1
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Shaikh AY, Björkling F, Zabicka D, Tomczak M, Urbas M, Domraceva I, Kreicberga A, Franzyk H. Structure-activity study of oncocin: On-resin guanidinylation and incorporation of homoarginine, 4-hydroxyproline or 4,4-difluoroproline residues. Bioorg Chem 2023; 141:106876. [PMID: 37797458 DOI: 10.1016/j.bioorg.2023.106876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023]
Abstract
Antimicrobial peptides (AMPs) often display guanidinium functionalities, and hence robust synthetic procedures are needed to facilitate access to analogues with unnatural homologues of arginine (Arg = R). Initially, a resin-bound Arg/Pro-rich fluoren-9-yl-methyloxycarbonyl-protected fragment (Fmoc-RPRPPR) of the AMP oncocin (i.e., VDKPPYLPRPRPPRRIYNR-NH2) was employed in a comparative on-resin assessment of commercial guanidinylation reagents head-to-head with the recently studied bis-Boc-protected triazole-based reagent, 1H-triazole-1-[N,N'-bis(tert-butoxycarbonyl)]-carboxamidine, which was synthesized by a chromatography-free procedure. This reagent was found to enable quantitative conversion in solid-phase peptide synthesis (SPPS) of peptides displaying homoarginine (Har) residues and/or an N-terminal guanidinium group. SPPS was used to obtain analogues of the 18-mer oncocin with single as well as multiple Arg → Har modifications. In addition, the effect of replacement of proline (Pro) residues in oncocin was explored by incorporating single or multiple trans-4-hydroxy-l-proline (Hyp) or 4,4-difluoro-l-proline (Dfp) residues, which both affected hydrophobicity. The resulting peptide library was tested against both Gram-negative and Gram-positive bacteria. Analysis of the minimal inhibitory concentrations (MICs) showed that analogues, displaying modifications at positions 4, 5 and 12 (originally Pro residues), had retained or slightly improved antimicrobial activity. Next, an oncocin analogue with two stabilizing l-Arg → d-Arg replacements in the C-terminal part was further modified by triple-replacement of Pro by either Dfp or Hyp in positions 4, 5, and 12. The resulting analogue displaying three Pro → Dfp modifications proved to possess the best activity profile: MICs of 1-2 µg/mL against E. coli and Klebsiella pneumoniae, less than 1% hemolysis at 800 µg/mL, and an IC50 above 1280 µg/mL in HepG2 cells. Thus, incorporation of bis-fluorinated Pro residues appears to constitute a novel tool in structure-activity studies aimed at optimization of Pro-rich AMPs.
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Affiliation(s)
- Ashif Y Shaikh
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark; Department of Chemistry, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Fredrik Björkling
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Dorota Zabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Magdalena Tomczak
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Malgorzata Urbas
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Ilona Domraceva
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Agrita Kreicberga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Henrik Franzyk
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark.
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2
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Mikame Y, Yamayoshi A. Recent Advancements in Development and Therapeutic Applications of Genome-Targeting Triplex-Forming Oligonucleotides and Peptide Nucleic Acids. Pharmaceutics 2023; 15:2515. [PMID: 37896275 PMCID: PMC10609763 DOI: 10.3390/pharmaceutics15102515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Recent developments in artificial nucleic acid and drug delivery systems present possibilities for the symbiotic engineering of therapeutic oligonucleotides, such as antisense oligonucleotides (ASOs) and small interfering ribonucleic acids (siRNAs). Employing these technologies, triplex-forming oligonucleotides (TFOs) or peptide nucleic acids (PNAs) can be applied to the development of symbiotic genome-targeting tools as well as a new class of oligonucleotide drugs, which offer conceptual advantages over antisense as the antigene target generally comprises two gene copies per cell rather than multiple copies of mRNA that are being continually transcribed. Further, genome editing by TFOs or PNAs induces permanent changes in the pathological genes, thus facilitating the complete cure of diseases. Nuclease-based gene-editing tools, such as zinc fingers, CRISPR-Cas9, and TALENs, are being explored for therapeutic applications, although their potential off-target, cytotoxic, and/or immunogenic effects may hinder their in vivo applications. Therefore, this review is aimed at describing the ongoing progress in TFO and PNA technologies, which can be symbiotic genome-targeting tools that will cause a near-future paradigm shift in drug development.
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Affiliation(s)
- Yu Mikame
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
| | - Asako Yamayoshi
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyomachi, Nagasaki 852-8521, Japan
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3
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Oyaghire SN, Quijano E, Perera JDR, Mandl HK, Saltzman WM, Bahal R, Glazer PM. DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101635. [PMID: 37920723 PMCID: PMC10621889 DOI: 10.1016/j.xcrp.2023.101635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Peptide nucleic acids (PNAs) can target and stimulate recombination reactions in genomic DNA. We have reported that γPNA oligomers possessing the diethylene glycol γ-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve γPNA accessibility, we explore the utility of γPNA oligomers possessing the hydroxymethyl-γ moiety for gene-editing applications. We demonstrate that a γPNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity than that of the diethylene glycol-γPNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-γPNA stimulates higher frequencies (≥ 1.5-fold) of gene modification than the diethylene glycol γPNA in mouse bone marrow cells.
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Affiliation(s)
- Stanley N. Oyaghire
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- These authors contributed equally
| | - Elias Quijano
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- These authors contributed equally
| | - J. Dinithi R. Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hanna K. Mandl
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - W. Mark Saltzman
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
- Department of Chemical & Environmental Engineering, Yale University, New Haven, CT 06511, USA
- Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Lead contact
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4
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Podlaski F, Cornwell S, Wong K, McKittrick B, Kim JH, Jung D, Jeon Y, Jung KB, Tolias P, Windsor WT. Peptide Nucleic Acids Containing Cationic/Amino-Alkyl Modified Bases Promote Enhanced Hybridization Kinetics and Thermodynamics with Single-Strand DNA. ACS OMEGA 2023; 8:33426-33436. [PMID: 37744819 PMCID: PMC10515352 DOI: 10.1021/acsomega.3c03184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
Peptide nucleic acids (PNAs) are antisense molecules with excellent polynucleotide hybridization properties; they are resistant to nuclease degradation but often have poor cell permeability leading to moderate cellular activity and limited clinical results. The addition of cationic substitutions (positive charges) to PNA molecules greatly increases cell permeability. In this report, we describe the synthesis and polynucleotide hybridization properties of a novel cationic/amino-alkyl nucleotide base-modified PNA (OPNA). This study was designed to quantitate the effect the cationic/amino-alkyl nucleotide base modification had on the kinetic and thermodynamic properties of OPNA-DNA hybridization using surface plasmon resonance and UV thermal melt studies. Kinetic studies reveal a favorable 10-30 fold increase in affinity for a single cationic modification on the base of an adenine, cytosine, or guanidine OPNA sequence compared to the nonmodified PNA strand. The increase in affinity is correlated directly with a favorable decrease in the dissociation rate constant and increase in the association rate constant. Introducing additional amino-alkyl base modifications further favors a decrease in the dissociation rate (3-10-fold per amino-alkyl). The thermodynamics driving the OPNA hybridization is promoted by an additional favorable -80 kJ/mol enthalpy of binding for a single amino-alkyl modification compared to the PNA strand. This increase in enthalpy is consistent with an ion-ion interaction with the DNA strand. These kinetic and thermodynamic hybridization studies reveal for the first time that this type of cationic/amino-alkyl base-modified PNA has favorable hybridization properties suitable for development as an antisense oligomer.
