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Scognamiglio PL, Vicidomini C, Roviello GN. Dancing with Nucleobases: Unveiling the Self-Assembly Properties of DNA and RNA Base-Containing Molecules for Gel Formation. Gels 2023; 10:16. [PMID: 38247739 PMCID: PMC10815473 DOI: 10.3390/gels10010016] [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: 12/12/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Nucleobase-containing molecules are compounds essential in biology due to the fundamental role of nucleic acids and, in particular, G-quadruplex DNA and RNA in life. Moreover, some molecules different from nucleic acids isolated from different vegetal sources or microorganisms show nucleobase moieties in their structure. Nucleoamino acids and peptidyl nucleosides belong to this molecular class. Closely related to the above, nucleopeptides, also known as nucleobase-bearing peptides, are chimeric derivatives of synthetic origin and more rarely isolated from plants. Herein, the self-assembly properties of a vast number of structures, belonging to the nucleic acid and nucleoamino acid/nucleopeptide family, are explored in light of the recent scientific literature. Moreover, several technologically relevant properties, such as the hydrogelation ability of some of the nucleobase-containing derivatives, are reviewed in order to make way for future experimental investigations of newly devised nucleobase-driven hydrogels. Nucleobase-containing molecules, such as mononucleosides, DNA, RNA, quadruplex (G4)-forming oligonucleotides, and nucleopeptides are paramount in gel and hydrogel formation owing to their distinctive molecular attributes and ability to self-assemble in biomolecular nanosystems with the most diverse applications in different fields of biomedicine and nanotechnology. In fact, these molecules and their gels present numerous advantages, underscoring their significance and applicability in both material science and biomedicine. Their versatility, capability for molecular recognition, responsiveness to stimuli, biocompatibility, and biodegradability collectively contribute to their prominence in modern nanotechnology and biomedicine. In this review, we emphasize the critical role of nucleobase-containing molecules of different nature in pioneering novel materials with multifaceted applications, highlighting their potential in therapy, diagnostics, and new nanomaterials fabrication as required for addressing numerous current biomedical and nanotechnological challenges.
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Affiliation(s)
| | - Caterina Vicidomini
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
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2
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Liu J, Li SM. Genomics-Guided Efficient Identification of 2,5-Diketopiperazine Derivatives from Actinobacteria. Chembiochem 2023; 24:e202200502. [PMID: 36098493 PMCID: PMC10092475 DOI: 10.1002/cbic.202200502] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/12/2022] [Indexed: 02/04/2023]
Abstract
Secondary metabolites derived from microorganism constitute an important part of natural products. Mining of the microbial genomes revealed a large number of uncharacterized biosynthetic gene clusters, indicating their greater potential to synthetize specialized or secondary metabolites (SMs) than identified by classic fermentation and isolation approaches. Various bioinformatics tools have been developed to analyze and identify such gene clusters, thus accelerating significantly the mining process. Heterologous expression of an individual biosynthetic gene cluster has been proven as an efficient way to activate the genes and identify the encoded metabolites that cannot be detected under normal laboratory cultivation conditions. Herein, we describe a concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways. Recent works focused on the identification of the nucleobase-related and dimeric DKPs are also presented.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.,Current address: Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
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3
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Willardiine and Its Synthetic Analogues: Biological Aspects and Implications in Peptide Chemistry of This Nucleobase Amino Acid. Pharmaceuticals (Basel) 2022; 15:ph15101243. [PMID: 36297355 PMCID: PMC9611319 DOI: 10.3390/ph15101243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/16/2022] Open
Abstract
Willardiine is a nonprotein amino acid containing uracil, and thus classified as nucleobase amino acid or nucleoamino acid, that together with isowillardiine forms the family of uracilylalanines isolated more than six decades ago in higher plants. Willardiine acts as a partial agonist of ionotropic glutamate receptors and more in particular it agonizes the non-N-methyl-D-aspartate (non-NMDA) receptors of L-glutamate: ie. the α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) and kainate receptors. Several analogues and derivatives of willardiine have been synthesised in the laboratory in the last decades and these compounds show different binding affinities for the non-NMDA receptors. More in detail, the willardiine analogues have been employed not only in the investigation of the structure of AMPA and kainate receptors, but also to evaluate the effects of receptor activation in the various brain regions. Remarkably, there are a number of neurological diseases determined by alterations in glutamate signaling, and thus, ligands for AMPA and kainate receptors deserve attention as potential neurodrugs. In fact, similar to willardiine its analogues often act as agonists of AMPA and kainate receptors. A particular importance should be recognized to willardiine and its thymine-based analogue AlaT also in the peptide chemistry field. In fact, besides the naturally-occurring short nucleopeptides isolated from plant sources, there are different examples in which this class of nucleoamino acids was investigated for nucleopeptide development. The applications are various ranging from the realization of nucleopeptide/DNA chimeras for diagnostic applications, and nucleoamino acid derivatization of proteins for facilitating protein-nucleic acid interaction, to nucleopeptide-nucleopeptide molecular recognition for nanotechnological applications. All the above aspects on both chemistry and biotechnological applications of willardine/willardine-analogues and nucleopeptide will be reviewed in this work.
