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Expedient Approaches to Bicyclic Nucleosides: Precursors to Nucleic Acid Modifications for Antisense-Based Therapeutics Natasha Narayanan, Ana Dmytrejchuk

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Expedient Approaches to Bicyclic Nucleosides: Precursors to Nucleic Acid Modifications for Antisense-Based Therapeutics Natasha Narayanan, Ana Dmytrejchuk Auburn University Journal of Undergraduate Scholarship | SPRING 2016 Auburn University Journal of Undergraduate Scholarship | SPRING 2016 Expedient Approaches to Bicyclic Nucleosides: Precursors to nucleic acid modifications for antisense-based therapeutics Natasha Narayanan, Ana Dmytrejchuk The human race is afflicted by countless Incorporating chemically modified The first and only reported synthesis diseases, many of which have genetic nucleosides in antisense strands has been involves 29 synthetic steps,1 which is origins. Small molecule therapeutics, shown to result in a stronger binding uneconomical in terms of both time and the traditional mode of treatment for interaction between the antisense strand money. In order to solve this problem, our genetic diseases, has focused on targeting and the mRNA, which translates to a more research is focused on the development of the pathogenic protein when it may be effective drug. The modifications we are short, streamlined synthetic approaches more effective to target the messenger interested in are tricyclic nucleic acids to TriNAs. RNA (mRNA) strand that codes for the (TriNAs), so named because the modified protein. This can be accomplished using ribose sugar contains three rings. Antisense The inexpensive ($0.40/gram) and a complementary DNA-based sequence strands that contain TriNAs show a higher commercially available nucleoside known as an antisense strand, which binds thermal stability when bound to mRNA 5-methyluridine (1) was selected as to the mRNA before it is translated into a compared to antisense strands containing the starting material for our synthesis protein. This binding event prevents the other reported modifications. However, a (Figure 1). Following protection with mRNA from undergoing translation, thus major drawback to the use of TriNAs as cyclohexanone dimethyl ketal to obtain inhibiting protein synthesis. potential drug candidates is the length of the protected cyclohexylidene acetal the synthesis used for their preparation. (2) and oxidation with Dess-Martin 1 2 3 4 5 6 7 8 9 10 Figure 1, Narayanan. Synthesis of bicyclic nucleoside precursor. 1 Auburn University Journal of Undergraduate Scholarship | SPRING 2016 periodinane, the resulting aldehyde (3) layer chromatography, and synthesized Statement of Research Advisor: was subjected to aldol reaction conditions compounds were purified by flash to afford diol (4). A protection reaction chromatography and analyzed using NMR Natasha has developed a short, efficient using trityl chloride yielded a mixture of spectroscopy and mass spectrometry. This synthesis of a bicyclic nucleoside separable diastereomers, and the trityl- project has yielded a nine-step synthesis intermediate that can serve as a precursor protected compound (5) was subjected to a key bicyclic nucleoside intermediate molecule to the tricyclic nucleoside to Dess-Martin oxidation conditions to that can be used as a precursor in the modifications that we hope to synthesize furnish aldehyde (6). Upon treatment with synthesis of TriNA analogues. Several in my lab. All of the compounds that allyltrimethylsilane and boron trifluoride different synthetic approaches to other Natasha has prepared are novel and have diethyl etherate (conditions that cleave bicyclic nucleosides are currently being not been reported in the primary literature. the trityl protecting group) in a Hosomi- investigated. - Bradley L. Merner, Department of Sakurai allylation, compound (7) was Chemistry and Biochemistry obtained and oxidized to afford aldehyde The development of a more efficient (8). Following a second Hosomi-Sakurai synthesis of TriNAs will save time and allylation, diene (9) was treated with money, reduce chemical waste, and ideally Grubbs second generation catalyst in a improve the overall yield of the desired ring-closing metathesis reaction to furnish compounds. Ultimately, we hope to use bicyclic nucleoside (10), which contains our optimized synthesis to build up large all of the carbon atoms and two of the quantities of TriNA analogues to be tested three rings present in the TriNA targets. as potential drug candidates in antisense All reactions were monitored by thin strands. References: Hanessian, S., Schroeder, B. R., Giacometti, R. D., Merner, B. L., Østergaard, M., Swayze, E. E., Seth, P. P. (2012) Structure- Based Design of a Highly Constrained Nucleic Acid Analogue: Improved Duplex Stabilization by Restricting Sugar Pucker and Torsion Angle γ. Angew. Chem. Int. Ed., 51, 11242-11245. 2.
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