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Affiliation(s)
- Frank Podlaski
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Stephen Cornwell
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Kenny Wong
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
| | - Brian McKittrick
- Department
of Global Sciences & Strategy, OliPass
Corporation, Yongin, Gyeonggi 17015, Republic of Korea
| | - Jae-Hun Kim
- Department
of Monomer Research, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Daram Jung
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Yeasel Jeon
- Department
of Oligo Sciences, OliPass Corporation, Yongin, Gyeonggi 17015, Republic
of Korea
| | - Kwang-Bok Jung
- Department
of Monomer Manufacture, OliPass Corporation, Suwon, Gyeonggi 16229, Republic
of Korea
| | - Peter Tolias
- Department
of Biology, School of Natural and Behavioral Sciences, Brooklyn College, CUNY, Brooklyn, New York 11210, United States
| | - William T. Windsor
- Department
of Chemistry and Chemical Biology, Stevens
Institute of Technology, 1 Castle Point Terrace, Hoboken, New Jersey 07030, United States
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5
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Del Bene A, D'Aniello A, Tomassi S, Merlino F, Mazzarella V, Russo R, Chambery A, Cosconati S, Di Maro S, Messere A. Ultrasound-assisted Peptide Nucleic Acids synthesis (US-PNAS). ULTRASONICS SONOCHEMISTRY 2023; 95:106360. [PMID: 36913782 PMCID: PMC10024050 DOI: 10.1016/j.ultsonch.2023.106360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Herein, we developed an innovative and easily accessible solid-phase synthetic protocol for Peptide Nucleic Acid (PNA) oligomers by systematically investigating the ultrasonication effects in all steps of the PNA synthesis (US-PNAS). When compared with standard protocols, the application of the so-obtained US-PNAS approach succeeded in improving the crude product purities and the isolated yields of different PNA, including small or medium-sized oligomers (5-mer and 9-mer), complex purine-rich sequences (like a 5-mer Guanine homoligomer and the telomeric sequence TEL-13) and longer oligomers (such as the 18-mer anti-IVS2-654 PNA and the 23-mer anti-mRNA 155 PNA). Noteworthy, our ultrasound-assisted strategy is compatible with the commercially available PNA monomers and well-established coupling reagents and only requires the use of an ultrasonic bath, which is a simple equipment generally available in most synthetic laboratories.
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Affiliation(s)
- Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Sandro Cosconati
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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6
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Moriya SS, Funaki K, Demizu Y, Kurihara M, Kittaka A, Sugiyama T. Synthesis and properties of PNA containing a dicationic nucleobase based on N 4-benzoylated cytosine. Bioorg Med Chem Lett 2023; 88:129287. [PMID: 37094725 DOI: 10.1016/j.bmcl.2023.129287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
We report the synthesis of a peptide nucleic acid (PNA) monomer containing N4-bis(aminomethyl)benzoylated cytosine (BzC2+ base). The BzC2+ monomer was incorporated into PNA oligomers using Fmoc-based solid-phase synthesis. The BzC2+ base in PNA had two positive charges and exhibited greater affinity for DNA G base than the natural C base. The BzC2+ base stabilized PNA-DNA heteroduplexes through electrostatic attractions, even in high salt conditions. The two positive charges on the BzC2+ residue did not compromise the sequence specificity of PNA oligomers. These insights will aid the future design of cationic nucleobases.
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Affiliation(s)
- Shun-Suke Moriya
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Kaoru Funaki
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Masaaki Kurihara
- Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, Yokohama, Kanagawa 244-0806, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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7
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Thibonnier M, Ghosh S. Strategy for Pre-Clinical Development of Active Targeting MicroRNA Oligonucleotide Therapeutics for Unmet Medical Needs. Int J Mol Sci 2023; 24:ijms24087126. [PMID: 37108289 PMCID: PMC10138879 DOI: 10.3390/ijms24087126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
We present here an innovative modular and outsourced model of drug research and development for microRNA oligonucleotide therapeutics (miRNA ONTs). This model is being implemented by a biotechnology company, namely AptamiR Therapeutics, in collaboration with Centers of Excellence in Academic Institutions. Our aim is to develop safe, effective and convenient active targeting miRNA ONT agents for the metabolic pandemic of obesity and metabolic-associated fatty liver disease (MAFLD), as well as deadly ovarian cancer.
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Affiliation(s)
| | - Sujoy Ghosh
- Duke-NUS Medical School, Singapore and Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
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8
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Pradeep SP, Malik S, Slack FJ, Bahal R. Unlocking the potential of chemically modified peptide nucleic acids for RNA-based therapeutics. RNA (NEW YORK, N.Y.) 2023; 29:434-445. [PMID: 36653113 PMCID: PMC10019372 DOI: 10.1261/rna.079498.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/12/2023] [Indexed: 05/27/2023]
Abstract
RNA therapeutics have emerged as next-generation therapy for the treatment of many diseases. Unlike small molecules, RNA targeted drugs are not limited by the availability of binding pockets on the protein, but rather utilize Watson-Crick (WC) base-pairing rules to recognize the target RNA and modulate gene expression. Antisense oligonucleotides (ASOs) present a powerful therapeutic approach to treat disorders triggered by genetic alterations. ASOs recognize the cognate site on the target RNA to alter gene expression. Nine single-stranded ASOs have been approved for clinical use and several candidates are in late-stage clinical trials for both rare and common diseases. Several chemical modifications, including phosphorothioates, locked nucleic acid, phosphorodiamidate, morpholino, and peptide nucleic acids (PNAs), have been investigated for efficient RNA targeting. PNAs are synthetic DNA mimics where the deoxyribose phosphate backbone is replaced by N-(2-aminoethyl)-glycine units. The neutral pseudopeptide backbone of PNAs contributes to enhanced binding affinity and high biological stability. PNAs hybridize with the complementary site in the target RNA and act by a steric hindrance--based mechanism. In the last three decades, various PNA designs, chemical modifications, and delivery strategies have been explored to demonstrate their potential as an effective and safe RNA-targeting platform. This review covers the advances in PNA-mediated targeting of coding and noncoding RNAs for a myriad of therapeutic applications.
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Affiliation(s)
- Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
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9
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Gluhacevic von Krüchten D, Roth M, Seitz O. DNA-Templated Reactions with High Catalytic Efficiency Achieved by a Loss-of-Affinity Principle. J Am Chem Soc 2022; 144:10700-10704. [PMID: 35696276 DOI: 10.1021/jacs.2c03188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleic-acid-templated chemical reactions are currently explored for applications in DNA-encoded drug discovery, nucleic acid diagnostics, and theranostics. Of particular interest are reactions enabling the template to gain catalytic activity, so that enzymatic amplification of low copy targets would no longer be necessary. Herein, we introduce a new reaction design relying on the template-controlled cleavage of PNA-spermine conjugates. With turnover frequencies in the range of 3-10 min-1 and a kcat/KM = 1.3 × 106 M-1 s-1, the loss of affinity upon reaction provides a catalytic efficiency equal to most enzymatic conversions and superior to nucleic-acid-templated reactions reported to date.
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Affiliation(s)
| | - Magdalena Roth
- Department of Chemistry, Humboldt University of Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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10
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Suparpprom C, Vilaivan T. Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications. RSC Chem Biol 2022; 3:648-697. [PMID: 35755191 PMCID: PMC9175113 DOI: 10.1039/d2cb00017b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.
