1445-07-4Relevant articles and documents
Total synthesis of pseudouridine: Via Heck-type C-glycosylation
Yu, Cheng-Ping,Chang, Hsin-Yun,Chien, Tun-Cheng
, p. 8796 - 8803 (2019)
The reaction of 2,4-dimethoxy-5-iodopyrimidine (8) and 3,5-di-O-tert-butyldimethylsilyl protected ribofuranoid glycal 4 was carried out with Pd(OAc)2 as the catalyst, PPh3 as the ligand and Et3N as the base in DMF at 70 °C followed by desilylation to afford exclusively the β-anomer of 5-(2,3-dideoxy-3-oxoribofuranosyl)-2,4-dimethoxypyrimidine (11) in a very good yield. The subsequent protecting group and functional group interconversions furnished pseudouridine (Ψ, 1).
Semi-enzymatic synthesis of pseudouridine
Clerc, Elliot P.,Riley, Andrew T.,Sanford, Tristan C.,Sumita, Minako,Woodard, Austin M.
, (2021)
Modifications of RNA molecules have a significant effect on their structure and function. One of the most common modifications is the isomerization from uridine to pseudouridine. Despite its prevalence in natural RNA sequences, organic synthesis of pseudouridine has been challenging because of the stereochemistry requirement and the sensitivity of reaction steps to moisture. Herein, a semi-enzymatic synthetic route is developed for the synthesis of pseudouridine using adenosine 5′-monophosphate and uracil as the starting materials and a reverse reaction catalyzed by the pseudouridine monophosphate glycosidase. This synthetic route has only three steps and the overall yield of β-pseudouridine production was 68.4%.
Structural elucidation of bisulfite adducts to pseudouridine that result in deletion signatures during reverse transcription of RNA
Fleming, Aaron M.,Alenko, Anton,Kitt, Jay P.,Orendt, Anita M.,Flynn, Peter F.,Harris, Joel M.,Burrows, Cynthia J.
, p. 16450 - 16460 (2019)
The recent report of RBS-Seq to map simultaneously the epitranscriptomic modifications N1-methyladenosine, 5-methylcytosine, and pseudouridine (ψ) via bisulfite treatment of RNA provides a key advance to locate these important modifications. The locations of ψ were found by a deletion signature generated during cDNA synthesis after bisulfite treatment for which the chemical details of the reaction are poorly understood. In the present work, the bisulfite reaction with ψ was explored to identify six isomers of bisulfite adducted to ψ. We found four of these adducts involved the heterocyclic ring, similar to the reaction with other pyrimidines. The remaining two adducts were bonded to the 1′ carbon, which resulted in opening of the ribose ring. The utilization of complementary 1D- and 2D-NMR, Raman, and electronic circular dichroism spectroscopies led to the assignment of the two ribose adducts being the constitutional isomers of an S- and an O-adduct of bisulfite to the ribose, and these are the final products after heating. A mechanistic proposal is provided to rationalize chemically the formation and stereochemistries of all six isomeric bisulfite adducts to ψ conversion of intermediate adducts to the two final products is proposed to involve E2, SN2′, and [2,3]-sigmatropic shift reactions. Lastly, a synthetic RNA template with ψ at a known location was treated with bisulfite, leading to a deletion signature after reverse transcription, supporting the RBS-Seq report. This classical bisulfite reaction used for epigenomic and epitranscriptomic sequencing diverges from the C nucleoside ψ to form stable bisulfite end products that yield signatures for next-generation sequencing.
