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Organic & Biomolecular Chemistry Organic & Biomolecular Chemistry View Article Online PAPER View Journal | View Issue Synthesis and biophysical properties of carbamate-locked nucleic acid (LNA) Cite this: Org. Biomol. Chem., 2019, 17, 5341 oligonucleotides with potential antisense applications† Cameron Thorpe, a Sven Epple, a Benjamin Woods,a Afaf H. El-Sagheera,b and Tom Brown *a Antisense oligonucleotides (ASOs) are becoming important drugs for hard to treat diseases. Modifications to their DNA backbones are essential to inhibit degradation in vivo, but they can reduce binding affinity to RNA targets. To address this problem we have combined the enzymatic resistance of carbamate (CBM) DNA backbone analogues with the thermodynamic stability conferred by locked nucleic acid sugars (LNA). Using a dinucleotide phosphoramidite strategy and automated solid phase synthesis, we have syn- Creative Commons Attribution 3.0 Unported Licence. thesised a set of oligonucleotides modified with multiple LNA-CBM units. The LNA sugars restore binding affinity to RNA targets, and in this respect LNA position with respect to the CBM linkage is important. Received 25th March 2019, Oligonucleotides containing carbamate flanked on its 5’and 3’-sides by LNA form stable duplexes with Accepted 9th April 2019 RNA and unstable duplexes with DNA, which is desirable for antisense applications. Carbamate-LNA DOI: 10.1039/c9ob00691e modified oligonucleotides also show increased stability in the presence of snake venom and foetal bovine rsc.li/obc serum compared to LNA or CBM backbones alone. Unfortunately, due to poor cell penetration8 combined with This article is licensed under a Introduction fast cellular degradation, unmodified sequences are less than Antisense oligonucleotides (ASOs) are short ∼20 mer ideal candidates for therapeutic applications. To overcome sequences that bind to complementary ribonucleic nucleic this, much research has focused on the incorporation of back- 9,10 Open Access Article. Published on 17 May 2019. Downloaded 9/29/2021 11:37:26 PM. acid (RNA) targets through Watson–Crick base pairing to bone modifications into ASOs. In regard to degradation of promote enzymatic degradation (RNase H), induce RNA inter- the phosphodiester backbone of ASOs by nuclease enzymes, ference (RNAi) or regulate protein expression (splice modu- chemical modification of sugar-phosphate backbones can sig- lation).1 Enabled by target specific binding, there are now nificantly improve biological stability. Several classes of anti- several FDA approved ASO-based drugs in the clinic treating a sense modifications have emerged, and have been used in FDA range of genetic and hereditary diseases.2 Eteplirsen (Exondys approved ASOs. Common modifications include 2′-O-methoxy 51)3 and Nusinersen (Spinraza)4 have been developed for the or 2′-O-(2-methoxyethyl) (MOE) ribose sugars, backbone modi- treatment of Duchenne muscular dystrophy and spinal muscu- fications such as phosphorothioates11 (Mipomersen and lar atrophy respectively. Antisense therapeutics are also Nusinersen) or phosphorodithioates and sugar alternatives making headway against severe hypercholesterolemia following such as morpholino (Eteplirsen) or threose nucleic acid – – the release of Mipomersen.5 Furthermore, with the recent (TNA).12,13 Amide14 18 and triazole19 21 artificial DNA back- approval in 2018 of Patisiran6 and Inotersen7 treating fatal her- bones also have potential, but are yet to reach maturity in the editary transthyretin-mediated amyloidosis, the ASO field antisense field. Further improvements to the design of chemi- demonstrates its versatility for treatment of diseases that could cally modified oligonucleotides (ONs), specifically those that be described as “undruggable” by small molecule approaches. increase hybridisation strength (RNA-target affinity) and stabi- lity in vivo are sought after, particularly if they also influence other properties such as cellular uptake.22 aDepartment of Chemistry, University of Oxford, 12 Mansfield Road, Locked nucleic acid (LNA), also known as bridged nucleic Oxford OX1 3TA, UK. E-mail: [email protected] acid (BNA), has been a transformative development in the bChemistry Branch, Department of Science and Mathematics, Faculty of Petroleum nucleic acid field. LNA is a bicyclic ribose analogue with a 2′- and Mining Engineering, Suez University, Suez 43721, Egypt ′ ′ †Electronic supplementary information (ESI) available. See DOI: 10.1039/ O-4 -methylene sugar bridge. The C3 -endo conformation is c9ob00691e preferred and consequently LNA displays unparalleled binding This journal is © The Royal Society of Chemistry 2019 Org. Biomol. Chem.,2019,17,5341–5348 | 5341 View Article Online Paper Organic & Biomolecular Chemistry affinity to complementary RNA strands; LNA modifications can Results and discussion stabilise duplexes by up to +7 °C per modification.23,24 Building on the seminal work of Wengel23,25 and Obika,26,27 Synthesis of LNA-CBM1 dinucleotides LNA has been used in a variety of applications including Compounds 13–16 (Scheme 1) were synthesised by ligation