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Affiliation(s)
- Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang Phitsanulok 65000 Thailand
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University Phayathai Road Pathumwan Bangkok 10330 Thailand
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11
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Munyaradzi O, Rundell S, Bong D. Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA. Chembiochem 2022; 23:e202100707. [PMID: 35167719 PMCID: PMC9136932 DOI: 10.1002/cbic.202100707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Indexed: 11/07/2022]
Abstract
We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.
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Affiliation(s)
- Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
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12
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Argueta-Gonzalez HS, Swenson CS, Song G, Heemstra JM. Stimuli-responsive assembly of bilingual peptide nucleic acids. RSC Chem Biol 2022; 3:1035-1043. [PMID: 35974999 PMCID: PMC9347363 DOI: 10.1039/d2cb00020b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Peptide nucleic acids (PNAs) are high-affinity synthetic nucleic acid analogs capable of hybridization with native nucleic acids. PNAs synthesized having amino acid sidechains installed at the γ-position along the backbone provide a template for a single biopolymer to simultaneously encode nucleic acid and amino acid sequences. Previously, we reported the development of “bilingual” PNAs through the synthesis of an amphiphilic sequence featuring separate blocks of hydrophobic and hydrophilic amino acid functional groups. These PNAs combined the sequence-specific binding activity of nucleic acids with the structural organization properties of peptides. Like other amphiphilic compounds, these γ-PNAs were observed to assemble spontaneously into micelle-like nanostructures in aqueous solutions and disassembly was induced through hybridization to a complementary sequence. Here, we explore whether assembly of these bilingual PNAs is possible by harnessing the nucleic acid code. Specifically, we designed an amphiphile-masking duplex system in which spontaneous amphiphile assembly is prevented through hybridization to a nucleic acid masking sequence. We show that the amphiphile is displaced upon introduction of a releasing sequence complementary to the masking sequence through toehold mediated displacement. Upon release, we observe that the amphiphile proceeds to assemble in a fashion consistent with our previously reported structures. Our approach represents a novel method for controlled stimuli-responsive assembly of PNA-based nanostructures. “Bilingual” biopolymers comprised of γ-modified peptide nucleic acids can harness peptide and nucleic acid codes to direct assembly and recognition. Herein, we demonstrate stimuli-responsive assembly through a toehold-mediated displacement motif.![]()
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Affiliation(s)
| | - Colin S. Swenson
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, Georgia, USA
| | - George Song
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, Georgia, USA
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Dr, Atlanta, Georgia, USA
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13
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Rundell S, Munyaradzi O, Bong D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs. Biochemistry 2021; 61:85-91. [PMID: 34955016 DOI: 10.1021/acs.biochem.1c00693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
General design principles for recognition at noncanonical interfaces of DNA and RNA remain elusive. Triplex hybridization of bifacial peptide nucleic acids (bPNAs) with oligo-T/U DNAs and RNAs is a robust recognition platform that can be used to define structure-function relationships in synthetic triplex formation. To this end, a set of minimal (mw < 1 kD) bPNA variants was synthesized to probe the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on hybridization with short, unstructured T-rich DNA and U-rich RNAs. Thermodynamic parameters extracted from optical melting analyses of bPNA variant hybrids indicated that there are two bPNA backbone modifications that significantly improve hybridization: alternating (d, l) configuration in open-chain dipeptides and homochiral dipeptide cyclization to diketopiperazine. Further, binding to DNA is preferred over RNA for all bPNA variants. Thymine-uracil substitutions in DNA substrates revealed that the methyl group of thymine accounts for 71% of ΔΔGDNA-RNA for open-chain bPNAs but only 40% of ΔΔGDNA-RNA for diketopiperazine bPNA, suggesting a greater sensitivity to RNA conformation and more optimized stacking in the cyclic bPNA. Together, these data reveal pressure points for tuning triplex hybridization at the chiral centers of bPNA, backbone conformation, stacking effects at the base triple, and the nucleic acid substrate itself. A structural blueprint for enhancing bPNA targeting of both DNA and RNA substrates includes syndiotactic base presentation (as found in homochiral diketopiperazines and d, l peptides), expansion of base stacking, and further investigation of bPNA backbone preorganization.
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Affiliation(s)
- Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio 43210, United States
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14
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Brodyagin N, Kataoka Y, Kumpina I, McGee DW, Rozners E. Cellular uptake of 2-aminopyridine-modified peptide nucleic acids conjugated with cell-penetrating peptides. Biopolymers 2021; 113:e23484. [PMID: 34914092 DOI: 10.1002/bip.23484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 01/31/2023]
Abstract
Cell-penetrating peptides (CPPs) have been extensively used to deliver peptide nucleic acid (PNA) in cells. We have previously found that replacement of cytosine in triplex-forming PNAs with 2-aminopyridine (M) not only enhanced RNA binding, but also improved cellular uptake of PNAs. In this study, we used confocal fluorescence microscopy to evaluate the ability of CPPs to further improve cellular uptake of M-modified PNAs. We found that PNAs conjugated with Tat and octa-arginine peptides were effectively taken up in MCF7 cells when supplied in cell media at 1 μM. Remarkably, M-modified PNA without any CPP conjugation also showed strong uptake when the concentration was increased to 5 μM. Majority of PNA conjugates remained localized in distinct cytoplasmic vesicles, as judged by dot-like fluorescence patterns. However, M-modified PNAs conjugated with Tat, octa-arginine, and even a simple tri-lysine peptide also showed dispersed fluorescence in cytoplasm and were taken up in nuclei where they localized in larger vesicles, most likely nucleoli. Endosomolytic peptides or chemicals (chloroquine and CaCl2 ) did not release the conjugates from cytosolic vesicles, which suggested that the PNAs were not entrapped in endosomes. We hypothesize that M-modified PNAs escape endosomes and accumulate in cellular compartments rich in RNA, such as nucleoli, stress granules, and P-bodies.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Yuka Kataoka
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Ilze Kumpina
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, The State University of New York, Binghamton, New York, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York, USA
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15
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The Challenges and Opportunities in the Development of MicroRNA Therapeutics: A Multidisciplinary Viewpoint. Cells 2021; 10:cells10113097. [PMID: 34831320 PMCID: PMC8619171 DOI: 10.3390/cells10113097] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/22/2021] [Accepted: 11/02/2021] [Indexed: 02/06/2023] Open
Abstract
microRNAs (miRs) are emerging as attractive therapeutic targets because of their small size, specific targetability, and critical role in disease pathogenesis. However, <20 miR targeting molecules have entered clinical trials, and none progressed to phase III. The difficulties in miR target identification, the moderate efficacy of miR inhibitors, cell type-specific delivery, and adverse outcomes have impeded the development of miR therapeutics. These hurdles are rooted in the functional complexity of miR's role in disease and sequence complementarity-dependent/-independent effects in nontarget tissues. The advances in understanding miR's role in disease, the development of efficient miR inhibitors, and innovative delivery approaches have helped resolve some of these hurdles. In this review, we provide a multidisciplinary viewpoint on the challenges and opportunities in the development of miR therapeutics.
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16
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Lai Q, Chen W, Zhang Y, Liu Z. Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors. Analyst 2021; 146:5822-5835. [PMID: 34581324 DOI: 10.1039/d1an00765c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.
