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Penchovsky R, Georgieva AV, Dyakova V, Traykovska M, Pavlova N. Antisense and Functional Nucleic Acids in Rational Drug Development. Antibiotics (Basel) 2024; 13:221. [PMID: 38534656 DOI: 10.3390/antibiotics13030221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
This review is focused on antisense and functional nucleic acid used for completely rational drug design and drug target assessment, aiming to reduce the time and money spent and increase the successful rate of drug development. Nucleic acids have unique properties that play two essential roles in drug development as drug targets and as drugs. Drug targets can be messenger, ribosomal, non-coding RNAs, ribozymes, riboswitches, and other RNAs. Furthermore, various antisense and functional nucleic acids can be valuable tools in drug discovery. Many mechanisms for RNA-based control of gene expression in both pro-and-eukaryotes and engineering approaches open new avenues for drug discovery with a critical role. This review discusses the design principles, applications, and prospects of antisense and functional nucleic acids in drug delivery and design. Such nucleic acids include antisense oligonucleotides, synthetic ribozymes, and siRNAs, which can be employed for rational antibacterial drug development that can be very efficient. An important feature of antisense and functional nucleic acids is the possibility of using rational design methods for drug development. This review aims to popularize these novel approaches to benefit the drug industry and patients.
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Affiliation(s)
- Robert Penchovsky
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Antoniya V Georgieva
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Vanya Dyakova
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Martina Traykovska
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Nikolet Pavlova
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
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Itoh M, Nakaura M, Imanishi T, Obika S. Target gene knockdown by 2',4'-BNA/LNA antisense oligonucleotides in zebrafish. Nucleic Acid Ther 2014; 24:186-91. [PMID: 24460393 DOI: 10.1089/nat.2013.0464] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Gene knockdowns using oligonucleotide-based approaches are useful for studying gene function in both in vitro cell culture systems and in vivo animal models. We evaluated the efficacy of 2',4'-bridged nucleic acids (BNA)-modified antisense oligonucleotides (AONs) for gene knockdown in zebrafish. We used the tcf7l1a gene as a model for testing the knockdown efficacy of 2',4'-BNA AONs and examined how the target sites/affinity and RNase H induction activity of 2',4'-BNA AONs affect knockdown efficacy. We found that tcf7l1a gene function was knocked down by 2',4'-BNA AONs that target the start codon and induce RNase H activity. Although nonspecific p53-mediated developmental defects were observed at higher doses, the effective dose of the 2',4'-BNA AONs for tcf7l1a is much lower than that of morpholino oligonucleotides. Our data thus show a potential application for 2',4'-BNA AONs in the downregulation of specific genes in zebrafish.
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Affiliation(s)
- Motoyuki Itoh
- 1 Graduate School of Pharmaceutical Sciences, Chiba University , Chuo-ku, Chiba, Japan
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Wheeler GN, Liu KJ. Xenopus: An ideal system for chemical genetics. Genesis 2012; 50:207-18. [DOI: 10.1002/dvg.22009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 02/05/2023]
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Koch T, Rosenbohm C, Hansen HF, Hansen B, Marie Straarup E, Kauppinen S. Locked Nucleic Acid: Properties and Therapeutic Aspects. THERAPEUTIC OLIGONUCLEOTIDES 2008. [DOI: 10.1039/9781847558275-00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Troels Koch
- Santaris Pharma A/S Bøge Allé 3 DK-2970 Hørsholm Denmark
| | | | | | - Bo Hansen
