1
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Diaferia C, Avitabile C, Leone M, Gallo E, Saviano M, Accardo A, Romanelli A. Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates. Chemistry 2021; 27:14307-14316. [PMID: 34314536 PMCID: PMC8597081 DOI: 10.1002/chem.202102481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/12/2022]
Abstract
Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the "suprastructures" typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer "gc" and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.
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Affiliation(s)
- Carlo Diaferia
- Department of PharmacyResearch Centre on Bioactive Peptides (CIRPeB)University of Naples “Federico II”Via Mezzocannone 1680134NaplesItaly
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR)Via Mezzocannone 1680134NaplesItaly
| | | | - Michele Saviano
- Institute of Crystallography (CNR)Via Amendola 12270126BariItaly
| | - Antonella Accardo
- Department of PharmacyResearch Centre on Bioactive Peptides (CIRPeB)University of Naples “Federico II”Via Mezzocannone 1680134NaplesItaly
| | - Alessandra Romanelli
- Department of Pharmaceutical SciencesUniversity of MilanVia Venezian 2120133MilanItaly
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2
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Zhan X, Deng L, Chen G. Mechanisms and applications of peptide nucleic acids selectively binding to double-stranded RNA. Biopolymers 2021; 113:e23476. [PMID: 34581432 DOI: 10.1002/bip.23476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022]
Abstract
RNAs form secondary structures containing double-stranded base paired regions and single-stranded regions. Probing, detecting and modulating RNA structures and dynamics requires the development of molecular sensors that can differentiate the sequence and structure of RNAs present in viruses and cells, as well as in extracellular space. In this review, we summarize the recent progress on the development of chemically modified peptide nucleic acids (PNAs) for the selective recognition of double-stranded RNA (dsRNA) sequences over both single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) sequences. We also briefly discuss the applications of sequence-specific dsRNA-binding PNAs in sensing and stabilizing dsRNA structures and inhibiting dsRNA-protein interactions.
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Affiliation(s)
- Xuan Zhan
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Liping Deng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
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3
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Klabenkova K, Fokina A, Stetsenko D. Chemistry of Peptide-Oligonucleotide Conjugates: A Review. Molecules 2021; 26:5420. [PMID: 34500849 PMCID: PMC8434111 DOI: 10.3390/molecules26175420] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022] Open
Abstract
Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.
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Affiliation(s)
- Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alesya Fokina
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
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4
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Winkle M, El-Daly SM, Fabbri M, Calin GA. Noncoding RNA therapeutics - challenges and potential solutions. Nat Rev Drug Discov 2021; 20:629-651. [PMID: 34145432 PMCID: PMC8212082 DOI: 10.1038/s41573-021-00219-z] [Citation(s) in RCA: 805] [Impact Index Per Article: 268.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Therapeutic targeting of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), represents an attractive approach for the treatment of cancers, as well as many other diseases. Over the past decade, substantial effort has been made towards the clinical application of RNA-based therapeutics, employing mostly antisense oligonucleotides and small interfering RNAs, with several gaining FDA approval. However, trial results have so far been ambivalent, with some studies reporting potent effects whereas others demonstrated limited efficacy or toxicity. Alternative entities such as antimiRNAs are undergoing clinical testing, and lncRNA-based therapeutics are gaining interest. In this Perspective, we discuss key challenges facing ncRNA therapeutics - including issues associated with specificity, delivery and tolerability - and focus on promising emerging approaches that aim to boost their success.