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Affiliation(s)
- Qingteng Lai
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Wei Chen
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China. .,Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Yanke Zhang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Zhengchun Liu
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
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17
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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18
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Perera JDR, Carufe KEW, Glazer PM. Peptide nucleic acids and their role in gene regulation and editing. Biopolymers 2021; 112:e23460. [PMID: 34129732 DOI: 10.1002/bip.23460] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022]
Abstract
The unique properties of peptide nucleic acid (PNA) makes it a desirable candidate to be used in therapeutic and biotechnological interventions. It has been broadly utilized for numerous applications, with a major focus in regulation of gene expression, and more recently in gene editing. While the classic PNA design has mainly been employed to date, chemical modifications of the PNA backbone and nucleobases provide an avenue to advance the technology further. This review aims to discuss the recent developments in PNA based gene manipulation techniques and the use of novel chemical modifications to improve the current state of PNA mediated gene targeting.
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Affiliation(s)
- J Dinithi R Perera
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kelly E W Carufe
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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19
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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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20
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Moriya SS, Shibasaki H, Kohara M, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A, Sugiyama T. Synthesis and characterization of PNA oligomers containing preQ 1 as a positively charged guanine analogue. Bioorg Med Chem Lett 2021; 39:127850. [PMID: 33662538 DOI: 10.1016/j.bmcl.2021.127850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
We report the synthesis of a peptide nucleic acid (PNA) monomer containing preQ1, a positively charged guanine analogue. The new monomer was incorporated into PNA oligomers using standard Fmoc-chemistry-based solid-phase synthesis. The preQ1 unit-containing PNA oligomers exhibited improved affinity for their complementary DNA through electrostatic attraction, and their sequence specificity was not compromised. It could be beneficial to incorporate preQ1 into PNA oligomers instead of guanine when creating antisense/antigene agents or research tools.
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Affiliation(s)
- Shun-Suke Moriya
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Hatsune Shibasaki
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Misaki Kohara
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-9501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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21
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Volpi S, Rozzi A, Rivi N, Neri M, Knoll W, Corradini R. Submonomeric Strategy with Minimal Protection for the Synthesis of C(2)-Modified Peptide Nucleic Acids. Org Lett 2021; 23:902-907. [PMID: 33417460 PMCID: PMC7880566 DOI: 10.1021/acs.orglett.0c04116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 11/28/2022]
Abstract
A novel synthesis of C(2)-modified peptide nucleic acids (PNAs) is proposed, using a submonomeric strategy with minimally protected building blocks, which allowed a reduction in the required synthetic steps. N(3)-unprotected, d-Lys- and d-Arg-based backbones were used to obtain positively charged PNAs with high optical purity, as inferred from chiral GC measurements. "Chiral-box" PNAs targeting the G12D point mutation of the KRAS gene were produced using this method, showing improved sequence selectivity for the mutated- vs wild-type DNA strand with respect to unmodified PNAs.
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Affiliation(s)
- Stefano Volpi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
| | - Andrea Rozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
| | - Nicola Rivi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
| | - Martina Neri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
| | - Wolfgang Knoll
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
- Biosensor
Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430, Tulln an der Donau, Austria
| | - Roberto Corradini
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43123, Italy
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22
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Das A, Pradhan B. Evolution of peptide nucleic acid with modifications of its backbone and application in biotechnology. Chem Biol Drug Des 2020; 97:865-892. [PMID: 33314595 DOI: 10.1111/cbdd.13815] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/17/2020] [Accepted: 12/05/2020] [Indexed: 01/23/2023]
Abstract
Peptide nucleic acids (PNAs) are getting prodigious interest currently in the biomedical and diagnostic field as an extremely powerful tool because of their potentiality to hybridize with natural nucleic acids. Although PNA has strong affinity and sequence specificity to DNA/RNA, there is a considerable ongoing effort to further enhance their special chemical and biological properties for potential application in numerous fields, notably in the field of therapeutics. The toolbox for backbone modified PNAs synthesis has been extended substantially in recent decades, providing a more efficient synthesis of peptides with numerous scaffolds and modifications. This paper reviews the various strategies that have been developed so far for the modification of the PNA backbone, challenging the search for new PNA systems with improved chemical and physical properties lacking in the original aegPNA backbone. The various practical issues and limitations of different PNA systems are also summarized. The focus of this review is on the evolution of PNA by its backbone modification to improve the cellular uptake, sequence specificity, and compatibility of PNA to bind to DNA/RNA. Finally, an insight was also gained into major applications of backbone modified PNAs for the development of biosensors.
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Affiliation(s)
- Anuradha Das
- National Institute of Science Education and Research Bhubaneswar (HBNI), Bhubaneswar, India
| | - Biswaranjan Pradhan
- S. K. Dash Center of Excellence of Biosciences and Engineering & Technology, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India
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23
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Volpi S, Cancelli U, Neri M, Corradini R. Multifunctional Delivery Systems for Peptide Nucleic Acids. Pharmaceuticals (Basel) 2020; 14:14. [PMID: 33375595 PMCID: PMC7823687 DOI: 10.3390/ph14010014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
The number of applications of peptide nucleic acids (PNAs)-oligonucleotide analogs with a polyamide backbone-is continuously increasing in both in vitro and cellular systems and, parallel to this, delivery systems able to bring PNAs to their targets have been developed. This review is intended to give to the readers an overview on the available carriers for these oligonucleotide mimics, with a particular emphasis on newly developed multi-component- and multifunctional vehicles which boosted PNA research in recent years. The following approaches will be discussed: (a) conjugation with carrier molecules and peptides; (b) liposome formulations; (c) polymer nanoparticles; (d) inorganic porous nanoparticles; (e) carbon based nanocarriers; and (f) self-assembled and supramolecular systems. New therapeutic strategies enabled by the combination of PNA and proper delivery systems are discussed.
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Affiliation(s)
| | | | | | - Roberto Corradini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.V.); (U.C.); (M.N.)
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24
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Das R, Gayakvad B, Shinde SD, Rani J, Jain A, Sahu B. Ultrashort Peptides—A Glimpse into the Structural Modifications and Their Applications as Biomaterials. ACS APPLIED BIO MATERIALS 2020; 3:5474-5499. [DOI: 10.1021/acsabm.0c00544] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bhavinkumar Gayakvad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Jyoti Rani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Alok Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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25
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Altrichter Y, Seitz O. Simultaneous Targeting of Two Master Regulators of Apoptosis with Dual-Action PNA- and DNA-Peptide Conjugates. Bioconjug Chem 2020; 31:1928-1937. [PMID: 32567853 PMCID: PMC7583637 DOI: 10.1021/acs.bioconjchem.0c00284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/21/2020] [Indexed: 01/31/2023]
Abstract
Conjugation of peptides with oligonucleotides offers opportunities for combining the strengths of both biopolymer classes. Herein, we show that the combination of a peptide-based module with an antisense oligonucleotide module provides for enhancements of potency and a widened scope of cell delivery options. The peptide unit comprises a Smac mimetic compound (SMCs) which antagonizes the action of inhibitor of apoptosis proteins (IAPs) frequently overexpressed in cancer cells. To counteract SMC resistance, the antisense module downregulates the cellular FLICE-like protein (c-FLIP), a master regulator of the extrinsic apoptosis pathway. We compared c-FLIP antisense units based on oligophosphorothioate (PSO) and peptide nucleic acid (PNA) architectures. Owing to the ease of synthesis, PNA conjugates combined with a cell penetrating peptide (CPP) offer a seemingly ideal solution for cell delivery of dual activity agents. However, our investigations revealed that such congeners have to be handled with care to avoid off-target effects. By contrast, PSO conjugates provided a more robust and specific activity for inducing death of SMC-resistant A549 cells due to a simultaneous activation of caspases and c-FLIP knockdown. We show that lipofection is a convenient approach for delivery of peptide-PSO conjugates into cells. The results highlight that the combination of the peptide and the DNA world confers properties inaccessible by the unconjugated components.
