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Tomassi S, Ieranò C, Del Bene A, D’Aniello A, Napolitano M, Rea G, Auletta F, Portella L, Capiluongo A, Mazzarella V, Russo R, Chambery A, Scala S, Di Maro S, Messere A. Tailoring the Structure of Cell Penetrating DNA and RNA Binding Nucleopeptides. Int J Mol Sci 2022; 23:ijms23158504. [PMID: 35955638 PMCID: PMC9369335 DOI: 10.3390/ijms23158504] [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: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Synthetic nucleic acid interactors represent an exciting research field due to their biotechnological and potential therapeutic applications. The translation of these molecules into drugs is a long and difficult process that justifies the continuous research of new chemotypes endowed with favorable binding, pharmacokinetic and pharmacodynamic properties. In this scenario, we describe the synthesis of two sets of homo-thymine nucleopeptides, in which nucleobases are inserted in a peptide structure, to investigate the role of the underivatized amino acid residue and the distance of the nucleobase from the peptide backbone on the nucleic acid recognition process. It is worth noting that the CD spectroscopy investigation showed that two of the reported nucleopeptides, consisting of alternation of thymine functionalized L-Orn and L-Dab and L-Arg as underivatized amino acids, were able to efficiently bind DNA and RNA targets and cross both cell and nuclear membranes.
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Affiliation(s)
- Stefano Tomassi
- Department of Pharmacy, University of Naples “Federico” II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Caterina Ieranò
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Antonia D’Aniello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Maria Napolitano
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Giuseppina Rea
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Federica Auletta
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Luigi Portella
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Anna Capiluongo
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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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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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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Hoffmann S, Witkowski W, Schubert H. Nucleinsäuremodelle; Analoge unterschiedlicher Strangpolaritäten. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/zfch.19740140213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Affiliation(s)
- Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, DK-2200, Copenhagen.
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Geotti-Bianchini P, Beyrath J, Chaloin O, Formaggio F, Bianco A. Design and synthesis of intrinsically cell-penetrating nucleopeptides. Org Biomol Chem 2008; 6:3661-3. [PMID: 18843393 DOI: 10.1039/b811639c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleopeptides, which are constituted of alpha-amino acids bearing nucleobases at their side chains, are able to penetrate into cells and to reach the nucleus without cytotoxic effects.
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Affiliation(s)
- Piero Geotti-Bianchini
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d'Immunologie et Chimie Thérapeutiques, 15 Rue René Descartes, 67000, Strasbourg, France
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Shvachkin YP, Mishin GP, Korshunova GA. Advances and Prospects in the Chemistry of Nucleoaminoacids and Nucleopeptides. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1982v051n02abeh002819] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pandit UK. Biomolecular approach to the design of potential drugs. PURE APPL CHEM 2007. [DOI: 10.1351/pac200779122119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The approach to drug design on the basis of molecular-level information on biological processes is being driven by the expanding knowledge of the details of molecular events in biological systems. We have directed attention to the design of potentially active compounds based on the aforementioned "biomolecular" concepts. Selected examples from our studies are discussed. This paper presents three case studies of approaches to the development of potential medicinal agents whose design has evolved from considerations of molecular mechanisms of processes in selected biological systems.
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Affiliation(s)
- Upendra K. Pandit
- Van't Hoff Institute of Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands
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Meier C, Engels JW. Peptidnucleinsäuren (PNAs) - ungewöhnliche Eigenschaften nichtionischer Oligonucleotid-Analoga. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.19921040810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Huang Y, Dey S, Zhang X, Sönnichsen F, Garner P. The alpha-helical peptide nucleic acid concept: merger of peptide secondary structure and codified nucleic acid recognition. J Am Chem Soc 2004; 126:4626-40. [PMID: 15070379 DOI: 10.1021/ja038434s] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A novel platform for nucleic acid recognition that integrates the alpha-helix secondary structure of peptides with the codified base-pairing capability of nucleic acids is reported. The resulting alpha-helical peptide nucleic acids (alpha PNAs) are composed of a repeating tetrapeptidyl unit, aa(1)-aa(2)-aa(3)-Ser(B), where aa(1) through aa(3) represent generic ancillary amino acids and B = nucleobases linked to Ser via a methylene bridge. Effective syntheses of constituent Fmoc-protected nucleoamino acids (Fmoc-Ser(B)-OH, where B = thymine, cytosine, and uracil) are described along with a protocol for the solid-phase synthesis of 21mer alpha PNAs containing five such nucleobases. By varying the ancillary amino acids, two distinct classes of alpha PNAs were constructed, having a net charge of -1 or +6, respectively, at physiological pH. The modular nature of the alpha PNA platform was illustrated by the synthesis of symmetrical disulfide-bridged alpha PNA dimers containing 10 nucleobases. Hybridization of these alpha PNAs with ssDNA has been examined by thermal denaturation, gel electrophoresis, and circular dichroism (CD) and the data indicated that alpha PNA binds to ssDNA in a cooperative manner with high affinity and sequence specificity. In general, b2 alpha PNAs bind faster and more strongly with ssDNA than do the corresponding b1 alpha PNAs. Parallel alpha PNA-DNA complexes are more stable than their antiparallel counterparts. CD studies also revealed that the hybridization event involves the folding of both species into their helical conformations. Finally, NMR experiments provided conclusive evidence of Watson-Crick base pairing in alpha PNA-ssDNA hybrids.
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Affiliation(s)
- Yumei Huang
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, USA
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Affiliation(s)
- Peter E. Nielsen
- Center for Biomolecular Recognition, Department of Medical Biochemistry & Genetics, Biochemical Laboratory B, The Panum Institute, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
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Affiliation(s)
- Nicola M. Howarth
- Cancer Drug Discovery, Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Laurence P. G. Wakelin
- Cancer Drug Discovery, Department of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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Meier C, Engels JW. Peptide Nucleic Acids(PNAs)?Unusual Properties of Nonionic Oligonucleotide Analogues. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/anie.199210081] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Lidak MY, Raukas ��, Krishane V�, Pa�gle RA, Raim TA, Kooli KA, Poritere SE. Synthesis of oligopeptides containing DL-?-(1-uracilyl)- and DL-?-(9-adeninyl)-?-alanine and lysine residues and study of their reaction with DNA. Chem Heterocycl Compd (N Y) 1983. [DOI: 10.1007/bf00513272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Kricheldorf HR, Fehrle M. New polymer syntheses. IV. Polypeptides of lysine and ornithine with pending pyrimidine bases. Biopolymers 1982. [DOI: 10.1002/bip.360211103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Doel M, Jones A, Walker R. The synthesis of peptides containing purine and pyrimidine derivatives of DL-alanine. Tetrahedron 1974. [DOI: 10.1016/s0040-4020(01)97440-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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