:38. [PMID: 18768082 PMCID: PMC2543017 DOI: 10.1186/1472-6807-8-38] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 09/03/2008] [Indexed: 12/12/2022]
Abstract
Background The transcription factor NF-kappaB is a very interesting target molecule for the design on anti-tumor, anti-inflammatory and pro-apoptotic drugs. However, the application of the widely-used molecular docking computational method for the virtual screening of chemical libraries on NF-kappaB is not yet reported in literature. Docking studies on a dataset of 27 molecules from extracts of two different medicinal plants to NF-kappaB-p50 were performed with the purpose of developing a docking protocol fit for the target under study. Results We enhanced the simple docking procedure by means of a sort of combined target- and ligand-based drug design approach. Advantages of this combination strategy, based on a similarity parameter for the identification of weak binding chemical entities, are illustrated in this work with the discovery of a new lead compound for NF-kappaB. Further biochemical analyses based on EMSA were performed and biological effects were tested on the compound exhibiting the best docking score. All experimental analysis were in fairly good agreement with molecular modeling findings. Conclusion The results obtained sustain the concept that the docking performance is predictive of a biochemical activity. In this respect, this paper represents the first example of successfully individuation through molecular docking simulations of a promising lead compound for the inhibition of NF-kappaB-p50 biological activity and modulation of the expression of the NF-kB regulated IL8 gene.
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Affiliation(s)
- Laura Piccagli
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Italy.
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29
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Moggio L, Romanelli A, Gambari R, Bianchi N, Borgatti M, Fabbri E, Mancini I, di Blasio B, Pedone C, Messere A. Alternate PNA-DNA chimeras (PNA-DNA)(n): synthesis, binding properties and biological activity. Biopolymers 2008; 88:815-22. [PMID: 17918186 DOI: 10.1002/bip.20857] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Peptide nucleic acids (PNAs) are oligonucleotide mimics in which the sugar-phosphate backbone has been replaced by a pseudo-peptide backbone. Among PNA-based molecules, PNA-DNA conjugates characterized by tracts of DNA bound to N and/or C terminus of PNA are very soluble in aqueous media, are able to recognize exclusively single strands of DNA and RNA in antiparallel fashion, activate RNAse H, bind to transcription factors and are more stable than DNA to nucleases degradation. Very little information is available on chimeras constituted of alternating monomers of PNA and DNA. In this article, we describe a simple fully automated strategy for the synthesis of 6-mer and 10-mer alternate PNA-DNA chimeras consisting of polythymine oligomers, stability assays in fetal calf serum, UV and CD studies of the single strand alternate chimeras and of alternate chimera/DNA and alternate chimera/RNA duplexes. Evidences supporting the formation of duplex hybrids were found. Furthermore, the ability of forming Hoogsteen base pairing with duplex DNA was investigated. Finally, we tested the ability of the PNA-DNA alternates in (a) interfering with reverse transcription of eukaryotic mRNA and (b) inhibiting DNA-protein interactions.
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Affiliation(s)
- Loredana Moggio
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy
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Chiaramoni NS, Speroni L, Taira MC, Alonso SDV. Liposome/DNA systems: correlation between association, hydrophobicity and cell viability. Biotechnol Lett 2007; 29:1637-44. [PMID: 17636387 DOI: 10.1007/s10529-007-9454-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 06/06/2007] [Accepted: 06/11/2007] [Indexed: 11/29/2022]
Abstract
Small unilamellar vesicles associated with plasmid DNA showed maximum association efficiency for a cationic mixture of egg phosphatidylcholine (EPC):1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE):di-1,2-dioleoyl-3-trimethyl ammonium propane (DOTAP) (16:8:1 molar ratio) [65%], followed by neutral lipids EPC:1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE):cholesterol (Chol) (2:2:1 molar ratio) [30%], and a polymerized formulation 1,2-bis(10,12-tricosadiynoyl)sn-glycero-3-phosphocholine (DC8,9PC):DMPE:Chol (2:2:1 molar ratio) [11%]. The hydrophobicity factor (HF) for these formulations followed the trend DC8,9PC:DMPE:CHOL < EPC:DMPE:Chol < EPC:DOPE DOTAP, and DNA association did not alter this trend. Results suggest that the higher the HF value, the more fluid the membrane and the higher the efficiency of DNA association. On the other hand, no differences were observed in cell toxicity with lipids up to 1 mg/ml in VERO cells.
