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Shi Y, Zhen X, Zhang Y, Li Y, Koo S, Saiding Q, Kong N, Liu G, Chen W, Tao W. Chemically Modified Platforms for Better RNA Therapeutics. Chem Rev 2024; 124:929-1033. [PMID: 38284616 DOI: 10.1021/acs.chemrev.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.
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Affiliation(s)
- Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyan Zhen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yiming Zhang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yongjiang Li
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310058, China
| | - Gang Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, National Innovation Platform for Industry-Education Integration in Vaccine Research, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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2
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Sonego JM, de Diego SI, Szajnman SH, Gallo-Rodriguez C, Rodriguez JB. Organoselenium Compounds: Chemistry and Applications in Organic Synthesis. Chemistry 2023; 29:e202300030. [PMID: 37378970 DOI: 10.1002/chem.202300030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/18/2023] [Accepted: 06/28/2023] [Indexed: 06/29/2023]
Abstract
Selenium, originally described as a toxin, turns out to be a crucial trace element for life that appears as selenocysteine and its dimer, selenocystine. From the point of view of drug developments, selenium-containing drugs are isosteres of sulfur and oxygen with the advantage that the presence of the selenium atom confers antioxidant properties and high lipophilicity, which would increase cell membrane permeation leading to better oral bioavailability. In this article, we have focused on the relevant features of the selenium atom, above all, the corresponding synthetic approaches to access a variety of organoselenium molecules along with the proposed reaction mechanisms. The preparation and biological properties of selenosugars, including selenoglycosides, selenonucleosides, selenopeptides, and other selenium-containing compounds will be treated. We have attempted to condense the most important aspects and interesting examples of the chemistry of selenium into a single article.
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Affiliation(s)
- Juan M Sonego
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
| | - Sheila I de Diego
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
| | - Sergio H Szajnman
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
| | - Carola Gallo-Rodriguez
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Centro de Investigaciones en Hidratos de Carbono (CIHIDECAR), C1428EHA, Buenos Aires, Argentina
| | - Juan B Rodriguez
- Departamento de Química Orgánica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR), C1428EHA, Buenos Aires, Argentina
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3
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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4
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Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
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Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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Conlon PF, Eguaogie O, Wilson JJ, Sweet JST, Steinhoegl J, Englert K, Hancox OGA, Law CJ, Allman SA, Tucker JHR, Hall JP, Vyle JS. Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography. Chem Sci 2019; 10:10948-10957. [PMID: 32190252 PMCID: PMC7066676 DOI: 10.1039/c9sc04098f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/11/2019] [Indexed: 01/20/2023] Open
Abstract
Oligodeoxynucleotides incorporating internucleotide phosphoroselenolate linkages have been prepared under solid-phase synthesis conditions using dimer phosphoramidites. These dimers were constructed following the high yielding Michaelis-Arbuzov (M-A) reaction of nucleoside H-phosphonate derivatives with 5'-deoxythymidine-5'-selenocyanate and subsequent phosphitylation. Efficient coupling of the dimer phosphoramidites to solid-supported substrates was observed under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle. In a further demonstration of the utility of M-A chemistry, the support-bound selenonucleoside was reacted with an H-phosphonate and then chain extended using phosphoramidite chemistry. Following initial unmasking of methyl-protected phosphoroselenolate diesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 to -3.1 °C per phosphoroselenolate) when introduced at the 5'-termini of A-form or mixed duplexes or at juxtaposed central loci within a B-form duplex (-1.0 °C per modification). As found with other nucleic acids incorporating selenium, expeditious crystallisation of a modified decanucleotide A-form duplex was observed and the structure solved to a resolution of 1.45 Å. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
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Affiliation(s)
- Patrick F Conlon
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Olga Eguaogie
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jordan J Wilson
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Jamie S T Sweet
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
| | - Julian Steinhoegl
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Klaudia Englert
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - Oliver G A Hancox
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - Christopher J Law
- School of Biological Sciences , Queen's University Belfast , 15 Chlorine Gardens , Belfast BT9 5AH , UK
| | - Sarah A Allman
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
| | - James H R Tucker
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK
| | - James P Hall
- Reading School of Pharmacy , University of Reading , Whiteknights , Reading RG6 6AP , UK .
- Diamond Light Source , Chilton , Didcot , Oxfordshire OX11 0DE , UK
| | - Joseph S Vyle
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast , BT9 5AG , UK .
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6
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Yamaguchi T, Obika S. Derivative Synthesis toward Enhancement of the Biophysical Properties of 2′,4′-Bridged Nucleic Acids. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
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