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Shiraishi T, Sato K, Hara RI, Wada T. Properties of artificial cationic oligodiaminosaccharides and oligopeptides that bind to A-type oligonucleotide duplexes. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023:1-18. [PMID: 36850058 DOI: 10.1080/15257770.2023.2182444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A critical strategy to improve the properties of oligonucleotide therapeutics is using cationic molecules as carriers. We developed artificial cationic molecules that bind to A-type oligonucleotide duplexes, such as siRNAs, in a stoichiometric ratio. In this study, we investigated the properties of oligo 2,6-diamino-D-galactoses (ODAGals) and L-2,4-diaminobutanoic acid oligomers (Dabs) and revealed their thermal and biological stabilization effects on A-type duplexes and their chemical stability. As a result, ODAGal and Dab with the same number of amino groups had the commensurate ability for the biological stabilization effect, whereas Dab enhanced the thermal stability of A-type duplexes more effectively than ODAGal.
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Affiliation(s)
- Tomomi Shiraishi
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
| | - Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan.,Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-Ku, Tokyo, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
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2
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Frenkel-Pinter M, Haynes JW, Mohyeldin AM, C M, Sargon AB, Petrov AS, Krishnamurthy R, Hud NV, Williams LD, Leman LJ. Mutually stabilizing interactions between proto-peptides and RNA. Nat Commun 2020; 11:3137. [PMID: 32561731 PMCID: PMC7305224 DOI: 10.1038/s41467-020-16891-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
The close synergy between peptides and nucleic acids in current biology is suggestive of a functional co-evolution between the two polymers. Here we show that cationic proto-peptides (depsipeptides and polyesters), either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared in pure form, can engage in direct interactions with RNA resulting in mutual stabilization. Cationic proto-peptides significantly increase the thermal stability of folded RNA structures. In turn, RNA increases the lifetime of a depsipeptide by >30-fold. Proto-peptides containing the proteinaceous amino acids Lys, Arg, or His adjacent to backbone ester bonds generally promote RNA duplex thermal stability to a greater magnitude than do analogous sequences containing non-proteinaceous residues. Our findings support a model in which tightly-intertwined biological dependencies of RNA and protein reflect a long co-evolutionary history that began with rudimentary, mutually-stabilizing interactions at early stages of polypeptide and nucleic acid co-existence.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jay W Haynes
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ahmad M Mohyeldin
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Martin C
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alyssa B Sargon
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton S Petrov
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramanarayanan Krishnamurthy
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Loren Dean Williams
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA. .,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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3
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Sato Y. Design of Fluorescent Peptide Nucleic Acid Probes Carrying Cyanine Dyes for Targeting Double-Stranded RNAs for Analytical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
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4
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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5
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Sato Y, Kaneko M, Sato T, Nakata S, Takahashi Y, Nishizawa S. Enhanced Binding Affinity of siRNA Overhang‐Binding Fluorescent Probes by Conjugation with Cationic Oligopeptides for Improved Analysis of the siRNA Delivery Process. Chembiochem 2018; 20:408-414. [DOI: 10.1002/cbic.201800560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Yusuke Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Mitsumasa Kaneko
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Takaya Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Saki Nakata
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Yuki Takahashi
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
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6
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Hara RI, Maeda Y, Fujimaki H, Wada T. Enhancement in RNase H activity of a DNA/RNA hybrid duplex using artificial cationic oligopeptides. Chem Commun (Camb) 2018; 54:8526-8529. [DOI: 10.1039/c8cc04082f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study assessed the effects of artificial cationic oligopeptides on a DNA/RNA hybrid duplex.