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Novel insights on nucleopeptide binding: A spectroscopic and in silico investigation on the interaction of a thymine-bearing tetrapeptide with a homoadenine DNA. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117975] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN. From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides. Molecules 2021; 26:3558. [PMID: 34200901 PMCID: PMC8230524 DOI: 10.3390/molecules26123558] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.
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Affiliation(s)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy
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6
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Borbone N, Piccialli G, Roviello GN, Oliviero G. Nucleoside Analogs and Nucleoside Precursors as Drugs in the Fight against SARS-CoV-2 and Other Coronaviruses. Molecules 2021; 26:986. [PMID: 33668428 PMCID: PMC7918729 DOI: 10.3390/molecules26040986] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses (CoVs) are positive-sense RNA enveloped viruses, members of the family Coronaviridae, that cause infections in a broad range of mammals including humans. Several CoV species lead to mild upper respiratory infections typically associated with common colds. However, three human CoV (HCoV) species: Severe Acute Respiratory Syndrome (SARS)-CoV-1, Middle East Respiratory Syndrome (MERS)-CoV, and SARS-CoV-2, are responsible for severe respiratory diseases at the origin of two recent epidemics (SARS and MERS), and of the current COronaVIrus Disease 19 (COVID-19), respectively. The easily transmissible SARS-CoV-2, emerging at the end of 2019 in China, spread rapidly worldwide, leading the World Health Organization (WHO) to declare COVID-19 a pandemic. While the world waits for mass vaccination, there is an urgent need for effective drugs as short-term weapons to combat the SARS-CoV-2 infection. In this context, the drug repurposing approach is a strategy able to guarantee positive results rapidly. In this regard, it is well known that several nucleoside-mimicking analogs and nucleoside precursors may inhibit the growth of viruses providing effective therapies for several viral diseases, including HCoV infections. Therefore, this review will focus on synthetic nucleosides and nucleoside precursors active against different HCoV species, paying great attention to SARS-CoV-2. This work covers progress made in anti-CoV therapy with nucleoside derivatives and provides insight into their main mechanisms of action.
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Affiliation(s)
- Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (N.B.); (G.P.)
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy; (N.B.); (G.P.)
| | | | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Napoli Federico II, Via Sergio Pansini 5, 80131 Naples, Italy;
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7
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Pomplun S, Gates ZP, Zhang G, Quartararo AJ, Pentelute BL. Discovery of Nucleic Acid Binding Molecules from Combinatorial Biohybrid Nucleobase Peptide Libraries. J Am Chem Soc 2020; 142:19642-19651. [PMID: 33166454 DOI: 10.1021/jacs.0c08964] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature has three biopolymers: oligonucleotides, polypeptides, and oligosaccharides. Each biopolymer has independent functions, but when needed, they form mixed assemblies for higher-order purposes, as in the case of ribosomal protein synthesis. Rather than forming large complexes to coordinate the role of different biopolymers, we dovetail protein amino acids and nucleobases into a single low molecular weight precision polyamide polymer. We established efficient chemical synthesis and de novo sequencing procedures and prepared combinatorial libraries with up to 100 million biohybrid molecules. This biohybrid material has a higher bulk affinity to oligonucleotides than peptides composed exclusively of canonical amino acids. Using affinity selection mass spectrometry, we discovered variants with a high affinity for pre-microRNA hairpins. Our platform points toward the development of high throughput discovery of sequence defined polymers with designer properties, such as oligonucleotide binding.
