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Challenges and Opportunities for Oligonucleotide-Based Therapeutics by Antisense and RNA Interference Mechanisms

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Chemical Biology of Nucleic Acids

Abstract

Oligonucleotide-based therapeutics may be one of the most promising approaches for the treatment of diseases. Although significant progress has been made in developing these agents as drugs, several hurdles remain to be overcome. One of the most promising approaches to overcome these difficulties is the preparation of modified oligonucleotides designed to increase cellular uptake and/or increase stability to nucleases. Herein, we report the developments done by our group in the synthesis of modified oligonucleotides directed to the generation of active compounds for gene inhibition. Specifically we will report the synthesis of novel nuclease-resistant oligonucleotides such as North bicyclo[3.1.0]hexane pseudosugars or N-coupled dinucleotide units. Also, the design of several siRNA conjugates carrying cell-penetrating peptides, lipids, intercalating agents, and carbohydrates will be described. Some of these novel derivatives show clear improvements in their biological and inhibitory properties.

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References

  • Aboul-Fadl T (2005) Antisense oligonucleotides: the state of the art. Curr Med Chem 12:2193–2214

    Article  CAS  PubMed  Google Scholar 

  • Aviñó A, Ocampo SM, Caminal C et al (2009) Stepwise synthesis of RNA conjugates carrying peptide sequences for RNA interference studies. Mol Divers 13:287–293

    Article  PubMed  Google Scholar 

  • Aviñó A, Ferreira R, Mazzini S et al (2010) Synthesis and structural properties of oligonucleotides covalently linked to acridine and quindoline derivatives through a threoninol linker. Bioorg Med Chem 18:7348–7356

    Article  PubMed  Google Scholar 

  • Aviñó A, Grijalvo S, Pérez-Rentero S et al (2011a) Synthesis of oligonucleotide-peptide conjugates for biomedical and technological applications. Methods Mol Biol 751:223–238

    Article  PubMed  Google Scholar 

  • Aviñó A, Ocampo SM, Lucas R et al (2011b) Synthesis and in vitro inhibition properties of siRNA conjugates carrying glucose and galactose with different presentation. Mol Divers 15:751–757

    Article  PubMed  Google Scholar 

  • Aviñó A, Ocampo SM, Perales JC et al (2012) Synthesis and in vitro inhibition properties of siRNA conjugates carrying acridine and quindoline moieties. Chem Biodivers 9:557–566

    Article  PubMed  Google Scholar 

  • Bernad A, Blanco L, Lázaro JM et al (1989) A conserved 3′-5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59:219–228

    Article  CAS  PubMed  Google Scholar 

  • Brody EN, Gold L (2000) Aptamers as therapeutic and diagnostic agents. J Biotechnol 74:5–13

    CAS  PubMed  Google Scholar 

  • Brucet M, Querol-Audí J, Serra M et al (2007) Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW domains. J Biol Chem 282:14547–14557

    Article  CAS  PubMed  Google Scholar 

  • Brumcot D, Manoharan M, Koteliansky V et al (2006) RNAi therapeutics: a potential new class of pharmaceutical drugs. Nat Chem Biol 2:711–719

    Article  Google Scholar 

  • Burnett JC, Rossi JJ (2012) RNA-based therapeutics: current progress and further prospects. Chem Biol 19:60–71

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chan JH, Lim S, Wong WS (2006) Antisense oligonucleotides: from design to therapeutic application. Clin Exp Pharmacol Physiol 33:533–540

    Article  CAS  PubMed  Google Scholar 

  • Chiu Y-L, Rana TM (2003) siRNA function in RNAi: a chemical modification analysis. RNA 9:1034–1048

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Corey DR (1995) 48000-Fold acceleration of hybridization by chemically-modified oligonucleotides. J Am Chem Soc 117:9373–9374

    Article  CAS  Google Scholar 

  • Davidson BL, McCray PB Jr (2011) Current protocols for RNA interference-based therapies. Nat Rev Genet 12:329–340

    Article  CAS  PubMed  Google Scholar 

  • Deleavey JF, Damha MJ (2012) Designing chemically modified oligonucleotides for targeted gene silencing. Chem Biol 19:937–954

    Article  CAS  PubMed  Google Scholar 

  • Eberle F, Giessler K, Deck C et al (2008) Modifications in small interfering RNA that separate immunostimulation from RNA interference. J Immunol 180:3229–3237

    Article  CAS  PubMed  Google Scholar 

  • Elmén J, Thonberg H, Ljungberg K et al (2005) Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality. Nucleic Acids Res 33:439–447

    Article  PubMed Central  PubMed  Google Scholar 

  • Gonzalez CR (2005) Enhanced efficacy associated with early treatment of neovascular age-related macular degeneration with pegaptanib sodium: an exploratory analysis. Retina 25:815–827

    Article  Google Scholar 

  • Grijalvo S, Eritja R (2012) Synthesis and in vitro inhibition properties of oligonucleotide conjugates carrying amphipathic proline-rich peptide derivatives of the sweet arrow peptide (SAP). Mol Divers 16(2):307–317