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Affiliation(s)
- Nadia S Chiaramoni
- Laboratory of Biomembranes (LBM), Universidad Nacional de Quilmes, Roque S. Peña 352, Bernal (C1876BXD), Buenos Aires, Argentina
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Piva R, Penolazzi L, Zennaro M, Bianchini E, Magri E, Borgatti M, Lampronti I, Lambertini E, Tavanti E, Gambari R. Induction of apoptosis of osteoclasts by targeting transcription factors with decoy molecules. Ann N Y Acad Sci 2007; 1091:509-16. [PMID: 17341640 DOI: 10.1196/annals.1378.092] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We review the effects of two transcription factor decoy oligonucleotides on apoptosis of human osteoclasts (OCs). The first decoy molecule was designed to inhibit nuclear factor kappa-B (NF-kappaB) binding to target sequence, the second to increase estrogen receptor (ER) alpha expression. We found that both decoy molecules are potent inducers of apoptosis of human OCs, associated with increase of caspase 3 activity and decrease of interleukin 6 expression. In addition, we provide evidence indicating that these oligonucleotides are active in vivo in inducing OCs apoptosis. Because OCs are essential for skeletal development and remodeling throughout the life of animal and man, the approach described is of potential clinical importance.
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Affiliation(s)
- Roberta Piva
- Department of Biochemistry and Molecular Biology, Section of Molecular Biology, Università degli Studi di Ferrara, Via Fossato di Mortara 74, 44100 Ferrara, Italy
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Petraccone L, Pagano B, Esposito V, Randazzo A, Piccialli G, Barone G, Mattia CA, Giancola C. Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras. J Am Chem Soc 2006; 127:16215-23. [PMID: 16287312 DOI: 10.1021/ja0545923] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PNA-DNA chimeras present the interesting properties of PNA, such as the high binding affinity to complementary single-strand (DNA or RNA), and the resistance to nuclease and protease degradation. At the same time, the limitations of an oligomer containing all PNA residues, such as low water solubility, self-aggregation, and low cellular uptake, are effectively overcome. Further, PNA-DNA chimeras possess interesting biological properties as antisense agents. We have explored the ability of PNA-DNA chimeric strands to assemble in quadruplex structures. The rate constant for association of the quadruplexes and their thermodynamic properties have been determined by CD spectroscopy and differential scanning calorimetry (DSC). Thermal denaturation experiments indicated higher thermal and thermodynamic stabilities for chimeric quadruplexes in comparison with the corresponding unmodified DNA quadruplex. Singular value decomposition analysis (SVD) suggests the presence of kinetically stable intermediate species in the quadruplex formation process. The experimental results have been discussed on the basis of molecular dynamic simulations. The ability of PNA-DNA chimeras to form stable quadruplex structures expands their potential utility as therapeutic agents.
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Affiliation(s)
- Luigi Petraccone
- Dipartimento di Scienze Farmaceutiche, Via Ponte Don Melillo, 84084, Fisciano (SA), Italy
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Mischiati C, Sereni A, Finotti A, Breda L, Cortesi R, Nastruzzi C, Romanelli A, Saviano M, Bianchi N, Pedone C, Borgatti M, Gambari R. Complexation to cationic microspheres of double-stranded peptide nucleic acid-DNA chimeras exhibiting decoy activity. J Biomed Sci 2005; 11:697-704. [PMID: 15316146 DOI: 10.1007/bf02256136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Accepted: 04/15/2004] [Indexed: 11/28/2022] Open
Abstract
The major aim of this paper was to determine whether cationic microspheres (CM), consisting of the permeable polymer Eudragit RS 100 plus the cationic surfactant dioctadecyl-dimethyl-ammonium bromide (DDAB(18)), could bind to double-stranded peptide nucleic acid PNA-DNA-PNA (PDP) chimeras exhibiting decoy activity against NF-kappaB transcription factors. Microspheres were produced by the 'solvent evaporation method' and centrifugation at 500, 1,000 and 3,000 rpm to obtain different-sized microparticles. Microsphere morphology, size and size distribution were determined by optical and electron microscopy observations. In order to determine their binding activity, double-stranded DNA-based and PDP-based decoy molecules were incubated with different amounts of microparticles in the presence of 100 ng of either (32)P-labeled DNA-DNA or DNA-PDP hybrid molecules or cold PDP-PDP hybrids. The complexes were analyzed by agarose gel electrophoresis. The resistance of (32)P-labeled DNA-DNA and DNA-PDP molecules in the presence of serum or cellular extracts was evaluated after binding to CM by gel electrophoresis analysis. DDAB(18) Eudragit RS 100 microspheres are able to bind to DNA-PDP and PDP-PDP hybrids, to deliver these molecules to target cells and to protect DNA-PDP molecules from enzymatic degradation in simulated biological fluids. In addition, when assayed in ex vivo conditions, DDAB(18) Eudragit RS 100 microspheres exhibited low toxicity. The results presented in this paper demonstrate that CM can be considered suitable formulations for pharmacogenomic therapy employing double-stranded PDP chimeras.