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Affiliation(s)
- Sebastian Pomplun
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zachary P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Genwei Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anthony J Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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8
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Bucci R, Bossi A, Erba E, Vaghi F, Saha A, Yuran S, Maggioni D, Gelmi ML, Reches M, Pellegrino S. Nucleobase morpholino β amino acids as molecular chimeras for the preparation of photoluminescent materials from ribonucleosides. Sci Rep 2020; 10:19331. [PMID: 33168883 PMCID: PMC7652887 DOI: 10.1038/s41598-020-76297-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/23/2020] [Indexed: 11/10/2022] Open
Abstract
Bioinspired smart materials represent a tremendously growing research field and the obtainment of new building blocks is at the molecular basis of this technology progress. In this work, colloidal materials have been prepared in few steps starting from ribonucleosides. Nucleobase morpholino β-amino acids are the chimera key intermediates allowing Phe-Phe dipeptides' functionalization with adenine and thymine. The obtained compounds self-aggregate showing enhanced photoluminescent features, such as deep blue fluorescence and phosphorescence emissions.
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Affiliation(s)
- Raffaella Bucci
- DISFARM-Dipartimento Di Scienze Farmaceutiche, Sezione Chimica Generale E Organica "A. Marchesini", Università Degli Studi Di Milano, Via Venezian 21, 20133, Milan, Italy
| | - Alberto Bossi
- Istituto Di Scienze E Tecnologie Chimiche "G. Natta" del Consiglio Nazionale Delle Ricerche (CNR-SCITEC), via Fantoli 16/15, 20138, Milan, Italy
- SmartMatLab Center, via C. Golgi 19, 20133, Milan, Italy
| | - Emanuela Erba
- DISFARM-Dipartimento Di Scienze Farmaceutiche, Sezione Chimica Generale E Organica "A. Marchesini", Università Degli Studi Di Milano, Via Venezian 21, 20133, Milan, Italy
| | - Francesco Vaghi
- DISFARM-Dipartimento Di Scienze Farmaceutiche, Sezione Chimica Generale E Organica "A. Marchesini", Università Degli Studi Di Milano, Via Venezian 21, 20133, Milan, Italy
| | - Abhijit Saha
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Institute of Chemistry, Jerusalem, Israel
| | - Sivan Yuran
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Institute of Chemistry, Jerusalem, Israel
| | - Daniela Maggioni
- SmartMatLab Center, via C. Golgi 19, 20133, Milan, Italy
- Dipartimento Di Chimica, Università Degli Studi Di Milano, Via Golgi 19, 20133, Milan, Italy
| | - Maria Luisa Gelmi
- DISFARM-Dipartimento Di Scienze Farmaceutiche, Sezione Chimica Generale E Organica "A. Marchesini", Università Degli Studi Di Milano, Via Venezian 21, 20133, Milan, Italy
| | - Meital Reches
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Institute of Chemistry, Jerusalem, Israel
| | - Sara Pellegrino
- DISFARM-Dipartimento Di Scienze Farmaceutiche, Sezione Chimica Generale E Organica "A. Marchesini", Università Degli Studi Di Milano, Via Venezian 21, 20133, Milan, Italy.
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9
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Musumeci D, Mokhir A, Roviello GN. Synthesis and nucleic acid binding evaluation of a thyminyl l-diaminobutanoic acid-based nucleopeptide. Bioorg Chem 2020; 100:103862. [PMID: 32428744 DOI: 10.1016/j.bioorg.2020.103862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/01/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023]
Abstract
Herein we present the synthesis of a l-diaminobutanoic acid (DABA)-based nucleopeptide (3), with an oligocationic backbone, realized by solid phase peptide synthesis using thymine-bearing DABA moieties alternating in the sequence with free ones. CD studies evidenced the ability of this oligothymine nucleopeptide, well soluble in aqueous solution, to alter the secondary structure particularly of complementary RNA (poly rA vs poly rU) and inosine-rich RNAs, like poly rI and poly rIC, and showed its preference in binding double vs single-stranded DNAs. Furthermore, ESI mass spectrometry revealed that 3 bound also G-quadruplex (G4) DNAs, with either parallel or antiparallel topologies (adopted in our experimental conditions by c-myc and tel22, respectively). However, it caused detectable changes only in the CD of c-myc (whose parallel G4 structure was also thermally stabilized by ~3 °C), while leaving unaltered the antiparallel structure of tel22. Interestingly, CD and UV analyses suggested that 3 induced a hybrid mixed parallel/antiparallel G4 DNA structure in a random-coil tel22 DNA obtained under salt-free buffer conditions. Titration of the random-coil telomeric DNA with 3 gave quantitative information on the stoichiometry of the obtained complex. Overall, the findings of this work suggest that DABA-based nucleopeptides are synthetic nucleic acid analogues potentially useful in antigene and antisense strategies. Nevertheless, the hexathymine DABA-nucleopeptide shows an interesting behaviour as molecular tool per se thanks to its efficacy in provoking G4 induction in random coil G-rich DNA, as well as for the possibility to bind and stabilize c-myc oncogene in a G4 structure.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, Federico II University, Via Cintia 21, 80126 Naples, Italy; Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Friedrich Alexander University, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, 80134 Naples, Italy.