    Article  CAS  PubMed  Google Scholar 

  • Grijalvo S, Ocampo SM, Perales JC et al (2010a) Synthesis of oligonucleotides carrying amino lipid groups at the 3′-end for RNA interference studies. J Org Chem 75:6806–6813

    Article  CAS  PubMed  Google Scholar 

  • Grijalvo S, Terrazas M, Aviñó A et al (2010b) Stepwise synthesis of oligonucleotide-peptide conjugates containing guanidinium or lipophilic groups in their 3′-termini. Bioorg Med Chem Lett 20(7):2144–2147

    Article  CAS  PubMed  Google Scholar 

  • Grijalvo S, Ocampo SM, Perales JC et al (2011) Synthesis of lipid-oligonucleotide conjugates for inhibition of gene expression. Chem Biodivers 8:287–299

    Article  CAS  PubMed  Google Scholar 

  • Hamzavi R, Dolle F, Tavitian B, Dahl O et al (2003) Modulation of the pharmacokinetic properties of PNA: preparation of galactosyl, mannosyl, fucosyl, N-acetylgalactosaminyl, and N-acetylglucosaminyl derivatives of aminoethylglycine peptide nucleic acid monomers and their incorporation into PNA oligomers. Bioconjug Chem 14:941–954

    Article  CAS  PubMed  Google Scholar 

  • Hangeland J, Levis JT, Lee YC et al (1995) Cell-type specific and ligand specific enhancement of cellular uptake of oligodeoxynucleoside-methylphosphonates covalently linked with a neoglycopeptide, YEE(ah-Ga1NAc)s. Bioconjug Chem 6:695–701

    Article  CAS  PubMed  Google Scholar 

  • Jiang K (2013) Biotech comes to its “antisense” after hard-won drug approval. Nat Med 19:252

    Article  PubMed  Google Scholar 

  • Kim HS, Ravi RG, Marquez VE et al (2002) Methanocarba modification of uracil and adenine nucleotides: high potency of Northern ring conformation at P2Y1, P2Y2, P2Y4, and P2Y11 but not P2Y6 receptors. J Med Chem 45:208–218

    Article  CAS  PubMed  Google Scholar 

  • Kumar P, Wu H, McBride JL, Jung KE, Kim MH, Davidson BL, Lee SK, Shankar P, Manjunath N (2007) Transvascular delivery of small interfering RNA to the central nervous system. Nature 448:39–43

    Article  CAS  PubMed  Google Scholar 

  • Lönnberg H (2009) Solid-phase of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics. Bioconjug Chem 20:1065–1094

    Article  PubMed  Google Scholar 

  • Lu K, Duan QP, Ma L et al (2010) Chemical strategies for the synthesis of peptide-oligonucleotide conjugates. Bioconjug Chem 21:187–202

    Article  CAS  PubMed  Google Scholar 

  • Maier MA, Yannopolus CG, Mohamed N et al (2003) Synthesis of antisense oligonucleotides conjugated to a multivalent carbohydrate cluster for cellular targeting. Bioconjug Chem 14:18–29

    Article  CAS  PubMed  Google Scholar 

  • Manoharan M (2002) Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery and mechanism of action. Antisense Nucleic Acid Drug Dev 129:103–128

    Article  Google Scholar 

  • Marquez VE, Siddiqui MA, Ezzitouni A et al (1996) Nucleosides with a twist. Can fixed forms of sugar ring pucker influence biological activity in nucleosides and oligonucleotides? J Med Chem 39:3739–3747

    Article  CAS  PubMed  Google Scholar 

  • Meares CF, Yokohama M (2012) Introduction to gene silencing and delivery. Acc Chem Res 45(7):959–1171, special issue in RNA delivery

    Article  CAS  PubMed  Google Scholar 

  • Ocampo SM, Romero C, Aviñó A et al (2012) Functionally enhanced siRNA targeting TNFα attenuates DSS-induced colitis and TLR-mediated immunostimulation in mice. Mol Ther 20:382–390

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Oishi M, Nagasaki Y, Itaka K et al (2005) Lactosylated poly(ethylene glycol)-siRNA conjugate through acid-labile β-thiopropionate linkage to construct pH-sensitive polyion complex micelles achieving enhanced gene silencing in hepatoma cells. J Am Chem Soc 127:1624–1625

    Article  CAS  PubMed  Google Scholar 

  • Pérez-Rentero S, Gállego I, Somoza A et al (2012) Interstrand interactions on DNA duplexes modified by TTF units at the 3′ or 5′-ends. RSC Adv 2:4069–4071

    Article  Google Scholar 

  • Pérez-Rentero S, Somoza A, Grijalvo S et al (2013) Biophysical and RNA Interference inhibitory properties of oligonucleotides carrying tetrathiafulvalene groups at terminal positions. J Chem 2013:article ID 650610, 11 pages. doi:10.1155/2013/650610

  • Raouane M, Desmaële D, Urbinati G et al (2012) Lipid conjugated oligonucleotides: a useful strategy for delivery. Bioconjug Chem 23:1091–1110

    Article  CAS  PubMed  Google Scholar 

  • Rettig GR, Behlke MA (2012) Progress towards in vivo use of siRNAs-II. Mol Ther 20:483–512