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Affiliation(s)
- Carlo Mischiati
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
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Marin VL, Roy S, Armitage BA. Recent advances in the development of peptide nucleic acid as a gene-targeted drug. Expert Opin Biol Ther 2004; 4:337-48. [PMID: 15006728 DOI: 10.1517/14712598.4.3.337] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Peptide nucleic acid (PNA) is a non-ionic mimic of DNA that binds to complementary DNA and RNA sequences with high affinity and selectivity. Targeting of single-stranded RNA leads to antisense effects, whereas PNAs directed toward double-stranded DNA exhibit antigene properties. Recent advances in cell uptake and in antisense and antigene effects in biological systems are summarised in this review. In addition to traditional targets, namely genomic DNA and messenger RNA, applications for PNA as a bacteriocidal antibiotic, for regulating splice site selection and as a telomerase inhibitor are described.
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Affiliation(s)
- Violeta L Marin
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA
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Cortesi R, Mischiati C, Borgatti M, Breda L, Romanelli A, Saviano M, Pedone C, Gambari R, Nastruzzi C. Formulations for natural and peptide nucleic acids based on cationic polymeric submicron particles. AAPS J 2004; 6:10-21. [PMID: 18465254 PMCID: PMC2750937 DOI: 10.1208/ps060102] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2003] [Accepted: 11/09/2003] [Indexed: 12/29/2022] Open
Abstract
This article describes the production and characterization of cationic submicron particles constituted with Eudragit RS 100, plus different cationic surfactants, such as dioctadecyl-dimethyl-ammonium bromide (DDAB18) and diisobutyphenoxyethyl-dimethylbenzyl ammonium chloride (DEBDA), as a transport and delivery system for DNA/DNA and DNA/peptide nucleic acid (PNA) hybrids and PNA-DNA chimeras. Submicron particles could offer advantages over other delivery systems because they maintain unaltered physicochemical properties for long time periods, allowing long-term storage, and are suitable for industrial production. Submicron particles were characterized in terms of size, size distribution, morphology, and zeta potential. Moreover, the in vitro activity and ability of submicron particles to complex different types of nucleic acids were described. Finally, the ability of submicron particles to deliver functional genes to cells cultured in vitro was determined by a luciferase activity assay, demonstrating that submicron particles possess superior transfection efficiency with respect to commercially available, liposome-based transfection kits.
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Affiliation(s)
- Rita Cortesi
- />Department of Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Carlo Mischiati
- />Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Monica Borgatti
- />Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | - Laura Breda
- />Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
| | | | - Michele Saviano
- />Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - Carlo Pedone
- />Institute of Biostructure and Bioimaging, CNR, Napoli, Italy
| | - Roberto Gambari
- />Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
- />Laboratory for the Development of Pharmacological and Pharmacogenomic Therapy of Thalassemia, Biotechnology Centre, University of Ferrara, Italy
| | - Claudio Nastruzzi
- />Department of Pharmaceutical Chemistry and Technology, University of Perugia Dipartimento di Chimica e Tecnologia del Farmaco, via del Liceo, 06100 Perugia, Italy
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Penolazzi L, Lambertini E, Borgatti M, Piva R, Cozzani M, Giovannini I, Naccari R, Siciliani G, Gambari R. Decoy oligodeoxynucleotides targeting NF-kappaB transcription factors: induction of apoptosis in human primary osteoclasts. Biochem Pharmacol 2003; 66:1189-98. [PMID: 14505798 DOI: 10.1016/s0006-2952(03)00470-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins belonging to the nuclear factor kappaB (NF-kappaB) superfamily are involved in osteoclast formation, playing a very important role for both differentiation of osteoclast precursors and survival of mature osteoclasts. Several drugs used to fight bone loss in a variety of human pathologies, including osteoporosis, act by increasing the frequency of osteoclast apoptosis, since it was demonstrated that small changes in osteoclast apoptosis can result in large changes in bone formation. In this respect, targeting of NF-kappaB transcription factor could be of great interest. Among nonviral gene therapy strategies recently proposed to inhibit or even block NF-kappaB activity, the transcription factor decoy (TFD) should be taken in great consideration. The main issue of the present study was to examine the effects of decoy DNA/DNA molecules targeting NF-kappaB on apoptosis of human osteoclasts (OCs), with the aim to interfere with the pathway regulating osteoclast differentiation and programmed cell death. To this aim, we used a mixture of receptor activator of NF-kappaB ligand (RANKL), macrophage colony-stimulating factor (M-CSF) and parathyroid hormone (PTH) to prepare human OCs from peripheral blood cells. Then, transfection with the decoy molecules targeting NF-kappaB was performed. The results obtained demonstrate that in primary cells expressing typical osteoclast markers such as TRAP and MMP9, NF-kappaB decoy significantly stimulated apoptosis. Inhibition of IL-6 expression and induction of Caspase 3 were found in OCs treated with NF-kappaB DNA/DNA decoys. We consider these data as the basis for setting up experimental conditions allowing nonviral gene therapy of several bone disorders.