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10
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Anticancer Activity of Chitosan, Chitosan Derivatives, and Their Mechanism of Action. Int J Biomater 2018; 2018:2952085. [PMID: 30693034 PMCID: PMC6332982 DOI: 10.1155/2018/2952085] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 11/26/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Tailoring of chitosan through the involvement of its amino, acetamido, and hydroxy groups can give derivatives of enhanced solubility and remarkable anticancer activity. The general mechanism of such activity is associated with the disturbances in normal functioning of cell cycle, interference to the central dogma of biological system from DNA to RNA to protein or enzymatic synthesis, and the disruption of hormonal path to biosynthesis to inhibit the growth of cancer cells. Both chitosan and its various derivatives have been reported to selectively permeate through the cancer cell membranes and show anticancer activity through the cellular enzymatic, antiangiogenic, immunoenhancing, antioxidant defense mechanism, and apoptotic pathways. They get sequestered from noncancer cells and provide their enhanced bioavailability in cancer cells in a sustained release manner. This review presents the putative mechanisms of anticancer activity of chitosan and mechanistic approaches of structure activity relation upon the modification of chitosan through functionalization, complex formation, and graft copolymerization to give different derivatives.
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Wang H, Feng Z, Qin Y, Wang J, Xu B. Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018; 57:4931-4935. [PMID: 29451962 PMCID: PMC6014697 DOI: 10.1002/anie.201712834] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Herein, we report that assemblies of nucleopeptides selectively sequester ATP in complex conditions (for example, serum and cytosol). We developed assemblies of nucleopeptides that selectively sequester ATP over ADP. Counteracting enzymes interconvert ATP and ADP to modulate the nanostructures formed by the nucleopeptides and the nucleotides. The nucleopeptides, sequestering ATP effectively in cells, slow down efflux pumps in multidrug-resistant cancer cells, thus boosting the efficacy of doxorubicin, an anticancer drug. Investigation of 11 nucleopeptides (including d- and l-enantiomers) yields five more nucleopeptides that differentiate ATP and ADP through either precipitation or gelation. As the first example of assemblies of nucleopeptides that interact with ATP and disrupt intracellular ATP dynamics, this work illustrates the use of supramolecular assemblies to interact with small and essential biological molecules for controlling cell behavior.
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Affiliation(s)
- Huaimin Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Zhaoqianqi Feng
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Yanan Qin
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Jiaqing Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Bing Xu
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
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12
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Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Abstract
As a novel class of biomaterials, nucleopeptides, via the conjugation of nucleobases and peptides, usually self-assemble to form nanofibres driven mainly by hydrogen bonds. Containing nucleobase(s), nucleopeptides have a unique property-interacting with nucleic acids. Here we report the design and characterization of nucleopeptides that self-assemble in water and are able to interact with single-stranded DNAs (ssDNAs). Containing nucleobases on their side chains, these nucleopeptides bind with the ssDNAs, and the ssDNAs reciprocally affect the self-assembly of nucleopeptides. In addition, the interactions between nucleopeptides and ssDNAs also decrease their proteolytic resistance against proteinase K, which further demonstrates the binding with ssDNAs. The nucleopeptides also interact with plasmid DNA and deliver hairpin DNA into cells. This work illustrates a new and rational approach to create soft biomaterials by the integration of nucleobases and peptides to bind with DNA, which may lead to the development of nucleopeptides for controlling DNA in cells.
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Affiliation(s)
- Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Xinming Li
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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14
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Lac-l-TTA, a novel lactose-based amino acid–sugar conjugate for anti-metastatic applications. Amino Acids 2017; 49:1347-1353. [DOI: 10.1007/s00726-017-2433-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/29/2017] [Indexed: 01/07/2023]
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15
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Roviello GN, Vicidomini C, Di Gaetano S, Capasso D, Musumeci D, Roviello V. Solid phase synthesis and RNA-binding activity of an arginine-containing nucleopeptide. RSC Adv 2016; 6:14140-14148. [PMID: 29057071 PMCID: PMC5635565 DOI: 10.1039/c5ra25809j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/15/2016] [Indexed: 01/22/2023] Open
Abstract
Here we report the solid phase synthesis and characterization (LC-ESIMS, CD) of a cationic nucleobase-containing α-peptide, composed of both l-arginine residues and l-lysine-based nucleoamino acids sequentially present in the structure. The binding properties of this novel basic nucleopeptide towards nucleic acids were investigated by CD spectroscopy which revealed the ability of the thymine-containing oligomer to bind both adenine-containing DNA (dA12) and RNA (poly rA) molecules inducing high conformational variations in the nucleic acid structures. Moreover, the artificial oligonucleotide inhibited the enzymatic activity of HIV reverse transcriptase, opening the door to the exploitation of novel antiviral strategies inspired to this molecular tool.