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Affiliation(s)
- Melanie Winkle
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Sherien M El-Daly
- Medical Biochemistry Department, Medical Research Division - Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences - National Research Centre, Cairo, Egypt
| | - Muller Fabbri
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
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5
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Janssens Y, Wynendaele E, Vanden Berghe W, De Spiegeleer B. Peptides as epigenetic modulators: therapeutic implications. Clin Epigenetics 2019; 11:101. [PMID: 31300053 PMCID: PMC6624906 DOI: 10.1186/s13148-019-0700-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Peptides originating from different sources (endogenous, food derived, environmental, and synthetic) are able to influence different aspects of epigenetic regulation. Endogenous short peptides, resulting from proteolytic cleavage of proteins or upon translation of non-annotated out of frame transcripts, can block DNA methylation and hereby regulate gene expression. Peptides entering the body by digestion of food-related proteins can modulate DNA methylation and/or histone acetylation while environmental peptides, synthesized by bacteria, fungi, and marine sponges, mainly inhibit histone deacetylation. In addition, synthetic peptides that reverse or inhibit different epigenetic modifications of both histones and the DNA can be developed as well. Next to these DNA and histone modifications, peptides can also influence the expression of non-coding RNAs such as lncRNAs and the maturation of miRNAs. Seen the advantages over small molecules, the development of peptide therapeutics is an interesting approach to treat diseases with a strong epigenetic basis like cancer and Alzheimer’s disease. To date, only a limited number of drugs with a proven epigenetic mechanism of action have been approved by the FDA of which two (romidepsin and nesiritide) are peptides. A large knowledge gap concerning epigenetic effects of peptides is present, and this class of molecules deserves more attention in the development as epigenetic modulators. In addition, none of the currently approved peptide drugs are under investigation for their potential effects on epigenetics, hampering drug repositioning of these peptides to other indications with an epigenetic etiology.
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Affiliation(s)
- Yorick Janssens
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Wim Vanden Berghe
- Protein Science, Proteomics and Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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6
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Mirihana Arachchilage G, Kharel P, Reid J, Basu S. Targeting of G-Quadruplex Harboring Pre-miRNA 92b by LNA Rescues PTEN Expression in NSCL Cancer Cells. ACS Chem Biol 2018. [PMID: 29529863 DOI: 10.1021/acschembio.7b00749] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the elevated levels of microRNAs (miRNAs) often cause various diseases, selective inhibition of miRNA maturation is an important therapeutic strategy. Commonly used anti-miRNA strategies are limited to targeting of mature miRNAs, as the upstream targeting of miRNA maturation with an oligonucleotide is challenging due to the presence of a stable pre-miRNA stem-loop structure. Previously, we reported that about 16% of known human pre-miRNAs have the potential to adopt G-quadruplex (GQ) structures alternatively to canonical stem-loops. Herein, we showed that a rationally designed locked nucleic acid (LNA) binds specifically the GQ conformation of pre-miRNA 92b and inhibits pre-miRNA maturation. Further, we showed that the LNA treatment rescues PTEN expression in non-small-cell lung cancer (NSCLC) cells, which is suppressed by the elevated level of miRNA 92b. Treatment of LNA significantly decreases the IC50 of doxorubicin for NSCLC cells. This strategy can be developed as a novel anti-miRNA therapeutic approach to target GQ harboring miRNAs. This can potentially be a more powerful approach than targeting of the mature miRNA, as it is an upstream targeting and can reduce both 3' and the 5' mature miRNA levels at once.