of siRNA-mediated gene silencing, CRISPR-Cas9,28 and triplex 3′-activated carbonyls 2 and 4 with 5′-nucleophilic amines 5 formation.29,30 A combination of LNA with a DNA backbone and 8 following a previously reported synthesis by Waldner mimic comprised of a six-atom triazole linkage improves et al.34 Starting material 1 was reacted with p-nitrophenyl duplex stability compared to the unmodified counterpart.20 In (PNP) chloroformate to give the activated nucleoside 2. contrast, Watts et al.31 found that addition of LNA to a four- Subsequent reaction with amine 5 under basic conditions atom triazole linkage caused duplex destabilisation. This indi- gave dinucleotide 9 which was converted to phosphoramidite cates that the contributions of linkage length and flexibility of 13 using standard phosphitylating conditions. For the DNA backbone analogues when combined with LNA as modu- LNA monomers, a divergent synthetic strategy was used. lators of duplex stability is still poorly understood. It is thus Compounds 3 and 6 were synthesised35 and compound 3 was important to expand the range of artificial backbones-LNA converted to an activated imidazole carbamate 4. Unlike DNA combinations beyond the triazole and amide systems.32,33 The analogue 2, activation of the 3′-OH by p-nitrophenyl (PNP) carbamate backbone is a four-atom, flexible, charge-neutral chloroformate was slow and resulted in poor yields. It has linkage with two constitutional isomers CBM1 (Fig. 1A) and been previously suggested that PNP carbonates could be sus- 36 CBM2 (Fig. 1E). Carbamate backbone incorporation into DNA ceptible to degradation in basic solvent, preventing efficient has previously been reported by Waldner and De Mesmaeker activation of the 3′-position. To overcome this, we opted for a et al.34 They found that duplex destabilisation occurs, but one pot strategy directly reacting alcohol 3 with CDI to form good stability against enzymatic degradation is achieved. imidazole carbamate 4 which was then used without further Hence, in isolation carbamates are less than ideal candidates purification. ffi 37 Creative Commons Attribution 3.0 Unported Licence. for antisense applications because of reduced binding a nity. Following work by Obika, LNA nucleoside 6 was reacted In pursuit of new modified oligonucleotide constructs, we with sodium azide to form its 5′-azide 7. Reduction of the sought to combine the enzymatic stability of carbamate back- azido group was performed as a one pot procedure by palla- bones with the favourable thermodynamic properties of LNA. dium-catalysed hydrogenation under H2 gas. Subsequent de- We now report the synthesis of a set of dinucleotide phosphor- protection of the 3′-benzyl group was then facilitated by the amidites designed to introduce the carbamate-LNA modifi- addition of NH4HCO2 to give amino nucleoside 8. cations in Fig. 1 into oligonucleotides sequences using stan- Combinations of the required DNA and LNA monomers 2, 4, 5, dard solid phase synthesis. The modified oligomers were syn- 8 were then used to give CBM1-linked dinucleotides analogues thesised and evaluated by ultraviolet melting (hybridisation) 10–12. As to be expected, coupling of the more sterically hin- This article is licensed under a studies in order to determine the most favourable carbamate- dered 3′-activated LNA monomer 4 was found to be slower but LNA combinations as modified DNA backbones. Enzymatic proceeded with comparable yields to the DNA analogues. digestion assays were carried out using snake venom and These compounds were then converted to their respective Open Access Article. Published on 17 May 2019. Downloaded 9/29/2021 11:37:26 PM. foetal bovine serum. phosphoramidites 14–16. Fig. 1 Carbamate-modified DNA backbones containing LNA sugars. Set 1 (A–D) and set 2 (E, F) comprise of dimers with the constitutional carba- mate isomers CBM1 and CBM2 respectively. A = DNA-CBM1-DNA, B = DNA-CBM1-LNA, C = LNA-CBM1-DNA, D = LNA-CBM1-LNA, E = DNA-CBM2- DNA, F = DNA-CBM2-LNA. 5342 | Org. Biomol. Chem.,2019,17,5341–5348 This journal is © The Royal Society of Chemistry 2019 View Article Online Organic & Biomolecular Chemistry Paper Creative Commons Attribution 3.0 Unported Licence. Scheme 1 Synthesis of CBM1-linked dinucleotides 13–16 using different combinations of 3’-activated carbonates 2, 4 and 5’-amines 5, 8. Reagents and conditions (i) p-nitrophenyl chloroformate, pyridine, 80 °C, 20 h, crude 2 60%; (ii) CDI, THF, rt, 20 h, crude 4 84%; (iii) NaN3, DMF, 65 °C, 20 h, 7 90%; (iv) H2, Pd(OH)2 (20%)/C MeOH, rt, 3 h; NH4HCO2,reflux, 4 h, 8 87%; (v) DMAP, pyridine, 80 °C, 20 h, 9 62%, 10 51%, 11 63%, 12 70%; (vi) Chloro (diisopropylamino)-β-cyanoethoxyphosphine, DIPEA, CH2Cl2, rt, 1 h, 13 54%, 14 57%, 15 36%, 16 88%. This article is licensed under a 22 Synthesis of LNA-CBM2 dinucleotide analogues destabilising than CBM1 and recent biophysical studies with ′ Compounds 24 and 27 (Scheme 2) were synthesised using a LNA-triazole backbones also showed that 5 -LNA adjacent to the modified linkage is highly destabilising in both DNA and Open Access Article. Published on 17 May 2019.
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