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Affiliation(s)
- G N Roviello
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - C Vicidomini
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - S Di Gaetano
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - D Capasso
- Università di Napoli "Federico II" , Dipartimento di Farmacia , 80134 Napoli , Italy
| | - D Musumeci
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
- Università di Napoli "Federico II" , Dipartimento di Scienze Chimiche , 80126 Napoli , Italy
| | - V Roviello
- Università di Napoli "Federico II" , Dipartimento di Ingegneria Chimica , dei Materiali e della Produzione Industriale (DICMaPI) , 80125 Napoli , Italy
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16
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Weckenmann NM, Nachtsheim BJ. Enantioselective Synthesis ofD-α-(Uracil-5-yl)glycine Derivatives and Their Racemization-Free Incorporation into a Model Peptide. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Yuan D, Du X, Shi J, Zhou N, Baoum AA, Al Footy KO, Badahdah KO, Xu B. Synthesis and evaluation of the biostability and cell compatibility of novel conjugates of nucleobase, peptidic epitope, and saccharide. Beilstein J Org Chem 2015; 11:1352-9. [PMID: 26425189 PMCID: PMC4578436 DOI: 10.3762/bjoc.11.145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/16/2015] [Indexed: 11/23/2022] Open
Abstract
This article reports the synthesis of a new class of conjugates containing a nucleobase, a peptidic epitope, and a saccharide and the evalution of their gelation, biostability, and cell compatibility. We demonstrate a facile synthetic process, based on solid-phase peptide synthesis of nucleopeptides, to connect a saccharide with the nucleopeptides for producing the target conjugates. All the conjugates themselves (1-8) display excellent solubility in water without forming hydrogels. However, a mixture of 5 and 8 self-assembles to form nanofibers and results in a supramolecular hydrogel. The proteolytic stabilities of the conjugates depend on the functional peptidic epitopes. We found that TTPV is proteolytic resistant and LGFNI is susceptible to proteolysis. In addition, all the conjugates are compatible to the mammalian cells tested.
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Affiliation(s)
- Dan Yuan
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | - Ning Zhou
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
| | | | | | | | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, MS015, Waltham, MA 02453, USA
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18
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Roviello GN, Musumeci D, Roviello V. Cationic peptides as RNA compaction agents: a study on the polyA compaction activity of a linear alpha,epsilon-oligo-L-lysine. Int J Pharm 2015; 485:244-8. [PMID: 25772417 DOI: 10.1016/j.ijpharm.2015.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 11/16/2022]
Abstract
In this work, we investigate the compaction activity of a sequential alpha,epsilon-peptide composed of l-lysines towards two RNA targets, in view of its possible pharmaceutical application in RNA-targeting and RNA delivery. The basic oligolysine, object of the present study, proved not only to be efficient in compacting the single-stranded polyA RNA, but also to strongly interact with the polyA·polyU complex, as evidenced by CD-binding and UV-melting experiments. In particular, the marked differences in the CD spectra of the RNA targets upon addition of the peptide, as well as the different UV melting behaviour for the polyA·polyU complex in the presence and absence of the peptide, sustain the hypothesis of a strong RNA compaction capacity of the alpha,epsilon-oligolysine. Finally, by using HPLC analysis, we found a good resistance of the peptide against the lytic action of human serum, an important requirement in view of in vitro/in vivo biological assays.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy.