- Santaris Pharma A/S Bøge Allé 3 DK-2970 Hørsholm Denmark
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Kaur H, Babu BR, Maiti S. Perspectives on chemistry and therapeutic applications of Locked Nucleic Acid (LNA). Chem Rev 2007; 107:4672-97. [PMID: 17944519 DOI: 10.1021/cr050266u] [Citation(s) in RCA: 231] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Harleen Kaur
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Grünweller A, Hartmann RK. Locked nucleic acid oligonucleotides: the next generation of antisense agents? BioDrugs 2007; 21:235-43. [PMID: 17628121 DOI: 10.2165/00063030-200721040-00004] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Locked nucleic acid (LNA) is the term for oligonucleotides that contain one or more nucleotide building blocks in which an extra methylene bridge fixes the ribose moiety either in the C3'-endo (beta-D-LNA) or C2'-endo (alpha-L-LNA) conformation. The beta-D-LNA modification results in significant increases in melting temperature of up to several degrees per LNA residue. The alpha-L-LNA stereoisomer, which also stabilizes duplexes, lends itself to use in triplex-forming oligonucleotides and transcription factor decoys, which have to maintain a B-type (C2'-endo) DNA conformation. LNA oligonucleotides are synthesized in different formats, such as all-LNA, LNA/DNA mixmers, or LNA/DNA gapmers. Essentially, all aspects of antisense technology have profited from LNA due to its unprecedented affinity, good or even improved mismatch discrimination, low toxicity, and increased metabolic stability. LNA is particularly attractive for in vivo applications that are inaccessible to RNA interference technology, such as suppression of aberrant splice sites or inhibition of oncogenic microRNAs. Furthermore, the extreme antisense-target duplex stability (formation of persistent steric blocks) conferred by beta-D-LNA also contributes to the capacity to invade stable secondary structures of RNA targets. The in vivo studies reported so far indeed point to LNA as a promising antisense player at the horizon of clinical applications.
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Affiliation(s)
- Arnold Grünweller
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
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Kaur H, Wengel J, Maiti S. LNA-modified oligonucleotides effectively drive intramolecular-stable hairpin to intermolecular-duplex state. Biochem Biophys Res Commun 2006; 352:118-22. [PMID: 17107660 DOI: 10.1016/j.bbrc.2006.10.155] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 10/27/2006] [Indexed: 11/21/2022]
Abstract
Sequence-specific hybridization of antisense and antigene agent to the target nucleic acid is an important therapeutic strategy to modulate gene expression. However, efficiency of such agents falls due to inherent intramolecular-secondary-structures present in the target that pose competition to intermolecular hybridization by complementary antisense/antigene agent. Performance of these agents can be improved by employing structurally modified complementary oligonucleotides that efficiently hybridize to the target and force it to transit from an intramolecular-structured-state to an intermolecular-duplex state. In this study, the potential of variably substituted locked nucleic acid-modified oligonucleotides (8mer) to hybridize and disrupt highly stable, secondary structure of nucleic acid has been biophysically characterized and compared with the conventionally used unmodified DNA oligonucleotides. The target here is a stem-loop hairpin oligonucleotide-a structure commonly present in most structured-nucleic acids and known to exhibit an array of biological functions. Using fluorescence-based studies and EMSA we prove that LNA-modified oligonucleotides hybridize to the target hairpin with higher binding affinity even at lower concentration and subsequently, force it to assume a duplex conformation. LNA-modified oligonucleotides may thus, prove as potential therapeutic candidates to manipulate gene expression by disruption of biologically relevant nucleic acid secondary structure.