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Affiliation(s)
- Letizia Penolazzi
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
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37
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Borgatti M, Rutigliano C, Bianchi N, Mischiati C, Baraldi PG, Romagnoli R, Gambari R. Inhibition of NF-kB/DNA Interactions and HIV-1 LTR Directed Transcription by Hybrid Molecules Containing Pyrrolo [2,1-c] [1,4] Benzodiazepine (PBD) and Oligopyrrole Carriers. Drug Dev Res 2003. [DOI: 10.1002/ddr.10280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Borgatti M, Lampronti I, Romanelli A, Pedone C, Saviano M, Bianchi N, Mischiati C, Gambari R. Transcription factor decoy molecules based on a peptide nucleic acid (PNA)-DNA chimera mimicking Sp1 binding sites. J Biol Chem 2003; 278:7500-9. [PMID: 12446679 DOI: 10.1074/jbc.m206780200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide nucleic acids (PNAs) are DNA-mimicking molecules in which the sugar-phosphate backbone is replaced by a pseudopeptide backbone composed of N-(2-aminoethyl)glycine units. We determined whether double-stranded molecules based on PNAs and PNA-DNA-PNA (PDP) chimeras could be capable of stable interactions with nuclear proteins belonging to the Sp1 transcription factor family and, therefore, could act as decoy reagents able to inhibit molecular interactions between Sp1 and DNA. Since the structure of PNA/PNA hybrids is very different from that of the DNA/DNA double helix, they could theoretically alter the molecular structure of the double-stranded PNA-DNA-PNA chimeras, perturbing interactions with specific transcription factors. We found that PNA-based hybrids do not inhibit Sp1/DNA interactions. In contrast, hybrid molecules based on PNA-DNA-PNA chimeras are very effective decoy molecules, encouraging further experiments focused on the possible use of these molecules for the development of potential agents for a decoy approach in gene therapy. In this respect, the finding that PDP-based decoy molecules are more resistant than DNA/DNA hybrids to enzymatic degradation appears to be of great interest. Furthermore, their resistance can even be improved after complexation with cationic liposomes to which PDP/PDP chimeras are able to bind by virtue of their internal DNA structure.
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Affiliation(s)
- Monica Borgatti
- Department of Biochemistry and Molecular Biology, Ferrara University, Via L.Borsari n.46, 44100 Ferrara, Italy
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Literature Alerts. J Microencapsul 2003. [DOI: 10.3109/02652040309178068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Piva R, Gambari R. Transcription factor decoy (TFD) in breast cancer research and treatment. Technol Cancer Res Treat 2002; 1:405-16. [PMID: 12625767 DOI: 10.1177/153303460200100512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Synthetic oligonucleotides have recently been the object of many investigations aimed to develop sequence-selective compounds able to modulate, either positively or negatively, transcription of eukaryotic and viral genes. Alteration of transcription could be obtained by using synthetic oligonucleotides mimicking target sites of transcription factors (the transcription factor decoy -TFD- approach). This could lead to either inhibition or activation of gene expression, depending on the biological functions of the target transcription factors. Since several transcription factors are involved in tumor onset and progression, this issue is of great interest in order to design anti-tumor compounds. In addition to oligonucleotides, peptide nucleic acids (PNA) can be proposed for the modulation of gene expression. In this respect, double-stranded PNA-DNA chimeras have been shown to be capable to exhibit strong decoy activity. In the case of treatment of breast cancer cells, decoy oligonucleotides mimicking CRE binding sites, promoter region of estrogen receptor alpha gene, NF-kB binding sites have been used with promising results. Therefore, the transcription factor decoy approach could be object of further studies to develop protocols for the treatment of breast cancer. In the future, transcription factors regulating cell cycle, hormone-dependent differentiation, tumor invasion and metastasis are expected to be suitable targets for transcription factor decoy.
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Affiliation(s)
- Roberta Piva
- Department of Biochemistry and Molecular Biology, Ferrara University, Via Luigi Borsari, 46, 44100 Ferrara, Italy
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