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Vu TD, Lin SC, Wu CC, Chu DT. RNA therapeutics for metabolic disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:181-196. [PMID: 38359998 DOI: 10.1016/bs.pmbts.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The prevalence of metabolic disorders is increasing exponentially and has recently reached epidemic levels. Over the decades, a large number of therapeutic options have been proposed to manage these diseases but still show several limitations. In this circumstance, RNA therapeutics have rapidly emerged as a new hope for patients with metabolic diseases. 57 years have elapsed from the discovery of mRNA, a large number of RNA-based drug candidates have been evaluated for their therapeutic effectiveness and clinical safety under clinical studies. To date, there are seven RNA drugs for treating metabolic disorders receiving official approval and entering the global market. Their targets include hereditary transthyretin-mediated amyloidosis (hATTR), familial chylomicronemia syndrome, acute hepatic porphyria, primary hyperoxaluria type 1 and hypercholesterolemia, which are all related to liver proteins. All of these seven RNA drugs are antisense oligonucleotides (ASO) and small interfering RNA (siRNA). These two types of treatment are both based on oligonucleotides complementary to target RNA through Watson-Crick base-pairing, but their mechanisms of action include different nucleases. Such treatments show greatest potential among all types of RNA therapeutics due to consecutive achievements in chemical modifications. Another method, mRNA therapeutics also promise a brighter future for patients with a handful of drug candidates currently under development.
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Affiliation(s)
- Thuy-Duong Vu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Sheng-Che Lin
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of Plastic and Reconstructive Surgery, Tainan Municipal An-Nan Hospital-China Medical University, Tainan, Taiwan
| | - Chia-Ching Wu
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan.
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Lee EM, Setterholm NA, Hajjar M, Barpuzary B, Chaput JC. Stability and mechanism of threose nucleic acid toward acid-mediated degradation. Nucleic Acids Res 2023; 51:9542-9551. [PMID: 37650628 PMCID: PMC10570051 DOI: 10.1093/nar/gkad716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/21/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
Xeno-nucleic acids (XNAs) have gained significant interest as synthetic genetic polymers for practical applications in biomedicine, but very little is known about their biophysical properties. Here, we compare the stability and mechanism of acid-mediated degradation of α-l-threose nucleic acid (TNA) to that of natural DNA and RNA. Under acidic conditions and elevated temperature (pH 3.3 at 90°C), TNA was found to be significantly more resistant to acid-mediated degradation than DNA and RNA. Mechanistic insights gained by reverse-phase HPLC and mass spectrometry indicate that the resilience of TNA toward low pH environments is due to a slower rate of depurination caused by induction of the 2'-phosphodiester linkage. Similar results observed for 2',5'-linked DNA and 2'-O-methoxy-RNA implicate the position of the phosphodiester group as a key factor in destabilizing the formation of the oxocarbenium intermediate responsible for depurination and strand cleavage of TNA. Biochemical analysis indicates that strand cleavage occurs by β-elimination of the 2'-phosphodiester linkage to produce an upstream cleavage product with a 2'-threose sugar and a downstream cleavage product with a 3' terminal phosphate. This work highlights the unique physicochemical properties available to evolvable non-natural genetic polymers currently in development for biomedical applications.
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Affiliation(s)
- Erica M Lee
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Noah A Setterholm
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Mohammad Hajjar
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Bhawna Barpuzary
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
- Department of Chemistry, University of California, Irvine, CA 92697-3958, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697-3958, USA
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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Sobkowski M. A convenient protection for 4-oxopyrimidine moieties in nucleosides by the pivaloyl group. ACTA ACUST UNITED AC 2010. [DOI: 10.1135/cccc2009084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Application of the pivaloyl group as a protection for the N3 position of thymidine and uridine was investigated. Pivaloylation of thymidine is a very rapid reaction proceeding under mild conditions with excellent regioselectivity for sugar or thymine moiety, depending on the amines used. Several pivaloylated thymidine derivatives were obtained by treatment of unprotected thymidine with pivaloyl chloride under various experimental conditions. Stability of the N3-pivaloyl protecting group under basic and acidic conditions was evaluated and the conditions for its selective removal were found.