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Affiliation(s)
| | - Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Joshua Reid
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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7
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Long non-coding RNA containing ultraconserved genomic region 8 promotes bladder cancer tumorigenesis. Oncotarget 2018; 7:20636-54. [PMID: 26943042 PMCID: PMC4991481 DOI: 10.18632/oncotarget.7833] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/03/2016] [Indexed: 12/12/2022] Open
Abstract
Ultraconserved regions (UCRs) have been shown to originate non-coding RNA transcripts (T-UCRs) that have different expression profiles and play functional roles in the pathophysiology of multiple cancers. The relevance of these functions to the pathogenesis of bladder cancer (BlCa) is speculative. To elucidate this relevance, we first used genome-wide profiling to evaluate the expression of T-UCRs in BlCa tissues. Analysis of two datasets comprising normal bladder tissues and BlCa specimens with a custom T-UCR microarray identified ultraconserved RNA (uc.) 8+ as the most upregulated T-UCR in BlCa tissues, although its expression was lower than in pericancerous bladder tissues. These results were confirmed on BlCa tissues by real-time PCR and by in situ hybridization. Although uc.8+ is located within intron 1 of CASZ1, a zinc-finger transcription factor, the transcribed non-coding RNA encoding uc.8+ is expressed independently of CASZ1. In vitro experiments evaluating the effects of uc.8+ silencing, showed significantly decreased capacities for cancer cell invasion, migration, and proliferation. From this, we proposed and validated a model of interaction in which uc.8+ shuttles from the nucleus to the cytoplasm of BlCa cells, interacts with microRNA (miR)-596, and cooperates in the promotion and development of BlCa. Using computational analysis, we investigated the miR-binding domain accessibility, as determined by base-pairing interactions within the uc.8+ predicted secondary structure, RNA binding affinity, and RNA species abundance in bladder tissues and showed that uc.8+ is a natural decoy for miR-596. Thus uc.8+ upregulation results in increased expression of MMP9, increasing the invasive potential of BlCa cells. These interactions between evolutionarily conserved regions of DNA suggest that natural selection has preserved this potentially regulatory layer that uses RNA to modulate miR levels, opening up the possibility for development of useful markers for early diagnosis and prognosis as well as for development of new RNA-based cancer therapies.
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8
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Toh DFK, Patil KM, Chen G. Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids. J Vis Exp 2017:56221. [PMID: 28994801 PMCID: PMC5752312 DOI: 10.3791/56221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNAs are emerging as important biomarkers and therapeutic targets. Thus, there is great potential in developing chemical probes and therapeutic ligands for the recognition of RNA sequence and structure. Chemically modified Peptide Nucleic Acid (PNA) oligomers have been recently developed that can recognize RNA duplexes in a sequence-specific manner. PNAs are chemically stable with a neutral peptide-like backbone. PNAs can be synthesized relatively easily by the manual Boc-chemistry solid-phase peptide synthesis method. PNAs are purified by reverse-phase HPLC, followed by molecular weight characterization by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF). Non-denaturing polyacrylamide gel electrophoresis (PAGE) technique facilitates the imaging of the triplex formation, because carefully designed free RNA duplex constructs and PNA bound triplexes often show different migration rates. Non-denaturing PAGE with ethidium bromide post staining is often an easy and informative technique for characterizing the binding affinities and specificities of PNA oligomers. Typically, multiple RNA hairpins or duplexes with single base pair mutations can be used to characterize PNA binding properties, such as binding affinities and specificities. 2-Aminopurine is an isomer of adenine (6-aminopurine); the 2-aminopurine fluorescence intensity is sensitive to local structural environment changes, and is suitable for the monitoring of triplex formation with the 2-aminopurine residue incorporated near the PNA binding site. 2-Aminopurine fluorescence titration can also be used to confirm the binding selectivity of modified PNAs towards targeted double-stranded RNAs (dsRNAs) over single-stranded RNAs (ssRNAs). UV-absorbance-detected thermal melting experiments allow the measurement of the thermal stability of PNA-RNA duplexes and PNA·RNA2 triplexes. Here, we describe the synthesis and purification of PNA oligomers incorporating modified residues, and describe biochemical and biophysical methods for characterization of the recognition of RNA duplexes by the modified PNAs.
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Affiliation(s)
- Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University;
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9
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Piras L, Avitabile C, D'Andrea LD, Saviano M, Romanelli A. Detection of oligonucleotides by PNA-peptide conjugates recognizing the biarsenical fluorescein complex FlAsH-EDT 2. Biochem Biophys Res Commun 2017; 493:126-131. [PMID: 28919425 DOI: 10.1016/j.bbrc.2017.09.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022]
Abstract
We report the application of the arsenical complex FlAsH-EDT2 for the identification of oligonucleotide sequences. We designed PNA sequences conjugated to either a tetracysteine motif and to split tetracysteine sequences, that are recognized by FlAsH. The effect of conjugation of the PNA to the tetracysteine peptide and RNA hybridization on the fluorescence of the arsenical complex has been investigated. The reconstitution of the tetracysteine motif, starting from 15-mer PNAs conjugated to split tetracysteine sequences and hybridized to a complementary oligonucleotide was also explored.