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Affiliation(s)
- Yannic Altrichter
- Department of Chemistry, Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
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26
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Bhingardeve P, Madhanagopal BR, Naick H, Jain P, Manoharan M, Ganesh K. Receptor-Specific Delivery of Peptide Nucleic Acids Conjugated to Three Sequentially Linked N-Acetyl Galactosamine Moieties into Hepatocytes. J Org Chem 2020; 85:8812-8824. [PMID: 32529829 DOI: 10.1021/acs.joc.0c00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide nucleic acids (PNAs) are DNA analogs that bind with high affinity to DNA and RNA in a sequence-specific manner but have poor cell permeability, limiting use as therapeutic agents. The work described here is motivated by recent reports of efficient gene silencing specifically in hepatocytes by small interfering RNAs conjugated to triantennary N-acetyl galactosamine (GalNAc), the ligand recognized by the asialoglycoprotein receptor (ASGPR). PNAs conjugated to either triantennary GalNAc at the N-terminus (the branched architecture) or monomeric GalNAc moieties anchored at Cγ of three consecutive PNA monomers of N-(2-aminoethyl)glycine (aeg) scaffolds (the sequential architecture) were synthesized on the solid phase. These formed duplexes with complementary DNA and RNA as shown by UV and circular dichroism spectroscopy. The fluorescently labeled analogs of GalNAc-conjugated PNAs were internalized by HepG2 cells that express the ASGPR but were not taken up by HEK-293 cells that lack this receptor. The sequential conjugate was internalized about 13-fold more efficiently than the branched conjugate into HepG2 cells, as demonstrated by confocal microscopy. The results presented here highlight the potential significance of the architecture of GalNAc conjugation for efficient uptake by target liver cells and indicate that GalNAc-conjugated PNAs have possible therapeutic applications.
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Affiliation(s)
- Pramod Bhingardeve
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| | - Hemanth Naick
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
| | - Prashant Jain
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, United States
| | - Krishna Ganesh
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India.,Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, Andhra Pradesh, India
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27
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Muangkaew P, Vilaivan T. Modulation of DNA and RNA by PNA. Bioorg Med Chem Lett 2020; 30:127064. [PMID: 32147357 DOI: 10.1016/j.bmcl.2020.127064] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.
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Affiliation(s)
- Penthip Muangkaew
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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28
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Abdelbaky AS, Prokhorov IA, Gnuskova EV, Esipova OV, Kirillova YG. Convenient and Efficient Syntheses of Peptide Nucleic Acid Purine Monomers. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666191014161442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Currently, peptide nucleic acids (PNAs) play an important role as therapeutic
agents, molecular tools for diagnosis and detection of genetic diseases as well as in biosensor
probes. This research aims to optimize the synthesis of aeg- and γ-(S)-Me PNA
monomers based on L-Ala, intended for oligomerization according to the Boc protocol.
The monomers were obtained through the condensation of the corresponding pseudopeptides
with carboxymethyl purine nucleic bases. During the work, the optimization of benzyloxycarbonyl-
N6-adenine-9-yl-acetic acid and benzyloxycarbonyl-N2-guanine-9-ylacetic
acid was carried out. The synthesis of benzyloxycarbonyl-N6-adenine-9-yl-acetic
acid was conducted in three stages based on adenine with an overall yield of 22%. At the
same time, the conditions for effective recrystallization of the mixture after alkylation of
benzyloxycarbonyl-N6-adenine with ethyl bromoacetic acid ether have been developed to isolate the desired
N9-regioisomer. Also, the optimization of a known method for producing benzyloxycarbonyl-N2-guanine-9-ylacetic
acid from 2-amino-6-chloropurine was carried out. The total yield of the five-stage scheme was 55%.
Condensation of aeg- and γ-(S)-Me pseudopeptides with benzyloxycarbonyl-N6-adenine-9-yl-acetic acid and
benzyloxycarbonyl-N2-guanine-9-yl-acetic acid was performed by the standard carbodiimide method,
DCC/HOBt in DMF followed by the removal of C-terminal methyl protective group by alkaline hydrolysis.
The structure of the new compounds obtained was confirmed by spectral analysis methods. This work provides
simple and optimized methods for obtaining protected carboxymethyl purine bases and increasing the efficiency
of the synthesis and synthesized purine PNA monomers in an acceptable yield.
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Affiliation(s)
- Ahmed S. Abdelbaky
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Ivan A. Prokhorov
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Elena V. Gnuskova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Olga V. Esipova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Yulia G. Kirillova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
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29
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Swenson CS, Velusamy A, Argueta-Gonzalez HS, Heemstra JM. Bilingual Peptide Nucleic Acids: Encoding the Languages of Nucleic Acids and Proteins in a Single Self-Assembling Biopolymer. J Am Chem Soc 2019; 141:19038-19047. [PMID: 31711285 DOI: 10.1021/jacs.9b09146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acids and proteins are the fundamental biopolymers that support all life on Earth. Nucleic acids store large amounts of information in nucleobase sequences while peptides and proteins utilize diverse amino acid functional groups to adopt complex structures and perform wide-ranging activities. Although nature has evolved machinery to read the nucleic acid code and translate it into amino acid code, the extant biopolymers are restricted to encoding amino acid or nucleotide sequences separately, limiting their potential applications in medicine and biotechnology. Here we describe the design, synthesis, and stimuli-responsive assembly behavior of a bilingual biopolymer that integrates both amino acid and nucleobase sequences into a single peptide nucleic acid (PNA) scaffold to enable tunable storage and retrieval of tertiary structural behavior and programmable molecular recognition capabilities. Incorporation of a defined sequence of amino acid side-chains along the PNA backbone yields amphiphiles having a "protein code" that directs self-assembly into micellar architectures in aqueous conditions. However, these amphiphiles also carry a "nucleotide code" such that subsequent introduction of a complementary RNA strand induces a sequence-specific disruption of assemblies through hybridization. Together, these properties establish bilingual PNA as a powerful biopolymer that combines two information systems to harness structural responsiveness and sequence recognition. The PNA scaffold and our synthetic system are highly generalizable, enabling fabrication of a wide array of user-defined peptide and nucleotide sequence combinations for diverse future biomedical and nanotechnology applications.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Arventh Velusamy
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | | | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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30
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Tahmasbi Rad A, Malik S, Yang L, Oberoi-Khanuja TK, Nieh MP, Bahal R. A universal discoidal nanoplatform for the intracellular delivery of PNAs. NANOSCALE 2019; 11:12517-12529. [PMID: 31188378 DOI: 10.1039/c9nr03667a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Peptide nucleic acids (PNAs) have gained considerable attention due to their remarkable potential in gene editing and targeting-based strategies. However, cellular delivery of PNAs remains a challenge in developing their broader therapeutic applications. Here, we investigated a novel complex made of lipid bicelles and PNA-based carriers for the efficient delivery of PNAs. For proof of concept, PNAs targeting microRNA (miR) 210 and 155 were tested. Comprehensive evaluation of positive as well as negative charge-containing bicelles with PNA : lipid ratios of 1 : 100, 1 : 1000, and 1 : 2500 was performed. The negatively charged bicelles with a PNA : lipid molar ratio of 1 : 2500 yielded a discoidal shape with a uniform diameter of ∼30 nm and a bilayer thickness of 5 nm, while the positively charged bicellar system contained irregular vesicles after the incorporation of PNA. Small-angle X-ray scattering (SAXS) analysis was performed to provide insight into how the hydrophobic PNAs interact with bicelles. Further, flow cytometry followed by confocal microscopy analyses substantiate the superior transfection efficiency of bicelles containing dye-conjugated antimiR PNAs. Functional analysis also confirmed miR inhibition by PNA oligomers delivered by bicelles. The nanodiscoidal complex opens a new pathway to deliver PNAs, which, on their own, are a great challenge to be endocytosed into cells.