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy; Dipartimento di Scienze Chimiche, Università di Napoli "Federico II", 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale(DICMaPI), Università di Napoli "Federico II", 80125 Napoli, Italy
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19
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Binding ability of a thymine-functionalized oligolysine towards nucleic acids. Bioorg Med Chem 2014; 22:997-1002. [DOI: 10.1016/j.bmc.2013.12.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 12/08/2013] [Accepted: 12/21/2013] [Indexed: 01/20/2023]
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20
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Verardo G, Gorassini A. Characterization of N-Boc/Fmoc/Z-N'-formyl-gem-diaminoalkyl derivatives using electrospray ionization multi-stage mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1136-1149. [PMID: 24259202 DOI: 10.1002/jms.3278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/23/2013] [Accepted: 08/27/2013] [Indexed: 06/02/2023]
Abstract
N-Boc/Fmoc/Z-N'-formyl-gem-diaminoalkyl derivatives, intermediates particularly useful in the synthesis of partially modified retro-inverso peptides, have been characterized by both positive and negative ion electrospray ionization (ESI) ion-trap multi-stage mass spectrometry (MS(n)). The MS(2) collision induced dissociation (CID) spectra of the sodium adduct of the formamides derived from the corresponding N-Fmoc/Z-amino acids, dipeptide and tripeptide acids show the [M + Na-NH2CHO](+) ion, arising from the loss of formamide, as the base peak. Differently, the MS(2) CID spectra of [M + Na](+) ion of all the N-Boc derivatives yield the abundant [M + Na-C4H8](+) and [M + Na-Boc + H](+) ions because of the loss of isobutylene and CO2 from the Boc protecting function. Useful information on the type of amino acids and their sequence in the N-protected dipeptidyl and tripeptidyl-N'-formamides is provided by MS(2) and subsequent MS(n) experiments on the respective precursor ions. The negative ion ESI mass spectra of these oligomers show, in addition to [M-H](-), [M + HCOO](-) and [M + Cl](-) ions, the presence of in-source CID fragment ions deriving from the involvement of the N-protecting group. Furthermore, MS(n) spectra of [M + Cl](-) ion of N-protected dipeptide and tripeptide derivatives show characteristic fragmentations that are useful for determining the nature of the C-terminal gem-diamino residue. The present paper represents an initial attempt to study the ESI-MS behavior of these important intermediates and lays the groundwork for structural-based studies on more complex partially modified retro-inverso peptides.
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Affiliation(s)
- Giancarlo Verardo
- Dipartimento di Chimica, Fisica e Ambiente, Università di Udine, Via del Cotonificio 108, I-33100, Udine, Italy
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21
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Roviello GN, Musumeci D, D'Alessandro C, Pedone C. Synthesis of a thymine-functionalized nucleoamino acid for the solid phase assembly of cationic nucleopeptides. Amino Acids 2013; 45:779-84. [PMID: 23722416 DOI: 10.1007/s00726-013-1520-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/21/2013] [Indexed: 10/26/2022]
Abstract
In this work, we report the synthesis of a thymine-functionalized nucleoamino acid suitable for the solid phase synthesis of nucleopeptides. The monomer was obtained in solution starting from commercial compounds and after NMR ((1)H and (13)C) and ESIMS (positive ions) characterization it was used for the assembly of a cationic nucleopeptide obtained by sequentially introducing underivatized L-lysine units and nucleoamino acid monomers. After detachment from the resin, performed in acidic conditions, the oligomer was purified by HPLC and characterized by LC-ESIMS (positive ions) which confirmed the identity of the thymine-based nucleopeptide. The cationic nucleobase-containing peptide, well soluble in water, was studied by CD spectroscopy which allowed us to exclude any helical pre-organization of the nucleopeptide in the experimental conditions used. Furthermore, CD behavior of the oligomer at different temperatures was also studied as described in this work.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Naples, Italy,
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22
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Kramer RA, Bleicher KH, Wennemers H. Design and Synthesis of Nucleoproline Amino Acids for the Straightforward Preparation of Chiral and Conformationally Constrained Nucleopeptides. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Roviello GN, Musumeci D, Bucci EM, Pedone C. Synthesis of a diaminopropanoic acid-based nucleoamino acid and assembly of cationic nucleopeptides for biomedical applications. Amino Acids 2012; 43:2537-43. [PMID: 22688861 DOI: 10.1007/s00726-012-1335-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 05/29/2012] [Indexed: 11/29/2022]
Abstract
In this work, we report a synthetic approach to a Fmoc-protected nucleoamino acid, based on L-diaminopropanoic acid, carrying the DNA nucleobase on the alpha-amino group by means of an amide bond, suitable for the solid-phase synthesis of novel nucleopeptides of potential interest in biomedicine. After ESI-MS and NMR characterization this building block was used for the assembly of a thymine-functionalized nucleopeptide, composed of nucleobase-containing L-diaminopropanoic acid moieties and underivatized L-lysine residues alternated in the backbone. Circular dichroism studies performed on the cationic nucleopeptide and adenine-containing DNA and RNA molecules suggested that the thymine-containing peptide is able to interact with both DNA and RNA. In particular, a significant conformational variation in the RNA structure was suggested by CD studies. Human serum stability assays were also conducted on the cationic nucleopeptide, which was found to be highly resistant to enzymatic degradation.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Naples, Italy.
