Post-Synthetic Nucleobase Modification of Oligodeoxynucleotides by Sonogashira Coupling and Influence of Alkynyl Modifications on the Duplex-Forming Ability.
alkynes
cross-coupling
nucleobases
oligonucleotides
Journal
Chemistry (Weinheim an der Bergstrasse, Germany)
ISSN: 1521-3765
Titre abrégé: Chemistry
Pays: Germany
ID NLM: 9513783
Informations de publication
Date de publication:
13 Nov 2023
13 Nov 2023
Historique:
received:
17
06
2023
medline:
15
11
2023
pubmed:
28
8
2023
entrez:
27
8
2023
Statut:
ppublish
Résumé
Recently, it was reported that the alkynyl modification of nucleobases mitigates the toxicity of antisense oligonucleotides (ASO) while maintaining the efficacy. However, the general effect of alkynyl modifications on the duplex-forming ability of oligonucleotides (ONs) is unclear. In this study, post-synthetic nucleobase modification by Sonogashira coupling in aqueous medium was carried out to efficiently evaluate the physiological properties of various ONs with alkynyl-modified nucleobases. Although several undesired reactions, including nucleobase cyclization, were observed, various types of alkynyl-modified ONs were successfully obtained via Sonogashira coupling of ONs containing iodinated nucleobases. Evaluation of the stability of the duplex formed by the synthesized alkynyl-modified ONs showed that the alkynyl modification of pyrimidine was less tolerated than that of purine, although both the modifications occurred in the major groove of the duplex. These results can be attributed to the bond angle of the alkyne on the pyrimidine and the close proximity of the alkynyl substituents to the phosphodiester backbone. The synthetic method developed in this study may contribute to the screening of the optimal chemical modification of ASO because various alkynyl-modified ONs that are effective in reducing the toxicity of ASO can be easily synthesized by this method.
Identifiants
pubmed: 37635089
doi: 10.1002/chem.202301928
doi:
Substances chimiques
Oligodeoxyribonucleotides
0
Oligonucleotides
0
Oligonucleotides, Antisense
0
Pyrimidines
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e202301928Subventions
Organisme : Japan Society for the Promotion of Science
ID : 22J11795
Organisme : Japan Society for the Promotion of Science
ID : 22KJ2142
Organisme : Nagai Memorial Research Scholarship from the Pharmaceutical Society of Japan
Organisme : the Japan Agency for Medical Research and Development (AMED)
ID : JP21ae0121022
Organisme : the Japan Agency for Medical Research and Development (AMED)
ID : JP21ae0121023
Organisme : the Japan Agency for Medical Research and Development (AMED)
ID : JP21ae0121024
Informations de copyright
© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.
Références
S. T. Crooke, B. F. Baker, R. M. Crooke, X. hai Liang, Nat. Rev. Drug Discovery 2021, 20, 427-453.
A. M. Quemener, L. Bachelot, A. Forestier, E. Donnou-Fournet, D. Gilot, M. D. Galibert, Wiley Interdiscip. Rev.: RNA 2020, 11, 1-22.
C. Rinaldi, M. J. A. Wood, Nat. Rev. Neurol. 2018, 14, 9-22.
B. Hu, L. Zhong, Y. Weng, L. Peng, Y. Huang, Y. Zhao, X. J. Liang, Signal Transduct. Target. Ther. 2020, 5, 101.
B. Hu, Y. Weng, X. H. Xia, X. jie Liang, Y. Huang, J. Gene Med. 2019, 21, 1-14.
R. R. Nikam, K. R. Gore, Nucleic Acid Ther. 2018, 28, 209-224.
S. Ni, Z. Zhuo, Y. Pan, Y. Yu, F. Li, J. Liu, L. Wang, X. Wu, D. Li, Y. Wan, L. Zhang, Z. Yang, B. T. Zhang, A. Lu, G. Zhang, ACS Appl. Mater. Interfaces 2021, 13, 9500-9519.