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Affiliation(s)
- Harleen Kaur
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Rapozzi V, Cogoi S, Xodo LE. Antisense locked nucleic acids efficiently suppress BCR/ABL and induce cell growth decline and apoptosis in leukemic cells. Mol Cancer Ther 2006; 5:1683-92. [PMID: 16891454 DOI: 10.1158/1535-7163.mct-06-0006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chronic myeloid leukemia (CML) develops when a hematopoietic stem cell acquires the Philadelphia chromosome carrying the BCR/ABL fusion gene. This gives the transformed cells a proliferative advantage over normal hematopoietic cells. Silencing the BCR/ABL oncogene by treatment with specific drugs remains an important therapeutic goal. In this work, we used locked nucleic acid (LNA)-modified oligonucleotides to silence BCR/ABL and reduce CML cell proliferation, as these oligonucleotides are resistant to nucleases and exhibit an exceptional affinity for cognate RNA. The anti-BCR/ABL oligonucleotides were designed as LNA-DNA gapmers, consisting of end blocks of 3/4 LNA monomers and a central DNA stretch of 13/14 deoxyribonucleotides. The gapmers were complementary to the b2a2 and b3a2 mRNA junctions with which they form hybrid duplexes that have melting temperatures of 79 degrees C and 75 degrees C, respectively, in a 20 mmol/L NaCl-buffered (pH 7.4) solution. Like DNA, the designed LNA-DNA gapmers were capable of activating RNase H and promote cleavage of the target b2a2 and b3a2 BCR/ABL mRNAs. The treatment of CML cells with junction-specific antisense gapmers resulted in a strong and specific reduction of the levels of BCR/ABL transcripts ( approximately 20% of control) and protein p210(BCR/ABL) ( approximately 30% of control). Moreover, the antisense oligonucleotides suppressed cell growth up to 40% of control and induced apoptosis, as indicated by the increase of caspase-3/7 activity in the treated cells. Finally, the b2a2-specific antisense gapmer used in combination with STI571 (imatinib mesylate), a tyrosine kinase inhibitor of p210(BCR/ABL), produced an enhanced antiproliferative effect in KYO-1 cells, which compared with K562 cells are refractory to STI571. The data of this study support the application of BCR/ABL antisense LNA-DNA gapmers, used either alone or in combination with STI571, as potential antileukemic agents.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/chemistry
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Apoptosis/genetics
- Benzamides
- Cell Proliferation/drug effects
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Oligonucleotides
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/therapeutic use
- Piperazines/therapeutic use
- Protein Kinase Inhibitors/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Pyrimidines/therapeutic use
- RNA, Messenger/antagonists & inhibitors
- Ribonuclease H/drug effects
- Transcription, Genetic/drug effects
- Tumor Cells, Cultured
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Affiliation(s)
- Valentina Rapozzi
- Department of Biomedical Sciences and Technologies, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
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Karkare S, Bhatnagar D. Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Appl Microbiol Biotechnol 2006; 71:575-86. [PMID: 16683135 DOI: 10.1007/s00253-006-0434-2] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 03/22/2006] [Accepted: 03/24/2006] [Indexed: 10/24/2022]
Abstract
Nucleic acid analogs and mimics are commonly the modifications of native nucleic acids at the nucleobase, the sugar ring, or the phosphodiester backbone. Many forms of promising nucleic acid analogs and mimics are available, such as locked nucleic acids (LNAs), peptide nucleic acids (PNAs), and morpholinos. LNAs, PNAs, and morpholinos can form both duplexes and triplexes and have improved biostability. They have become a general and versatile tool for DNA and RNA recognition. LNA is a general and versatile tool for specific, high-affinity recognition of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA). LNA can be used for designing LNA oligoes for hybridization studies or as real time polymerase chain reaction probes in the form of Taqman probes. LNA also has therapeutic and diagnostic applications. PNA is another type of DNA analog with neutral charge. The extreme stability of PNA makes it an ideal candidate for the antisense and antigene application. PNA is used as probe for gene cloning, mutation detection, and in homologous recombination studies. It was also used to design transcription factor decoy molecules for target gene induction. Morpholino, another structural type, was devised to circumvent cost problems associated with DNA analogs. It has become the premier knockdown tool in developmental biology due to its cytosolic delivery in the embryos by microinjection. Thus, the nucleic acid analogs provide an advantage to design and implementation, therapies, and research assays, which were not implemented due to limitations associated with standard nucleic acids chemistry.
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Affiliation(s)
- Shantanu Karkare
- Apticraft Systems (P) Ltd. 142, Electronics Complex, Indore, 452010, India.