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Zatsepin TS, Romanova EA, Oretskaya TS. Synthesis of 2'-O-alkylnucleosides. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc2002v071n06abeh000714] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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McGee DPC, Zhai Y. REACTION OF ANHYDRONUCLEOSIDES WITH MAGNESIUM ALKOXIDES: REGIOSPECIFIC SYNTHESIS OF 2′-O-ALKYLPYRIMIDINE NUCLEOSIDES. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cramer H, Pfleiderer W. Nucleosides. Part LXI. A Simple Procedure for the Monomethylation of Protected and Unprotected Ribonucleosides in the 2?-O- and 3?-O-Position Using Diazomethane and the Catalyst Stannous Chloride. Helv Chim Acta 1996. [DOI: 10.1002/hlca.19960790808] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lubini P, Zürcher W, Egli M. Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines. CHEMISTRY & BIOLOGY 1994; 1:39-45. [PMID: 9383369 DOI: 10.1016/1074-5521(94)90039-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The stability of hybrids of 2'-O-methyl-ribonucleotides with complementary RNA is considerably higher than that of the corresponding DNA.RNA duplexes. The 2'-O-modified ribonucleotides are thus an attractive class of compounds for antisense applications. Understanding how these substituents stabilize the structure of the hybrid duplex may be important in the design of ribonucleotides with novel properties. RESULTS The crystal structure of a dimer of the self-complementary DNA strand d(GCGT)O2'mer(A)d(TACGC), which has a 2'-O-methylated ribonucleotide incorporated at position 5, was determined at 2.1 A resolution. This strand forms a duplex with an overall A-type conformation; the methyl groups of the two modified adenosines point into the relatively wide minor groove. Both 2'-methoxy groups are hydrogen-bonded to solvent molecules. These results allowed us to build a model of a fully 2'-O-methylated RNA double helix. CONCLUSIONS Insertion of 2'-O-modified RNA residues into a stretch of DNA can nucleate a local A-type conformation, in part because modification with a bulky residue at this position stabilizes a C3'-endo type sugar pucker. The increased stability of fully 2'-O-methylated RNA may result from hydrophobic interactions between substituents in the minor groove. As the 2'-O-methyl groups are directed into the minor groove, it may be worthwhile to introduce tailor-made 2'-O-substituents into RNA; it might be possible to design groups that both stabilize the hybrid duplexes and carry a nuclease function, further improving the efficacy of these modified RNAs in antisense applications.
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Affiliation(s)
- P Lubini
- Organic Chemistry Laboratory, ETH Swiss Federal Institute of Technology, Zürich, Switzerland
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Abstract
A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sources, and initial literature citations for structural characterization or occurrence, and for chemical synthesis. The listing is categorized by type of RNA: tRNA, rRNA, mRNA, snRNA, and other RNAs. A total of 93 different modified nucleosides have been reported in RNA, with the largest number and greatest structural diversity in tRNA, 79; and 28 in rRNA, 12 in mRNA, 11 in snRNA and 3 in other small RNAs.
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Affiliation(s)
- P A Limbach
- Department of Medicinal Chemistry, University of Utah, Salt Lake City 84112
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Ghosh MK, Cohen JS. Oligodeoxynucleotides as antisense inhibitors of gene expression. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1992; 42:79-126. [PMID: 1574591 DOI: 10.1016/s0079-6603(08)60574-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M K Ghosh
- Pharmacology Department, Georgetown University Medical School, Washington, D.C. 20007
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Sproat BS, Iribarren AM, Garcia RG, Beijer B. New synthetic routes to synthons suitable for 2'-O-allyloligoribonucleotide assembly. Nucleic Acids Res 1991; 19:733-8. [PMID: 1708121 PMCID: PMC333704 DOI: 10.1093/nar/19.4.733] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
New synthetic routes have been devised for the high yield preparation of protected 2'-O-allylribonucleoside-3'-O-phosphoramidites, exemplified by the ribonucleosides guanosine and 2,6-diaminopurine riboside (2-aminoadenosine). Key features are the use of versatile intermediates and an easy allylation step. The development of a novel synthon based on 2'-O-allyl-2,6-diaminopurine riboside enables short 2'-O-allyl-oligoribonucleotide probes to be synthesized with adenine replaced by 2-aminoadenine. Thus very stable hybrids with complementary RNA target sequences can be formed due to the formation of the three hydrogen bond 2-amino A.U base pairs.
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Affiliation(s)
- B S Sproat
- European Molecular Biology Laboratory, Heidelberg, FRG
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Sproat BS, Beijer B, Iribarren A. New synthetic routes to protected purine 2'-O-methylriboside-3'-O-phosphoramidites using a novel alkylation procedure. Nucleic Acids Res 1990; 18:41-9. [PMID: 2308835 PMCID: PMC330201 DOI: 10.1093/nar/18.1.41] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A highly selective alkylation procedure has been developed enabling new synthetic routes to be established for protected purine 2'-O-methylriboside-3'-O-phosphoramidites; building blocks for the assembly of 2'-O-methyloligoribonucleotides. The new procedure avoids the use of the highly toxic and potentially explosive reagent diazomethane and is far superior to the use of silver oxide/methyl iodide. Moreover, the use of highly versatile key intermediates will enable the synthesis of a wide variety of base modified analogues as well as other 2'-O-alkylriboside derivatives.
