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Locked Nucleic Acid: Modality, Diversity, and Drug Discovery Downloaded from orbit.dtu.dk on: Oct 02, 2021 Locked nucleic acid: modality, diversity, and drug discovery Hagedorn, Peter H.; Persson, Robert; Funder, Erik D.; Albæk, Nanna; Diemer, Sanna L.; Hansen, Dennis J.; Møller, Marianne R; Papargyri, Natalia; Christiansen, Helle; Hansen, Bo R. Total number of authors: 13 Published in: Drug Discovery Today Link to article, DOI: 10.1016/j.drudis.2017.09.018 Publication date: 2018 Document Version Peer reviewed version Link back to DTU Orbit Citation (APA): Hagedorn, P. H., Persson, R., Funder, E. D., Albæk, N., Diemer, S. L., Hansen, D. J., Møller, M. R., Papargyri, N., Christiansen, H., Hansen, B. R., Hansen, H. F., Jensen, M. A., & Koch, T. (2018). Locked nucleic acid: modality, diversity, and drug discovery. Drug Discovery Today, 23(1), 101-114. https://doi.org/10.1016/j.drudis.2017.09.018 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Drug Discovery Today Volume 00, Number 00 October 2017 REVIEWS Teaser LNA-modified antisense oligonucleotides (LNAs) are widely used in RNA therapeu- tics. The structural diversity of LNAs affects most drug properties. Exploiting this diversity offers new opportunities for discovering LNA-based drugs. KEYNOTE REVIEW Locked nucleic acid: modality, diversity, and drug discovery Reviews 1 2 1 Peter Hagedorn has a Peter H. Hagedorn , Robert Persson , Erik D. Funder , MSc in theoretical physics 1 1 1 and biophysics from the Nanna Albæk , Sanna L. Diemer , Dennis J. Hansen , Niels Bohr Institute at the 1 3 University of Copenhagen, Marianne R. Møller , Natalia Papargyri , and a PhD in molecular 1 1 1 biology and bioinformatics Helle Christiansen , Bo R. Hansen , Henrik F. Hansen , from Ris½ National 1 1 Laboratory, Denmark. For Mads A. Jensen and Troels Koch the past 6 years, Peter has been exploring the structural diversity of LNA-modified antisense 1 Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, oligonucleotides and how this impacts measured properties, with a particular focus on developing 2970 Hørsholm, Denmark 2 predictive mathematical models that capture this Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center diversity. Copenhagen, 2970 Hørsholm, Denmark 3 Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark Robert Persson has a PhD in microbiology and biochemistry from the University of Lund, Over the past 20 years, the field of RNA-targeted therapeutics has Sweden. He has worked advanced based on discoveries of modified oligonucleotide chemistries, with the intracellular transport of secretory and an ever-increasing understanding of how to apply cellular assays to proteins and viral identify oligonucleotides with improved pharmacological properties membrane proteins and with the pharmacokinetics of proteins and in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity oligonucleotides for more than 25 years. During the past 8 years, Robert has focused on the bioanalysis, and potency, is widely used for this purpose. Our understanding of RNA biodistribution, and pharmacokinetics of LNA biology has also expanded tremendously, resulting in new approaches to oligonucleotides. engage RNA as a therapeutic target. Recent observations indicate that each Troels Koch has a PhD in bioorganic chemistry from oligonucleotide is a unique entity, and small structural differences the University of Copenhagen, Denmark. He between oligonucleotides can often lead to substantial differences in their has worked in the area of pharmacological properties. Here, we outline new principles for drug nucleic acid chemistry and biology for 20 years. He co- discovery exploiting oligonucleotide diversity to identify rare molecules founded Santaris Pharma A/S, which pioneered the with unique pharmacological properties. locked nucleic acid (LNA) platform and LNA therapeutics. Santaris was acquired by Roche in August 2014, and he is presently vice president and head of research at the Roche Innovation Centre in Introduction Copenhagen. His main responsibilities are to develop the chemical and biological properties of LNA, The flow of genetic information is a highly complex process. Of the approximately 43 000 improve and upgrade the LNA platform, refine LNA human genes currently annotated by the Ensembl project (release 89), approximately 