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Affiliation(s)
- Armin Tahmasbi Rad
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA. and Polymer Program, Institute of Materials Sciences, University of Connecticut, 191 Auditorium Road, Storrs, CT 06269, USA
| | - Shipra Malik
- School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA.
| | - Lin Yang
- National Synchrotron Light Source - II, Brookhaven National Laboratory, Upton, NY, USA
| | | | - Mu-Ping Nieh
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA. and Polymer Program, Institute of Materials Sciences, University of Connecticut, 191 Auditorium Road, Storrs, CT 06269, USA and Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Raman Bahal
- School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA.
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31
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RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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32
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Dong B, Nie K, Shi H, Yao X, Chao L, Liang B, Liu Z. Synthesis and characterization of (R)-miniPEG-containing chiral γ-peptide nucleic acids using the Fmoc strategy. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.04.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Abdelbaky AS, Prokhorov IA, Smirnov IP, Koroleva KM, Shvets VI, Kirillova YG. Synthesis of α-(R)-/γ-(S)-Dimethyl Substituted Peptide Nucleic Acid Submonomer Using Mitsunobu Reaction. LETT ORG CHEM 2019. [DOI: 10.2174/1570178616666190118155031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
One of the major challenges facing modern biochemical and biomedical technologies are
finding molecular tools for diagnosis and detection of genetic diseases. In this connection, several classes
of oligonucleotides have been developed that can recognize and bind to DNA and RNA with high
affinity and sequence selectivity and withstand enzymatic degradation by proteases and nucleases;
however, few can traverse the cell membrane on their own. One such promising class of nucleic acid
mimics developed in the last two decades which showed good results in vitro, are the peptide nucleic
acids (PNAs). New chiral α- and γ-peptide Nucleic Acid (PNA) submonomer with methyl substituents
in pseudopeptide backbone were synthesized via Mitsunobu reaction. The α-(R)-/γ-(S)-configuration of
the chiral centres will ensure the preorganization of the PNA oligomer into a right-handed helix. The
results obtained showed that Boc/Fmoc-submonomer compatible with Boc-protocol PNAs solid-phase
synthesis on an MBHA resin. We synthesized simple and efficient α-R-, γ-S-disubstituted PNA submonomer
based on L-Ala and D-Ala with the construction of the intermediate pseudopeptide moiety
by Mitsunobu reaction for subsequent use in the Boc-Protocol of solid phase PNA synthesis.
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Affiliation(s)
- Ahmed S. Abdelbaky
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Ivan A. Prokhorov
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Igor P. Smirnov
- Department of Biophysics, Federal Research and Clinical Center of Physical-Chemical Medicine, 119571 Moscow, Russian Federation
| | - Kristina M. Koroleva
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Vitaliy I. Shvets
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Yulia G. Kirillova
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
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34
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Malik S, Oyaghire S, Bahal R. Applications of PNA-laden nanoparticles for hematological disorders. Cell Mol Life Sci 2019; 76:1057-1065. [PMID: 30498995 PMCID: PMC11105400 DOI: 10.1007/s00018-018-2979-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/07/2018] [Accepted: 11/23/2018] [Indexed: 12/26/2022]
Abstract
Safe and efficient genome editing has been an unmitigated goal for biomedical researchers since its inception. The most prevalent strategy for gene editing is the use of engineered nucleases that induce DNA damage and take advantage of cellular DNA repair machinery. This includes meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems. However, the clinical viability of these nucleases is marred by their off-target cleavage activity (≥ 50% in RNA-guided endonucleases). In addition, in vivo applications of CRISPR require systemic administration of Cas9 protein, mRNA, or DNA, which presents a significant delivery challenge. The development of nucleic acid probes that can recognize specific double-stranded DNA (dsDNA) regions and activate endogenous DNA repair machinery holds great promise for gene editing applications. Triplex-forming oligonucleotides (TFOs), which were introduced more than 25 years ago, are among the most extensively studied oligomeric dsDNA-targeting agents. TFOs bind duplex DNA to create a distorted helical structure, which can stimulate DNA repair and the exchange of a nearby mutated region-otherwise leading to an undesired phenotype-for a short single-stranded donor DNA that contains the corrective nucleotide sequence. Recombination can be induced within several hundred base-pairs of the TFO binding site and has been shown to depend on triplex-induced initiation of the nucleotide excision repair pathway and engagement of the homology-dependent repair pathway. Since TFOs do not possess any direct nuclease activity, their off-target effects are minimal when compared to engineered nucleases. This review comprehensively covers the advances made in peptide nucleic acid-based TFOs for site-specific gene editing and their therapeutic applications.
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Affiliation(s)
- Shipra Malik
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Stanley Oyaghire
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA.
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35
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Yu Z, Hsieh WC, Asamitsu S, Hashiya K, Bando T, Ly DH, Sugiyama H. Orthogonal γPNA Dimerization Domains Empower DNA Binders with Cooperativity and Versatility Mimicking that of Transcription Factor Pairs. Chemistry 2018; 24:14183-14188. [PMID: 30003621 PMCID: PMC9724550 DOI: 10.1002/chem.201801961] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/26/2018] [Indexed: 12/21/2022]
Abstract
Synthetic molecules capable of DNA binding and mimicking cooperation of transcription factor (TF) pairs have long been considered a promising tool for manipulating gene expression. Our previously reported Pip-HoGu system, a programmable DNA binder pyrrole-imidazole polyamides (PIPs) conjugated to host-guest moiety, defined a general framework for mimicking cooperative TF pair-DNA interactions. Here, we supplanted the cooperation modules with left-handed (LH) γPNA modules: i.e., PIPs conjugated with nucleic acid-based cooperation system (Pip-NaCo). LH γPNA was chosen because of its bioorthogonality, sequence-specific interaction, and high binding affinity toward the partner strand. From the results of the Pip-NaCo system, cooperativity is highly comparable to the natural TF pair-DNA system, with a minimum energetics of cooperation of -3.27 kcal mol-1 . Moreover, through changing the linker conjugation site, binding mode, and the length of γPNAs sequence, the cooperative energetics of Pip-NaCo can be tuned independently and rationally. The current Pip-NaCo platform might also have the potential for precise manipulation of biological processes through the construction of triple to multiple heterobinding systems.
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Affiliation(s)
- Zutao Yu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Wei-Che Hsieh
- Institute for Biomolecular Design and Discovery (IBD), Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Danith H Ly
- Institute for Biomolecular Design and Discovery (IBD), Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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36
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Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. J Chem Theory Comput 2018; 14:3603-3620. [PMID: 29791152 DOI: 10.1021/acs.jctc.8b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
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Affiliation(s)
- Maciej Jasiński
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Centre of New Technologies , University of Warsaw , Warsaw , Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Warsaw , Poland
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37
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Thadke SA, Perera JDR, Hridya VM, Bhatt K, Shaikh AY, Hsieh WC, Chen M, Gayathri C, Gil RR, Rule GS, Mukherjee A, Thornton CA, Ly DH. Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington's Disease. Biochemistry 2018; 57:2094-2108. [PMID: 29562132 PMCID: PMC6091552 DOI: 10.1021/acs.biochem.8b00062] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report the development of a new class of nucleic acid ligands that is comprised of Janus bases and the MPγPNA backbone and is capable of binding rCAG repeats in a sequence-specific and selective manner via, inference, bivalent H-bonding interactions. Individually, the interactions between ligands and RNA are weak and transient. However, upon the installation of a C-terminal thioester and an N-terminal cystine and the reduction of disulfide bond, they undergo template-directed native chemical ligation to form concatenated oligomeric products that bind tightly to the RNA template. In the absence of an RNA target, they self-deactivate by undergoing an intramolecular reaction to form cyclic products, rendering them inactive for further binding. The work has implications for the design of ultrashort nucleic acid ligands for targeting rCAG-repeat expansion associated with Huntington's disease and a number of other related neuromuscular and neurodegenerative disorders.