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Affiliation(s)
- Linda Piras
- Institute of Crystallography (IC), CNR, Via Amendola 122/O, 70126, Bari, Italy
| | - Concetta Avitabile
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Luca Domenico D'Andrea
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Michele Saviano
- Institute of Crystallography (IC), CNR, Via Amendola 122/O, 70126, Bari, Italy
| | - Alessandra Romanelli
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134, Napoli, Italy.
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10
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Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis. Molecules 2017; 22:molecules22071144. [PMID: 28698463 PMCID: PMC6152032 DOI: 10.3390/molecules22071144] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/12/2022] Open
Abstract
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs. Herein, for the first time, is proposed the use of peptide nucleic acids (PNAs) to protect specific sequences in the 3’UTR (untranslated region) of the CFTR messenger RNA (mRNA) by action of miRNAs. Two PNAs (7 and 13 bases long) carrying the tetrapeptide Gly-SerP-SerP-Gly at their C-end, fully complementary to the 3’UTR sequence recognized by miR-509-3p, have been synthesized and the structural features of target PNA/RNA heteroduplexes have been investigated by spectroscopic and molecular dynamics studies. The co-transfection of the pLuc-CFTR-3´UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression.
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11
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Patil KM, Chen G. Recognition of RNA Sequence and Structure by Duplex and Triplex Formation: Targeting miRNA and Pre-miRNA. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-34175-0_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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12
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Ringhieri P, Avitabile C, Saviano M, Morelli G, Romanelli A, Accardo A. The influence of liposomal formulation on the incorporation and retention of PNA oligomers. Colloids Surf B Biointerfaces 2016; 145:462-469. [PMID: 27236097 DOI: 10.1016/j.colsurfb.2016.05.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/04/2016] [Accepted: 05/11/2016] [Indexed: 11/28/2022]
Abstract
Liposomal formulations composed of phospholipids with different unsaturation degrees, head groups and at different cholesterol content have been tested for the encapsulation of Peptide Nucleic Acid (PNA) oligomers. The best loading capability (177μg, ER%=87.2) was obtained for pure liposomes of phosphatidylglycerol (DOPG) with negatively charged head group. The insertion of a 10-20% of cholesterol in DOPG based liposomes provides a slight decrease (∼160μg) of the PNA loading. On the other hand, the cholesterol addition (20-30%) slows down the PNA's release (∼27%) in fetal bovine serum from the liposomal formulation. Based on the encapsulation and the release properties, PEGylated DOPG liposomes with a percentage of cholesterol of 10-20% are the optimal formulation for the loading of PNA-a210.
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Affiliation(s)
- Paola Ringhieri
- 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
| | - Concetta Avitabile
- Institute of Biostructure and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Michele Saviano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126 Bari, 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
| | - 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.
| | - 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.
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13
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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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14
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Avitabile C, Cimmino A, Romanelli A. Oligonucleotide analogues as modulators of the expression and function of noncoding RNAs (ncRNAs): emerging therapeutics applications. J Med Chem 2014; 57:10220-40. [PMID: 25280271 DOI: 10.1021/jm5006594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
ncRNAs are emerging as key regulators of physiological and pathological processes and therefore have been identified as pharmacological targets and as markers for some diseases. Oligonucleotide analogues represent so far the most widely employed tool for the modulation of the expression of ncRNAs. In this perspective we briefly describe most of the known classes of ncRNAs and then we discuss the design and the applications of oligonucleotide analogues for their targeting. The effects of modifications of the chemical structure of the oligonucleotides on properties such as the binding affinity toward targets and off targets, and the stability to degradation and their biological effects (when known) are discussed. Examples of molecules currently used in clinical trials are also reported.