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Erdmann V, Barciszewski J, Brosius J. Locked nucleic acid: high-affinity targeting of complementary RNA for RNomics. Handb Exp Pharmacol 2006; 173:405-22. [PMID: 16594628 PMCID: PMC7120141 DOI: 10.1007/3-540-27262-3_21] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Locked nucleic acid (LNA) is a nucleic acid analog containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA-mimicking sugar conformation. This conformational restriction is translated into unprecedented hybridization affinity towards complementary single-stranded RNA molecules. That makes fully modified LNAs, LNA/DNA mixmers, or LNA/RNA mixmers uniquely suited for mimicking RNA structures and for RNA targeting in vitro or in vivo. The focus of this chapter is on LNA antisense, LNA-modified DNAzymes (LNAzymes), LNA-modified small interfering (si)RNA (siLNA), LNA-enhanced expression profiling by real-time RT-PCR and detection and analysis of microRNAs by LNA-modified probes.
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Affiliation(s)
- Volker Erdmann
- Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Scienes, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jürgen Brosius
- Institute of Experimental Pathology, Molecular Neurobiology (ZMBE), University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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Jepsen JS, Pfundheller HM, Lykkesfeldt AE. Downregulation of p21(WAF1/CIP1) and estrogen receptor alpha in MCF-7 cells by antisense oligonucleotides containing locked nucleic acid (LNA). Oligonucleotides 2005; 14:147-56. [PMID: 15294077 DOI: 10.1089/1545457041526281] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Locked nucleic acid (LNA) is a nucleic acid analog with very high affinity to complementary RNA and a promising compound in the field of antisense research. The intracellular localization and quantitative uptake of oligonucleotides containing LNA were found to be equivalent to those of phosphorothioate oligonucleotides (PS AONs). The antisense efficiency of LNA-containing oligonucleotides was systematically compared with standard PS AONs targeting expression of two endogenous proteins in the human breast cancer cell line MCF-7, namely, the cyclin-dependent kinase inhibitor p21(WAF1/CIP1) and the estrogen receptor alpha (ERalpha). For downregulation of both target proteins, the most efficient design was achieved with oligonucleotides containing LNA monomers in the extremities and a central gap of PS-linked DNA monomers, so called LNA gapmers. Such LNA gapmers caused more potent downregulation of the targeted proteins than PS AONs, whereas fully modified LNA AONs or LNA mixmers (LNA nucleotides interspersed) were inactive.
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Affiliation(s)
- Jan Stenvang Jepsen
- Department of Tumor Endocrinology, Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen, Denmark.
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Jepsen JS, Sørensen MD, Wengel J. Locked nucleic acid: a potent nucleic acid analog in therapeutics and biotechnology. Oligonucleotides 2005; 14:130-46. [PMID: 15294076 DOI: 10.1089/1545457041526317] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Locked nucleic acid (LNA) is a class of nucleic acid analogs possessing very high affinity and excellent specificity toward complementary DNA and RNA, and LNA oligonucleotides have been applied as antisense molecules both in vitro and in vivo. In this review, we briefly describe the basic physiochemical properties of LNA and some of the difficulties that may be encountered when applying LNA technology. The central part of the review focuses on the use of LNA molecules in regulation of gene expression, including delivery to cells, stability, unspecific effects, toxicity, pharmacokinetics, and design of LNA oligonucleotides. The last part evaluates LNA as a diagnostic tool in genotyping.
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Affiliation(s)
- Jan Stenvang Jepsen
- Department of Tumor Endocrinology, Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen, Denmark.
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14
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Abstract
Locked nucleic acid (LNA) is a nucleic acid analogue that displays unprecedented hybridization affinity towards complementary DNA and RNA. Structural studies have shown LNA to be an RNA mimic, fitting seamlessly into an A-type duplex geometry. Several reports have revealed LNA as a most promising molecule for the development of oligonucleotide-based therapeutics. For example, Tat-dependent transcription and telomerase activity have been efficiently suppressed by LNA oligomers, and efficient cleavage of highly structured RNA has been achieved using LNA-modified DNAzymes ('LNAzyme'). Furthermore, convincing examples of the application of LNA to nucleic acid diagnostics have been reported, including high capturing efficiencies and unambiguous scoring of single-nucleotide polymorphisms.
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Affiliation(s)
- Michael Petersen
- Nucleic Acid Center, Dept of Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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