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Robles J, Mased M, Beltrán M et al (1997) Synthesis and enzymatic stability of phosphodiester-linked peptide-oligonucleotide hybrids. Bioconjug Chem 8:785–788

    Article  CAS  PubMed  Google Scholar 

  • Said HF, Saleh AF, Abes R et al (2010) Cell penetrating peptides: overview and applications to the delivery of oligonucleotides. Cell Mol Life Sci 67:715–726

    Article  Google Scholar 

  • Sanghvi Y (2011) A status update of modified oligonucleotides for chemotherapeutics applications. Curr Protoc Nucleic Acid Chem Chapter 4:Unit 4.1.1-22

    PubMed  Google Scholar 

  • Shukla S, Sumaria CS, Pradeepkumar PI (2010) Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook. ChemMedChem 5:328–349

    Article  CAS  PubMed  Google Scholar 

  • Singh SK, Nielsen P, Koshkin AA et al (1998) LNA (locked nucleic acids): synthesis and high affinity nucleic acid recognition. Chem Commun 34:455–456

    Google Scholar 

  • Sioud M (2010) Advances in RNA sensing by the immune system: separation of siRNA unwanted effects from RNA interference. Methods Mol Biol 629:33–52

    Article  CAS  PubMed  Google Scholar 

  • Somoza A, Terrazas M, Eritja R (2010) Modified siRNAs for the study of the PAZ domain. Chem Commun 46:4270–4272

    Article  CAS  Google Scholar 

  • Soutschek J, Akinc A, Bramlage B et al (2004) Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature 432:173–178

    Article  CAS  PubMed  Google Scholar 

  • Tabernero J, Shapiro GI, LoRuss PM et al (2013) First-in-man trial of an RNA interference targeting VEGF and KSP in cancer patients with liver involvement. Cancer Discov 3:406–417

    Article  CAS  PubMed  Google Scholar 

  • Terrazas M, Aviñó A, Siddiqui M et al (2011a) A direct, efficient method for the preparation of siRNAs containing ribo-like North bicyclo[3.1.0]hexane pseudosugars. Org Lett 13:2888–2891

    Article  CAS  PubMed  Google Scholar 

  • Terrazas M, Ocampo SM, Perales JC et al (2011b) Effect of North bicyclo[3.1.0]hexane pseudosugars on RNA interference. A novel class of siRNA modification. Chembiochem 12:1056–1065

    Article  CAS  PubMed  Google Scholar 

  • Terrazas M, Alagia A, Faustino I et al (2013) Functionalization of the 3′-ends of DNA and RNA strands with N-ethyl-N bridged nucleosides: a promising approach to avoid 3′-exonuclease-catalyzed hydrolysis and to improve the biological properties of therapeutic oligonucleotides. Chembiochem 14:510–520

    Article  CAS  PubMed  Google Scholar 

  • Tiemann K, Rossi JJ (2009) RNAi-based therapeutics-current status, challenges and prospects. EMBO Mol Med 1:142–151

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ugarte-Uribe B, Pérez-Rentero S, Lucas R et al (2010) Synthesis, cell-surface binding and cellular uptake of fluorescently labeled glucose DNA conjugates with different carbohydrate presentation. Bioconjug Chem 21:1280–1287

    Article  CAS  PubMed  Google Scholar 

  • Ugarte-Uribe B, Grijalvo S, Busto JV et al (2013) Double-tailed lipid modification as a promising candidate for oligonucleotide delivery in mammalian cells. Biochim Biophys Acta 1830(10):4872–4884

    Article  CAS  PubMed  Google Scholar 

  • Vengut-Climent E, Terrazas M, Lucas R et al (2013) Synthesis, RNAi activity and nuclease-resistant properties of apolar carbohydrates siRNA conjugates. Bioorg Med Chem Lett 23:4048–4051

    Article  CAS  PubMed  Google Scholar 

  • Whitehead KA, Langer R, Anderson DG (2009) Nat Rev Drug Discov 8:129–138

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This research was supported by the European Commission (Grants FP7-FUNMOL 213382 and NMP4-LA-2011-262943, MULTIFUN), by the Spanish Ministry of Education (grant CTQ2010-20541, CTQ2009-13705), by CSIC (intramural PIF06-045), and by the Generalitat de Catalunya (2009/SGR/208). We would like to thank our collaborators for their continuous support on the synthesis and evaluation of the biophysical and biological properties of modified oligonucleotides, especially Dr. S. Ocampo, Dr. J.C. Perales, Dr. E. Fernandez, Dr. C. Romero, Dr. B. Uriarte-Uribe, Dr. I. Alkorta, Dr. F. Goñi, Dr. V.E. Marquez, and Dr. M. Orozco.

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Correspondence to Ramon Eritja .

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Eritja, R. et al. (2014). Challenges and Opportunities for Oligonucleotide-Based Therapeutics by Antisense and RNA Interference Mechanisms. In: Erdmann, V., Markiewicz, W., Barciszewski, J. (eds) Chemical Biology of Nucleic Acids. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-54452-1_13

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