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Affiliation(s)
- Concetta Avitabile
- Università di Napoli "Federico II" , Dipartimento di Farmacia, via Mezzocannone 16, 80134 Napoli, Italy
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15
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Devi G, Zhou Y, Zhong Z, Toh DFK, Chen G. RNA triplexes: from structural principles to biological and biotech applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:111-28. [DOI: 10.1002/wrna.1261] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 06/30/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
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16
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Avitabile C, Fabbri E, Bianchi N, Gambari R, Romanelli A. Inhibition of miRNA maturation by peptide nucleic acids. Methods Mol Biol 2014; 1095:157-64. [PMID: 24166311 DOI: 10.1007/978-1-62703-703-7_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Molecules able to interfere in miRNA genesis and function are potent tools to unravel maturation and processing pathways. Antisense oligonucleotides or analogs are actually employed for the inhibition of miRNA function. Here we illustrate how Peptide Nucleic Acids oligomers targeting pre-miRNA are exploited to inhibit miRNA maturation.
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Affiliation(s)
- Concetta Avitabile
- Dipartimento delle Scienze Biologiche, Università di Napoli "Federico II", Napoli, Italy
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17
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Diaz JP, Chirayil R, Chirayil S, Tom M, Head KJ, Luebke KJ. Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha. RNA (NEW YORK, N.Y.) 2014; 20:528-39. [PMID: 24497550 PMCID: PMC3964914 DOI: 10.1261/rna.042911.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We have found a small molecule that specifically inhibits cleavage of a precursor to the oncogenic miRNA, miR-21, by the microprocessor complex of Drosha and DGCR8. We identified novel ligands for the apical loop of this precursor from a screen of 14,024 N-substituted oligoglycines (peptoids) in a microarray format. Eight distinct compounds with specific affinity were obtained, three having affinities for the targeted loop in the low micromolar range and greater than 15-fold discrimination against a closely related hairpin. One of these compounds completely inhibits microprocessor cleavage of a miR-21 primary transcript at concentrations at which cleavage of another miRNA primary transcript, pri-miR-16, is little affected. The apical loop of pri-miR-21, placed in the context of pri-miR-16, is sufficient for inhibition of microprocessor cleavage by the peptoid. This compound also inhibits cleavage of pri-miR-21 containing the pri-miR-16 apical loop, suggesting an additional site of association within pri-miR-21. The reported peptoid is the first example of a small molecule that inhibits microprocessor cleavage by binding to the apical loop of a pri-miRNA.
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18
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Perspectives in targeting miRNA function. Bioorg Med Chem 2013; 21:6115-8. [PMID: 23602624 DOI: 10.1016/j.bmc.2013.03.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 03/20/2013] [Accepted: 03/21/2013] [Indexed: 12/21/2022]
Abstract
First oligonucleotide analogues that inhibit miRNA function are currently investigated in clinical trials. In addition, several alternative methods are under development that may allow for controlling miRNA function by small molecules-mediated inhibiting of its biogenesis. In this perspectives article, we provide a short overview on recent developments in this field.
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19
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Sugiyama T, Kittaka A. Chiral peptide nucleic acids with a substituent in the N-(2-aminoethy)glycine backbone. Molecules 2012; 18:287-310. [PMID: 23271467 PMCID: PMC6269907 DOI: 10.3390/molecules18010287] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 12/19/2012] [Accepted: 12/19/2012] [Indexed: 11/16/2022] Open
Abstract
A peptide nucleic acid (PNA) is a synthetic nucleic acid mimic in which the sugar-phosphate backbone is replaced by a peptide backbone. PNAs hybridize to complementary DNA and RNA with higher affinity and superior sequence selectivity compared to DNA. PNAs are resistant to nucleases and proteases and have a low affinity for proteins. These properties make PNAs an attractive agent for biological and medical applications. To improve the antisense and antigene properties of PNAs, many backbone modifications of PNAs have been explored under the concept of preorganization. This review focuses on chiral PNAs bearing a substituent in the N-(2-aminoethyl)glycine backbone. Syntheses, properties, and applications of chiral PNAs are described.
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Affiliation(s)
- Toru Sugiyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-3-5465-8743
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi-ku, Tokyo 173-8605, Japan; E-Mail:
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