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Kumar S, Koh J, Kim H, Gupta MK, Dutta PK. A new chitosan-thymine conjugate: synthesis, characterization and biological activity. Int J Biol Macromol 2012; 50:493-502. [PMID: 22285484 DOI: 10.1016/j.ijbiomac.2012.01.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2012] [Indexed: 01/28/2023]
Abstract
Conjugation of chitosan with nucleobases is expected to expand its not only antimicrobial activity but also anti-cancer activity. Here, we report the synthesis of a novel chitosan-thymine conjugate by the reaction between chitosan and thymine-1-yl-acetic acid followed by acylation. The synthesized conjugate was characterized by FTIR, XRD, (1)H NMR, TGA and SEM. The microbiological screening results demonstrated the antimicrobial activity of the conjugate against bacteria viz., Escherichia coli, Staphylococcus aureus, and fungi viz., Aspergillus niger. The chitosan-thymine conjugate also inhibited (p<0.05) the proliferation of human liver cancer cells (HepG2) in a dose-dependent manner but had no cellular toxicity in non-cancerous mouse embryonal fibroblast cells (NIH 3T3). Thus, the chitosan-nucleobase conjugate may open a new perspective in biomedical applications.
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Affiliation(s)
- Santosh Kumar
- Department of Textile Engineering, Konkuk University, Seoul 143-701, South Korea
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25
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Roviello GN, Roviello G, Musumeci D, Bucci EM, Pedone C. Dakin-West reaction on 1-thyminyl acetic acid for the synthesis of 1,3-bis(1-thyminyl)-2-propanone, a heteroaromatic compound with nucleopeptide-binding properties. Amino Acids 2012; 43:1615-23. [PMID: 22349760 DOI: 10.1007/s00726-012-1237-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 01/30/2012] [Indexed: 10/14/2022]
Abstract
This work deals with the Dakin-West synthesis, starting from the nucleoamino acid 1-thyminyl acetic acid, as well the NMR, ESI MS, and X-ray characterization of a heteroaromatic compound denominated by us T(2)CO, comprising two thymine moieties anchored to a 2-propanonic unit, the spectroscopic properties of which were studied by UV as a function of temperature and ionic strength. Preliminary binding-studies with molecules of biomedical interest such as nucleic acids and proteins, performed on samples containing T(2)CO, suggested that this molecule is able to interact very weakly with double-stranded RNA, whereas it does not seem to bind other nucleic acids or proteins. Moreover, by studies with fresh human serum we found that T(2)CO is resistant to enzymatic degradation till 24 h, whereas UV metal binding-studies, performed using solutions of copper (II) chloride dihydrate and nickel (II) chloride hexahydrate, revealed a certain ability of T(2)CO to bind copper (II) cation. Finally, by CD spectroscopy we investigated the influence of T(2)CO on the already described supramolecular networks based on L-serine-containing nucleopeptides. More particularly, we found that T(2)CO is able to increase the level of structuration of the non-covalent supramolecular assembly of the chiral nucleopeptides, which is a feature of remarkable interest for the development of innovative drug delivery tools.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Naples, Italy.
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26
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Li X, Kuang Y, Shi J, Gao Y, Lin HC, Xu B. Multifunctional, biocompatible supramolecular hydrogelators consist only of nucleobase, amino acid, and glycoside. J Am Chem Soc 2011; 133:17513-8. [PMID: 21928792 PMCID: PMC3238097 DOI: 10.1021/ja208456k] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The integration of nucleobase, amino acid, and glycoside into a single molecule results in a novel class of supramolecular hydrogelators, which not only exhibit biocompatibility and biostability but also facilitate the entry of nucleic acids into cytosol and nuclei of cells. This work illustrates a simple way to generate an unprecedented molecular architecture from the basic biological building blocks for the development of sophisticated soft nanomaterials, including supramolecular hydrogels.
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Affiliation(s)
- Xinming Li
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Yi Kuang
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Yuan Gao
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Hsin-Chieh Lin
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
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27
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Kumar S, Kim H, Gupta MK, Dutta PK, Koh J. WITHDRAWN: A new chitosan-thymine conjugate: Synthesis, characterization and biological activity. Int J Biol Macromol 2011:S0141-8130(11)00371-0. [PMID: 21986543 DOI: 10.1016/j.ijbiomac.2011.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 09/24/2011] [Indexed: 10/17/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicyv.