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Affiliation(s)
- B S Sproat
- European Molecular Biology Laboratory, Heidelberg, FRG
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Inoue H, Hayase Y, Imura A, Iwai S, Miura K, Ohtsuka E. Synthesis and hybridization studies on two complementary nona(2'-O-methyl)ribonucleotides. Nucleic Acids Res 1987; 15:6131-48. [PMID: 3627981 PMCID: PMC306073 DOI: 10.1093/nar/15.15.6131] [Citation(s) in RCA: 278] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
2'-O-Methyl derivatives of the common ribonucleosides except for guanosine were synthesized via the 2'-O-methylation of appropriately-protected nucleosides with CH3I in the presence of Ag2O. The 2'-O-methylguanosine derivative was prepared by the monomethylation of a 2',3'-cis-diol system with diazomethane. These derivatives were converted to protected 2'-O-methylribonucleoside 3'-phosphates and used for oligonucleotide synthesis on polymer supports. Thus, oligo(2'-O-methyl-ribonucleotides) having the sequence identical to the consensus sequence of the 5'-splice junction CAGGUAAGU and its complement were synthesized in a stepwise manner using the phosphotriester method. Thermal stabilities (Tm's) of the duplex of these 2'-O-methyl ribo-oligomers and eight related duplexes containing ribo- or deoxyribo-oligomers were examined. It was found that the 2'-O-methyl oligoribonucleotides can be utilized as an alternative to an oligoribonucleotide probe in RNA hybridizations as the hybrid formed has a high, or a higher Tm, the probe is much easier to synthesize and it is less likely to be enzymatically degraded.
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Yamauchi K, Nakagima T, Kinoshita M. Selective 2′-O-Methylation of Pyrimidine-Ribonucleosides by Trimethylsulfonium Hydroxide in the Presence of Mg2+and Ca2+Ions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1986. [DOI: 10.1246/bcsj.59.2947] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Kamimura T, Masegi T, Hata T. PROTECTION OF IMIDE GROUP OF URACIL MOIETY BY MEANS OF 2,2,2-TRICHLORO-TERT-BUTYLOXYCARBONYL CHLORIDE: A SELECTIVE SYNTHESIS OF 2′-O-METHYLURIDINE. CHEM LETT 1982. [DOI: 10.1246/cl.1982.965] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Tanabe T, Yamauchi K, Kinoshita M. Methylation of Pyrimidine 2′-Deoxynucleosides with Trimethyl Phosphate. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1979. [DOI: 10.1246/bcsj.52.204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Robins MJ, Lee AS, Norris FA. Catalytic monomethylation of the cis-glycol system by diazomethane. Effects of novel inorganic catalysts on isomer ratios. Carbohydr Res 1975. [DOI: 10.1016/s0008-6215(00)87030-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ritzmann G, Klein RS, Ohrui H, Fox JJ. Nucleosides LXXXVI. A direct synthesis of 2′-unsubstituted pyrimidine ribonucleosides by use of a sugar 1,2-ketal. Tetrahedron Lett 1974. [DOI: 10.1016/s0040-4039(01)93125-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Haines A. Synthesis of 1-(2′-O-methyl-β-d-ribofuranosyl)-uracil (2′-O-methyluridine) and 3-(2′-O-methyl-β-d-ribofuranosyl)uracil. Tetrahedron 1973. [DOI: 10.1016/s0040-4020(01)93406-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Robins MJ, Naik SR. Nucleic acid related compounds. 1. Methylation and transformation of 4-methoxy-2-pyrimidinone 1- -D-ribofuranoside into 2'-O-methyl nucleoside components of ribonucleic acid, their analogs, and derivatives. Biochemistry 1971; 10:3591-7. [PMID: 5146572 DOI: 10.1021/bi00795a017] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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26
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Naik SR, Robins MJ. Nucleic acid related compounds. II. A rapid and quantitative preparation of 2'-0- and 3'-0-methyl nucleosides. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 246:341-3. [PMID: 5132908 DOI: 10.1016/0005-2787(71)90144-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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27
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Howlett HA, Johnson MW, Trim AR, Eagles J, Self R. Mass spectral analysis of modified ribonucleosides obtained by degradation of 14 alkali-stable dinucleotides isolated from yeast ribonucleic acid. Anal Biochem 1971; 39:429-40. [PMID: 5555471 DOI: 10.1016/0003-2697(71)90433-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Nichols JL, Lane BG. Characterization of N4,O2'-dimethylcytidine, a rare nucleoside constituent of Escherichia coli 16-S RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 166:605-15. [PMID: 4301908 DOI: 10.1016/0005-2787(68)90367-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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29
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Gray MW, Lane BG. 5-carboxymethyluridine, a novel nucleoside derived from yeast and wheat embryo transfer ribonucleates. Biochemistry 1968; 7:3441-53. [PMID: 4300701 DOI: 10.1021/bi00850a020] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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