Y. Zhang, B. S. Lai, M. Juhas, Molecules 2019, 24, 941.
J. Zhou, J. Rossi, Nat. Rev. Drug Discovery 2017, 16, 181-202.
A. Khvorova, J. K. Watts, Nat. Biotechnol. 2017, 35, 238-248.
S. Ochoa, V. T. Milam, Molecules 2020, 25, 1-23.
W. Brad Wan, P. P. Seth, J. Med. Chem. 2016, 59, 9645-9667.
M. Terrazas, E. T. Kool, Nucleic Acids Res. 2009, 37, 346-353.
F. Odeh, H. Nsairat, W. Alshaer, M. A. Ismail, E. Esawi, B. Qaqish, A. Al Bawab, S. I. Ismail, Molecules 2020, 25, DOI 10.3390/molecules25010003.
M. Hocek, J. Org. Chem. 2014, 79, 9914-9921.
S. Cornélie, J. Hoebeke, A. M. Schacht, B. Bertin, J. Vicogne, M. Capron, G. Riveau, J. Biol. Chem. 2004, 279, 15124-15129.
J. Cavagnaro, C. Berman, D. Kornbrust, T. White, S. Campion, S. Henry, Nucleic Acid Ther. 2014, 24, 313-325.
Y. Ito, Y. Hari, Chem. Rec. 2022, 202100325, 1-15.
K. Bartosik, K. Debiec, A. Czarnecka, E. Sochacka, G. Leszczynska, Molecules 2020, 25, 3344.
S. I. Khan, M. W. Grinstaff, J. Am. Chem. Soc. 1999, 121, 4704-4705.
A. E. Beilstein, M. W. Grinstaff, Chem. Commun. 2000, 509-510.
M. Rist, N. Amann, H. A. Wagenknecht, Eur. J. Org. Chem. 2003, 2498-2504.
O. Schiemann, N. Piton, Y. Mu, G. Stock, J. W. Engels, T. F. Prisner, J. Am. Chem. Soc. 2004, 126, 5722-5729.
E. Mayer, L. Valis, C. Wagner, M. Rist, N. Amann, H. A. Wagenknecht, ChemBioChem 2004, 5, 865-868.
T. Kottysch, C. Ahlborn, F. Brotzel, C. Richert, Chem. A Eur. J. 2004, 10, 4017-4028.
H. Okamura, G. H. Trinh, Z. Dong, W. Fan, F. Nagatsugi, Molecules 2023, 28, DOI 10.3390/molecules28041766.
N. Piton, Y. Mu, G. Stock, T. F. Prisner, O. Schiemann, J. W. Engels, Nucleic Acids Res. 2007, 35, 3128-3143.
A. Krause, A. Hertl, F. Muttach, A. Jäschke, Chem. Eur. J. 2014, 20, 16613-16619.
L. Wicke, J. W. Engels, Bioconjugate Chem. 2012, 23, 627-642.
C. Grünewald, T. Kwon, N. Piton, U. Förster, J. Wachtveitl, J. W. Engels, Bioorg. Med. Chem. 2008, 16, 19-26.
M. Ejlersen, C. Lou, Y. S. Sanghvi, Y. Tor, J. Wengel, Chem. Commun. 2018, 54, 8003-8006.
N. Probst, R. Lartia, O. Théry, M. Alami, E. Defrancq, S. Messaoudi, Chem. A Eur. J. 2018, 24, 1795-1800.
A. Omumi, D. G. Beach, M. Baker, W. Gabryelski, R. A. Manderville, J. Am. Chem. Soc. 2011, 133, 42-50.
L. Lercher, J. F. McGouran, B. M. Kessler, C. J. Schofield, B. G. Davis, Angew. Chem. Int. Ed. 2013, 52, 10553-10558.
M. B. Walunj, A. A. Tanpure, S. G. Srivatsan, Nucleic Acids Res. 2018, 46, e65.