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Affiliation(s)
- Santosh Kumar
- Department of Textile Engineering, Konkuk University,Seoul 143-701,South Korea
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28
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Li X, Kuang Y, Lin HC, Gao Y, Shi J, Xu B. Supramolecular nanofibers and hydrogels of nucleopeptides. Angew Chem Int Ed Engl 2011; 50:9365-9. [PMID: 21948432 PMCID: PMC3251214 DOI: 10.1002/anie.201103641] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/19/2011] [Indexed: 02/03/2023]
Affiliation(s)
| | | | | | | | | | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA, Fax: (+) 01-781-736-5201
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29
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Li X, Kuang Y, Lin HC, Gao Y, Shi J, Xu B. Supramolecular Nanofibers and Hydrogels of Nucleopeptides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103641] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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Roviello GN, Musumeci D, Bucci EM, Pedone C. Synthesis and characterization of a novel ester-based nucleoamino acid for the assembly of aromatic nucleopeptides for biomedical applications. Int J Pharm 2011; 415:206-10. [PMID: 21689737 DOI: 10.1016/j.ijpharm.2011.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/01/2011] [Accepted: 06/03/2011] [Indexed: 01/12/2023]
Abstract
In this work, we report a technological approach to a novel Fmoc-protected nucleoamino acid, based on l-tyrosine, carrying the DNA nucleobase on the hydroxyl group by means of an ester bond, suitable for the solid-phase synthesis of novel aromatic nucleopeptides of potential interest in biomedicine. After ESI-MS and NMR characterization this building block was used for the assembly of a thymine-functionalized tetrapeptide, composed of nucleobase-containing and underivatized l-tyrosine moieties alternated in the backbone.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
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31
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Roviello GN, Ricci A, Bucci EM, Pedone C. Synthesis, biological evaluation and supramolecular assembly of novel analogues of peptidyl nucleosides. MOLECULAR BIOSYSTEMS 2011; 7:1773-8. [PMID: 21431179 DOI: 10.1039/c1mb05007a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work concerns the synthesis, the supramolecular assembly and the evaluation of some biological properties, such as DNA and RNA-binding ability and human serum stability, of novel nucleopeptides. These compounds are of potential interest for the well-known properties that similar compounds, such as natural peptidyl nucleosides, possess in biology and medicine and also for the possibility to realize nucleopeptide-based supramolecular systems useful for drug and gene delivery applications. More particularly, all four nucleobase-containing peptides were synthesized by solid phase synthesis, purified by HPLC and characterized by NMR and ESI-MS. Subsequently, nucleopeptide self-assembly as well as DNA and RNA-binding ability were investigated by CD spectroscopy and further information on the formation of molecular networks, based on the peptidyl nucleoside analogues and nucleic acids, was obtained by Laser Light Scattering. Finally, nucleopeptide enzymatic stability was studied and a half life of about 2 hours was found in the presence of 50% fresh human serum.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
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32
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Roviello GN, Musumeci D, Bucci EM, Pedone C. Evidences for supramolecular organization of nucleopeptides: synthesis, spectroscopic and biological studies of a novel dithymine L-serine tetrapeptide. MOLECULAR BIOSYSTEMS 2011; 7:1073-80. [PMID: 21203614 DOI: 10.1039/c0mb00214c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work concerns a dithymine tetrapeptide, which can be seen as a new analogue of a dinucleoside monophosphate, made of both unfunctionalized and thymine-containing L-serine units alternated in the sequence. The new nucleopeptide was obtained on the solid phase by two different synthetic strategies. The first one is suitable to easily realize nucleopeptides with homonucleobase sequences, obtained by assembling an oligoserine backbone and then simultaneously coupling the free serine hydroxyl groups with the carboxymethylated nucleobase. The other strategy, which makes use of a Fmoc-protected nucleo-L-serine monomer, allows for the obtainment of nucleopeptides with mixed nucleobase sequences. CD spectroscopic studies and laser light scattering experiments, performed on solutions of the novel nucleopeptide, suggested the formation of supramolecular networks based on the self-assembly of the dithymine tetrapeptide molecules. Furthermore, CD binding studies with natural nucleic acids revealed a very weak interaction between the nucleopeptide and DNA (but not RNA). Molecular networks based on this biodegradable and water-soluble nucleopeptide, which is more resistant in plasma than standard tetrapeptides (and oligopeptides), contain a hydrophobic core which could provide the necessary environment to incorporate poorly water-soluble drugs, as evidenced by fluorescence spectroscopy. Furthermore, our studies evidenced that the structure of the tetrapeptide-based supramolecular assembly can be modified by metal ions as evidenced by UV interaction studies with Cu(2+).
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
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33
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Diezmann F, Seitz O. DNA-guided display of proteins and protein ligands for the interrogation of biology. Chem Soc Rev 2011; 40:5789-801. [DOI: 10.1039/c1cs15054e] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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