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Affiliation(s)
- Shivaji A. Thadke
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - J. Dinithi R. Perera
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - V. M. Hridya
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India
| | - Kirti Bhatt
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Ashif Y. Shaikh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Che Hsieh
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Mengshen Chen
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Chakicherla Gayathri
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Roberto R. Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S. Rule
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India
| | - Charles A. Thornton
- Department of Neurology, Box 645, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Danith H. Ly
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Institute for Biomolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
- Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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38
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Soudah T, Mogilevsky M, Karni R, Yavin E. CLIP6-PNA-Peptide Conjugates: Non-Endosomal Delivery of Splice Switching Oligonucleotides. Bioconjug Chem 2017; 28:3036-3042. [PMID: 29211451 DOI: 10.1021/acs.bioconjchem.7b00638] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient delivery of oligonucleotides still remains a challenge in the field of oligonucleotide based therapy. Peptide nucleic acid (PNA), a DNA analogue that is typically synthesized by solid phase peptide chemistry, has been conjugated to a variety of cell penetrating peptides (CPP) as a means of improving its cellular uptake. These CPPs typically deliver their cargoes into cells by an endosomal-dependent mechanism resulting in lower bioavailability of the cargo. Herein, we designed and synthesized PNA-peptide conjugates as splice switching oligonucleotides (SSO) targeting the Mnk2 gene, a therapeutic target in cancer. In humans, the MKNK2 gene, is alternatively spliced, generating isoforms with opposite biological activities: Mnk2a and Mnk2b. It was found that the Mnk2a isoform is down-regulated in breast, lung, brain, and colon tumors and is a tumor suppressor, whereas MnK2b is oncogenic. We have designed and synthesized PNAs that were conjugated to either of the following peptides: a nuclear localization sequence (NLS) or a cytosol localizing internalization peptide (CLIP6). CLIP6-PNA demonstrates effective cellular uptake and exclusively employs a nonendosomal mechanism to cross the cellular membranes of glioblastoma cells (U87). Simple incubation of PNA-peptide conjugates in human glioblastoma cells up-regulates the Mnk2a isoform leading to cancer cell death.
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Affiliation(s)
- Terese Soudah
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Maxim Mogilevsky
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Rotem Karni
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
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39
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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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40
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Hnedzko D, McGee DW, Karamitas YA, Rozners E. Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids. RNA (NEW YORK, N.Y.) 2017; 23:58-69. [PMID: 27742909 PMCID: PMC5159649 DOI: 10.1261/rna.058362.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/08/2016] [Indexed: 05/07/2023]
Abstract
Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research, and biotechnology. However, specific recognition of structured RNA is challenging, and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well-suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 107 M-1) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same sequence (Ka = 0.05 to 1.1 × 107 M-1). The binding of double-stranded RNA by M-modified PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 104 M-1 sec-1) compared to the notoriously slow triple helix formation by oligodeoxynucleotides (kon ∼ 103 M-1 sec-1). M-modified PNA-peptide conjugates were not cytotoxic and were efficiently delivered in the cytosol of HEK293 cells at 10 µM. Surprisingly, M-modified PNAs without peptide conjugation were also taken up by HEK293 cells, which, to the best of our knowledge, is the first example of heterocyclic base modification that enhances the cellular uptake of PNA. Our results suggest that M-modified PNA-peptide conjugates are promising probes for sequence-selective recognition of double-stranded RNA in live cells and other biological systems.
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Affiliation(s)
- Dziyana Hnedzko
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Dennis W McGee
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Yannis A Karamitas
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, USA
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41
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Mercurio ME, Tomassi S, Gaglione M, Russo R, Chambery A, Lama S, Stiuso P, Cosconati S, Novellino E, Di Maro S, Messere A. Switchable Protecting Strategy for Solid Phase Synthesis of DNA and RNA Interacting Nucleopeptides. J Org Chem 2016; 81:11612-11625. [DOI: 10.1021/acs.joc.6b01829] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maria Emilia Mercurio
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Stefano Tomassi
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Gaglione
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosita Russo
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Angela Chambery
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Stefania Lama
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via De Crecchio 7, 80127 Napoli, Italy
| | - Paola Stiuso
- Department
of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via De Crecchio 7, 80127 Napoli, Italy
| | - Sandro Cosconati
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Napoli, Italy
| | - Salvatore Di Maro
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- Department
of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
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42
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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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43
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Bose T, Banerjee A, Nahar S, Maiti S, Kumar VA. β,γ-Bis-substituted PNA with configurational and conformational switch: preferred binding to cDNA/RNA and cell-uptake studies. Chem Commun (Camb) 2016; 51:7693-6. [PMID: 25848728 DOI: 10.1039/c5cc00891c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
(S,S)- and (R,R)-β,γ-Bis-substituted PNAs were synthesized from the C-2 symmetric vicinal diamine system embedded in 1,4 dihydroxybutane and 1,4-dimethoxybutane scaffolds. (R,R)-β,γ-Bis-methoxymethyl-PNA derived from d-tartaric acid was found to be in the right configuration and conformation to be an excellent mimic of PNA, endowed with superior ability to enter into cells.
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Affiliation(s)
- Tanaya Bose
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pashan Road, Pune, 411008, India.
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44
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Parsel SM, Grandis JR, Thomas SM. Nucleic acid targeting: towards personalized therapy for head and neck cancer. Oncogene 2015; 35:3217-26. [PMID: 26592450 PMCID: PMC4877278 DOI: 10.1038/onc.2015.424] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/29/2015] [Accepted: 10/05/2015] [Indexed: 12/13/2022]
Abstract
In light of a detailed characterization of genetic aberrations in cancer, nucleic acid targeting represents an attractive therapeutic approach with significant translational potential. Head and neck squamous cell carcinoma (HNSCC) is a leading cause of cancer deaths worldwide with stagnant 5-year survival rates. Advances in conventional treatment have done little to improve survival and combined chemoradiation is associated with significant adverse effects. Recent reports have characterized the genetic alterations in HNSCC and demonstrated that mutations confer resistance to conventional and molecular targeted therapies. The ability to use specific nucleic acid sequences to inhibit cancer-associated genes including non-druggable targets facilitates personalized medicine approaches with less adverse effects. Additionally, advances in drug delivery mechanisms have increased the transfection efficiency aiding in greater therapeutic responses. Given these advances, the stage has been set to translate the information garnered from genomic studies into personalized treatment strategies. Genes involved in the tumor protein 53 (TP53) and epidermal growth factor receptor (EGFR) pathways have been extensively investigated and many promising preclinical studies have shown tumor inhibition through genetic modulation. We, and others, have demonstrated that targeting oncogene expression with gene therapy approaches is feasible in patients. Other methods such as RNA interference have proven to be effective and are potential candidates for clinical studies. This review summarizes the major advances in sequence-specific gene modulation in the preclinical setting and in clinical trials in head and neck cancer patients.