M. B. Walunj, S. G. Srivatsan, Bioconjugate Chem. 2020, 31, 2513-2521.
K. Götte, S. Chines, A. Brunschweiger, Tetrahedron Lett. 2020, 61, 151889-151897.
P. R. Fitzgerald, B. M. Paegel, Chem. Rev. 2021, 121, 7155-7177.
T. Yoshida, K. Morihiro, Y. Naito, A. Mikami, Y. Kasahara, T. Inoue, S. Obika, Nucleic Acids Res. 2022, 50, 7224-7234.
A. Dieckmann, P. H. Hagedorn, Y. Burki, C. Brügmann, M. Berrera, M. Ebeling, T. Singer, F. Schuler, Mol. Ther. Nucleic Acids 2018, 10, 45-54.
N. Papargyri, M. Pontoppidan, M. R. Andersen, T. Koch, P. H. Hagedorn, Mol. Ther. Nucleic Acids 2020, 19, 706-717.
K. Liu, L. Zheng, Q. Liu, J. W. De Vries, J. Y. Gerasimov, A. Herrmann, J. Am. Chem. Soc. 2014, 136, 14255-14262.
M. C. Linder, Mutat. Res. - Fundam. Mol. Mech. Mutagen. 2012, 733, 83-91.
B. M. Trost, M. T. Sorum, C. Chan, A. E. Harms, G. Rühter, J. Am. Chem. Soc. 1997, 119, 698-708.
D. A. Berry, K. Y. Jung, D. S. Wise, A. D. Sercel, W. H. Pearson, H. Mackie, J. B. Randolph, R. L. Somers, Tetrahedron Lett. 2004, 45, 2457-2461.
Z. Jahnz-Wechmann, G. Framski, P. Januszczyk, J. Boryski, Eur. J. Med. Chem. 2015, 97, 388-396.
K. W. Anderson, S. L. Buchwald, Angew. Chem. Int. Ed. 2005, 44, 6173-6177.
A. L. Casalnuovo, J. C. Calabrese, J. Am. Chem. Soc. 1990, 112, 4324-4330.
E. Kuntz, U. S. Patent. 1981, 4248802.
R. Martin, S. L. Buchwald, Acc. Chem. Res. 2008, 41, 1461-1473.
K. H. Shaughnessy, Eur. J. Org. Chem. 2006, 1827-1835.
E. Alacid, C. Nájera, Adv. Synth. Catal. 2006, 348, 2085-2091.
N. C. Bruno, M. T. Tudge, S. L. Buchwald, Chem. Sci. 2013, 4, 916-920.
P. Yang, X. Wang, B. Li, Y. Yang, J. Yue, Y. Suo, H. Tong, G. He, X. Lu, G. Chen, Chem. Sci. 2021, 12, 5804-5810.
N. J. Whitcombe, K. K. Hii, S. E. Gibson, Tetrahedron 2001, 57, 7449-7476.
H. Xu, F. Ma, N. Wang, W. Hou, H. Xiong, F. Lu, J. Li, S. Wang, P. Ma, G. Yang, R. A. Lerner, Adv. Sci. 2019, 6, 6-11.
N. Favalli, G. Bassi, T. Zanetti, J. Scheuermann, D. Neri, Helv. Chim. Acta 2019, 102, e1900033.
M. Schilz, H. Plenio, J. Org. Chem. 2012, 77, 2798-2807.
T. W. Barnes, D. H. Turner, J. Am. Chem. Soc. 2001, 123, 9186-9187.
R. W. Wagner, M. D. Matteucci, J. G. Lewis, A. J. Gutierrez, C. Moulds, B. C. Froehler, Science 1993, 260, 1510-1513.
R. W. Wagner, M. D. Matteucci, D. Grant, T. Huang, B. C. Froehler, Nat. Biotechnol. 1996, 14, 840-844.