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Affiliation(s)
- Rintaro Iwata Hara
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
- Department of Neurology and Neurological Science
| | - Yusuke Maeda
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
| | - Haruna Fujimaki
- Graduate School of Frontier Sciences
- The University of Tokyo
- Kashiwa
- Japan
| | - Takeshi Wada
- Faculty of Pharmaceutical Sciences
- Tokyo University of Science
- Noda
- Japan
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7
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Sbicca L, González AL, Gresika A, Di Giorgio A, Closa JT, Tejedor RE, Andréola ML, Azoulay S, Patino N. Exploring the impact of the side-chain length on peptide/RNA binding events. Phys Chem Chem Phys 2017; 19:18452-18460. [PMID: 28681892 DOI: 10.1039/c7cp03726k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The impact of the amino-acid side-chain length on peptide-RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model. Our studies demonstrate that increasing the length of all peptide side-chains improves unexpectedly the binding affinity (KD) but reduces the degree of compactness of the peptide-RNA complex. Overall, the side-chain length appears to modulate in an unpredictable way the ability of the peptide to compete with the cognate TAR RNA partner. Beyond the establishment of non-intuitive fundamental relationships, our results open up new perspectives in the design of effective RNA ligand competitors, since a large number of them have already been identified but few studies report on the modulation of the biological activity by modifying in the same way the length of all chains connecting RNA recognition motives to the central scaffold of a ligand.
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Affiliation(s)
- Lola Sbicca
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, 06108 Nice, France.
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8
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Muse O, Zengeya T, Mwaura J, Hnedzko D, McGee DW, Grewer CT, Rozners E. Sequence selective recognition of double-stranded RNA at physiologically relevant conditions using PNA-peptide conjugates. ACS Chem Biol 2013; 8:1683-6. [PMID: 23721369 DOI: 10.1021/cb400144x] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conjugation of short peptide nucleic acids (PNA) with tetralysine peptides strongly enhanced triple helical binding to RNA at physiologically relevant conditions. The PNA hexamers and heptamers carrying cationic nucleobase and tetralysine modifications displayed high binding affinity for complementary double-stranded RNA without compromising sequence selectivity. The PNA-peptide conjugates had unique preference for binding double-stranded RNA, while having little, if any, affinity for double-stranded DNA. The cationic PNAs were efficiently taken up by HEK293 cells, whereas little uptake was observed for unmodified PNA.
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Affiliation(s)
- Oluwatoyosi Muse
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Thomas Zengeya
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Juddy Mwaura
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Dziyana Hnedzko
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Dennis W. McGee
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Christof T. Grewer
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
| | - Eriks Rozners
- Departments of †Chemistry and ‡Biological Sciences, Binghamton University, The State University
of New York, Binghamton, New York 13902, United
States
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9
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Maeda Y, Iwata R, Wada T. Synthesis and properties of cationic oligopeptides with different side chain lengths that bind to RNA duplexes. Bioorg Med Chem 2013; 21:1717-23. [DOI: 10.1016/j.bmc.2013.01.053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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10
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Diaminopropionic acid lipopeptides: characterization studies of polyplexes aimed at pDNA delivery. Bioorg Med Chem Lett 2012; 22:5635-8. [PMID: 22858100 DOI: 10.1016/j.bmcl.2012.06.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/27/2012] [Accepted: 06/29/2012] [Indexed: 11/20/2022]
Abstract
Here we report a novel class of peptides-d-diaminopropionic acids (Dap)-for gene delivery. These peptides have attractive properties for gene delivery, and the advantage that they can be easily manipulated in relation to their composition, abiding with tailored-design. We characterized the toxicological and biophysical properties of DNA particles resulting from the interaction of the nucleic acid with a series of Dap(8) peptides conjugated to different alkyl groups. These peptides formed small and homogenous DNA particle populations that protected against DNase I degradation at non-toxic concentrations. However, despite the similarity between these peptides and others that are arginine-rich, and efficient vectors, functional studies suggest the need for additional modifications in the carriers to improve their DNA delivery efficiency. Taken together, these studies underscore the relevance of the overall structure of the carrier and the complexity of designing from scratch a carrier.
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