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Affiliation(s)
- S M Parsel
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, KS, USA
| | - J R Grandis
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - S M Thomas
- Department of Otolaryngology, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
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45
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Ellipilli S, vasudeva Murthy R, Ganesh KN. Perfluoroalkylchain conjugation as a new tactic for enhancing cell permeability of peptide nucleic acids (PNAs) via reducing the nanoparticle size. Chem Commun (Camb) 2015; 52:521-4. [PMID: 26535419 DOI: 10.1039/c5cc05342k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Perfluoro undecanoyl chain conjugated peptide nucleic acids (PNAs) show 2.5 to 3 fold higher cellular uptake efficiency in NIH 3T3 and HeLa cells compared to simple undecanoyl PNAs. Fluorination of PNAs leads to the formation of lower size (∼100-250 nm) nanoparticles compared to larger size (∼500 nm) nanoparticles from non-fluorinated PNAs, thereby improving the efficiency of cell penetration.
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Affiliation(s)
- Satheesh Ellipilli
- Chemical Biology Unit, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pune 411008, Maharashtra, India
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46
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Kirillova Y, Boyarskaya N, Dezhenkov A, Tankevich M, Prokhorov I, Varizhuk A, Eremin S, Esipov D, Smirnov I, Pozmogova G. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs): Synthesis and DNA Binding. PLoS One 2015; 10:e0140468. [PMID: 26469337 PMCID: PMC4607454 DOI: 10.1371/journal.pone.0140468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022] Open
Abstract
New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA.
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Affiliation(s)
- Yuliya Kirillova
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- * E-mail:
| | - Nataliya Boyarskaya
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Andrey Dezhenkov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Mariya Tankevich
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Ivan Prokhorov
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Anna Varizhuk
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
- Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Sergei Eremin
- Department of Biotechnology and Bionanotechnology, Moscow State University of Fine Chemical Technologies, Moscow, Russia
| | - Dmitry Esipov
- Department of Bioorganic Chemistry, Biology Faculty, Moscow State University, Moscow, Russia
| | - Igor Smirnov
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
| | - Galina Pozmogova
- Department of Molecular Biology and Genetics, SRI of Physical-Chemical Medicine, Moscow, Russia
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47
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Ellipilli S, Ganesh KN. Fluorous Peptide Nucleic Acids: PNA Analogues with Fluorine in Backbone (γ-CF2-apg-PNA) Enhance Cellular Uptake. J Org Chem 2015; 80:9185-91. [PMID: 26322827 DOI: 10.1021/acs.joc.5b01614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorous PNA analogues possessing fluorine as inherent part of aminopropylglycine (apg) backbone (γ-CF2-apg PNA) have been synthesized and evaluated for biophysical and cell penetrating properties. These form duplexes of higher thermal stability with cRNA than cDNA, although destabilized compared to duplexes of standard aeg-PNA. Cellular uptake of the fluorinated γ-CF2-apg PNAs in NIH 3T3 and HeLa cells was 2-3-fold higher compared to that of nonfluorinated apg PNA, with NIH 3T3 cells showing better permeability compared to HeLa cells. The backbone fluorinated PNAs, which are first in this class, when combined with other chemical modifications may have potential for future PNA-based antisense agents.
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Affiliation(s)
- Satheesh Ellipilli
- Chemical Biology Unit, Indian Institute of Science Education and Research (IISER) , Dr. Bhabha Road, Pune 411008, Maharashtra India
| | - Krishna N Ganesh
- Chemical Biology Unit, Indian Institute of Science Education and Research (IISER) , Dr. Bhabha Road, Pune 411008, Maharashtra India
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48
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Vilaivan T. Pyrrolidinyl PNA with α/β-Dipeptide Backbone: From Development to Applications. Acc Chem Res 2015; 48:1645-56. [PMID: 26022340 DOI: 10.1021/acs.accounts.5b00080] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The specific pairing between two complementary nucleobases (A·T, C·G) according to the Watson-Crick rules is by no means unique to natural nucleic acids. During the past few decades a number of nucleic acid analogues or mimics have been developed, and peptide nucleic acid (PNA) is one of the most intriguing examples. In addition to forming hybrids with natural DNA/RNA as well as itself with high affinity and specificity, the uncharged peptide-like backbone of PNA confers several unique properties not observed in other classes of nucleic acid analogues. PNA is therefore suited to applications currently performed by conventional oligonucleotides/analogues and others potentially beyond this. In addition, PNA is also interesting in its own right as a new class of oligonucleotide mimics. Unlimited opportunities exist to modify the PNA structure, stimulating the search for new systems with improved properties or additional functionality not present in the original PNA, driving future research and applications of these in nanotechnology and beyond. Although many structural variations of PNA exist, significant improvements to date have been limited to a few constrained derivatives of the privileged N-2-aminoethylglycine PNA scaffold. In this Account, we summarize our contributions in this field: the development of a new family of conformationally constrained pyrrolidinyl PNA having a nonchimeric α/β-dipeptide backbone derived from nucleobase-modified proline and cyclic β-amino acids. The conformational constraints dictated by the pyrrolidine ring and the β-amino acid are essential requirements determining the binding efficiency, as the structure and stereochemistry of the PNA backbone significantly affect its ability to interact with DNA, RNA, and in self-pairing. The modular nature of the dipeptide backbone simplifies the synthesis and allows for rapid structural optimization. Pyrrolidinyl PNA having a (2'R,4'R)-proline/(1S,2S)-2-aminocyclopentanecarboxylic backbone (acpcPNA) binds to DNA with outstanding affinity and sequence specificity. It also binds to RNA in a highly sequence-specific fashion, albeit with lower affinity than to DNA. Additional characteristics include exclusive antiparallel/parallel selectivity and a low tendency for self-hybridization. Modification of the nucleobase or backbone allowing site-specific incorporation of labels and other functions to acpcPNA via click and other conjugation chemistries is possible, generating functional PNAs that are suitable for various applications. DNA sensing and biological applications of acpcPNA have been demonstrated, but these are still in their infancy and the full potential of pyrrolidinyl PNA is yet to be realized. With properties competitive with, and in some aspects superior to, the best PNA technology available to date, pyrrolidinyl PNA offers great promise as a platform system for future elaboration for the fabrication of new functional materials, nanodevices, and next-generation analytical tools.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research
Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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49
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Manna A, Rapireddy S, Sureshkumar G, Ly DH. Synthesis of optically pure γPNA monomers: a comparative study. Tetrahedron 2015; 71:3507-3514. [PMID: 30792557 PMCID: PMC6379906 DOI: 10.1016/j.tet.2015.03.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We report a systematic study examining two synthetic routes, reductive amination and Mitsunobu coupling, for preparation of chiral γ-peptide nucleic acid (γPNA) monomers and oligomers. We found that the reductive amination route is prone to epimerization, even under mild experimental conditions. The extent of epimerization could be minimized by utilizing a bulky protecting group such as PhFl; however, it is difficult to remove in the subsequent oligomer synthesis stage. On the other hand, we found that the Mitsunobu route produced optically superior products using standard carbamate protecting groups.
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Affiliation(s)
- Arunava Manna
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Gopalsamy Sureshkumar
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400
Fifth Avenue, Pittsburgh, Pennsylvania 15213
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50
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Cγ-Aminopropylene peptide nucleic acid (amp-PNA): chiral cationic PNAs with superior PNA:DNA/RNA duplex stability and cellular uptake. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.03.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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