An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation
Friedt, Jenna,Leavens, Fern M. V.,Mercier, Evan,Wieden, Hans-Joachim,Kothe, Ute
, p. 3857 - 3870 (2014)
Pseudouridine synthases introduce the most common RNA modification and likely use the same catalytic mechanism. Besides a catalytic aspartate residue, the contributions of other residues for catalysis of pseudouridine formation are poorly understood. Here, we have tested the role of a conserved basic residue in the active site for catalysis using the bacterial pseudouridine synthase TruB targeting U55 in tRNAs. Substitution of arginine 181 with lysine results in a 2500-fold reduction of TruB's catalytic rate without affecting tRNA binding. Furthermore, we analyzed the function of a second-shell aspartate residue (D90) that is conserved in all TruB enzymes and interacts with C56 of tRNA. Site-directed mutagenesis, biochemical and kinetic studies reveal that this residue is not critical for substrate binding but influences catalysis significantly as replacement of D90 with glutamate or asparagine reduces the catalytic rate 30- and 50-fold, respectively. In agreement with molecular dynamics simulations of TruB wild type and TruB D90N, we propose an electrostatic network composed of the catalytic aspartate (D48), R181 and D90 that is important for catalysis by finetuning the D48-R181 interaction. Conserved, negatively charged residues similar to D90 are found in a number of pseudouridine synthases, suggesting that this might be a general mechanism. The Author(s) 2013. Published by Oxford University Press.
Total Synthesis of Pseudouridimycin
Jia, Yue-Mei,Li, Yi-Xian,Wang, Xu-Kun,Yu, Chu-Yi
, p. 511 - 515 (2022/01/28)
Pseudouridimycin (1), a potent antibiotic against both Gram-positive and Gram-negative bacteria including multi-drug-resistant strains with a new mode of action isolated from Streptomyces sp., was synthesized by a convergent strategy from 5′-amino-pseudouridine 5 and N-hydroxy-dipeptide 26 in 23% total yield. The key intermediate 26 was synthesized by hydroxylaminolysis of the nitrone derived from glutamine and subsequent glycylation with glycine chloride. The synthetic method provides an efficient and practical way for the synthesis of N-hydroxylated peptidyl nucleoside.
SYNTHESIS AND STRUCTURE OF HIGH POTENCY RNA THERAPEUTICS
-
, (2019/01/15)
This invention provides expressible polynucleotides, which can express a target protein or polypeptide. Synthetic mRNA constructs for producing a protein or polypeptide can contain one or more 5′ UTRs, where a 5′ UTR may be expressed by a gene of a plant. In some embodiments, a 5′ UTR may be expressed by a gene of a member of Arabidopsis genus. The synthetic mRNA constructs can be used as pharmaceutical agents for expressing a target protein or polypeptide in vivo.
Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives
Chang, Yu-Cheng,Herath, Jayatilake,Wang, Tony H.-H.,Chow, Christine S.
, p. 2676 - 2686 (2008/09/21)
A series of 3-substituted uridine and pseudouridine derivatives, based on the naturally occurring 3-(3-amino-3-carboxypropyl) modification, were synthesized. Their aqueous solution conformations were determined by using circular dichroism and NMR spectroscopy. Functional group composition and chain length were shown to have only a subtle influence on the distribution of syn/anti conformations of the modified nucleosides. The dominating factor appears to be the glycosidic linkage (C- vs. N-glycoside) in determining the nucleoside conformation.
Nucleic acid labeling compounds
-
, (2008/06/13)
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. Methods for making such heterocyclic compounds are also disclosed. The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
A highly stereocontrolled and efficient synthesis of α- and β-pseudouridines
Hanessian, Stephen,Machaalani, Roger
, p. 8321 - 8323 (2007/10/03)
A five-step practical and stereocontrolled synthesis of α- and β-pseudouridines from D-ribonolactone is described. The key step involves a highly stereoselective reduction of a hemiketal C-nucleoside intermediate in each case. Multi-gram quantities of β-pseudouridine can now be made available.
A practical synthesis of the modified RNA nucleoside pseudouridine
Grohar, Patrick J.,Chow, Christine S.
, p. 2049 - 2052 (2007/10/03)
An alternative synthesis of the modified RNA nucleoside pseudouridine is reported. This procedure employs coupling of an iodinated pyrimidine and a suitably protected lactone. The resulting hemiacetal is reduced and deprotected to yield pseudouridine.