47% antisense drug discovery processes, and establish a RNA therapeutics drug pipeline in Roche. encodes proteins, and the rest are all transcribed into different types of noncoding RNA (ncRNA) [1]. It is clear that these ncRNAs represent a long and growing list of different types of RNA with various functional roles and regulatory interactions [2,3]. This knowledge has provided a stronger basis for the specific annotation of the relationships between structure, type, and function of RNAs and human disease [4]. This is one reason for the increased interest in RNA Corresponding author: Koch, T. ([email protected]) 1359-6446/ã 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). https://doi.org/10.1016/j.drudis.2017.09.018 www.drugdiscoverytoday.com 1 Please cite this article in press as: Hagedorn, P.H. et al. Locked nucleic acid: modality, diversity, and drug discovery, Drug Discov Today (2017), https://doi.org/10.1016/j.drudis.2017.09.018 DRUDIS-2093; No of Pages 14 REVIEWS Drug Discovery Today Volume 00, Number 00 October 2017 therapeutics, which focuses not only on classic protein-coding Chemistry sets boundaries for success mRNA intervention, but also on how the manipulation of non- In the first generation of single-stranded therapeutic oligonucleo- coding regulatory RNA can provide novel drugs for previously tides, the phosphorothioate (PS) internucleoside linkage was the untreatable diseases. only chemical modification [8,21–24]. The PS modification A rational strategy to target RNA is by synthetic oligonucleo- replaces one of the nonbridging oxygen atoms with sulfur in tides. Although RNA exists in a complex biological matrix, en- the internucleoside phosphate (Fig. 1ai). This modification creates Reviews dogenous enzymatic RNA-processing mechanisms can be a chiral center at phosphorous producing two isomers: Rp and Sp. exploited and recruited by the heteroduplex formation between Thus, for every PS linkage introduced in an oligonucleotide, two RNA and synthetic oligonucleotides. RNA exhibits high turnover diastereoisomers are formed. Given that conventional solid-phase KEYNOTE REVIEW rates and is more labile than DNA [5]; thus, inhibitory effects PS synthesis is not stereoselective, an n-mer PS oligonucleotide n–1 induced by the oligonucleotide binding complement can be contains random mixtures of 2 diastereoisomers [25–30]. How- executed rapidly and effectively. Zamecnik and Stevenson [6] ever, recent developments have now made it possible to synthesize were the first to show that a single-stranded synthetic DNA individual stereoisomers with high stereoselectivity [31–34], and oligonucleotide could inhibit the expression of RNA, resulting with good yields [35–37]. Diastereoisomers are different chemical in the stimulation of substantial research and development ac- compounds and the diversity of properties for a given PS oligonu- tivity [7–13]. cleotide will be a gradient spanning from a little to a very large The past four decades of research and development in oligo- difference in property. Generally, oligonucleotides with a Sp nucleotide-based RNA therapeutics has produced groundbreak- configuration provided better exonuclease resistance compared ing results. The recent successes are based on improvements in with oligonucleotides with a Rp configuration, whereas Rp iso- three essential parameters for antisense technologies: (i) medici- mers were better substrates for DNA-dependent RNA poly- nal chemistry efforts have devised much-improved nucleic acid merases, RNase H, and stimulated immune responses [38–40]. modifications for antisense oligonucleotides (AONs), of which Compared with the random mixtures, Rp oligonucleotides exhib- the high-affinity LNA [14–17] is among the most widely used; (ii) ited higher melting temperature (Tm) against RNA, whereas Sp the knowledge revolution of the functions and biological molec- analogs had lower Tm. In the first-generation oligonucleotide ular mechanisms of RNA; and (iii) the translational drug discov- drugs, the PS modification was normally not stereocontrolled. ery part (i.e., discovery processes and models used in drug Except for rare examples [41], this class of drugs has not provided discovery). The latter relates to bioinformatics drug design, pre- an adequate TI for AONs [42]. Two reasons for this were that
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