The Medicinal Chemistry of Artificial Nucleic Acids and Therapeutic Oligonucleotides

Abstract

Nucleic acids play a central role in human biology, making them suitable and attractive tools for therapeutic applications. While conventional drugs generally target proteins and induce transient therapeutic effects, nucleic acid medicines can achieve long-lasting or curative effects by targeting the genetic bases of diseases. However, native oligonucleotides are characterized by low in vivo stability due to nuclease sensitivity and unfavourable physicochemical properties due to their polyanionic nature, which are obstacles to their therapeutic use. A myriad of synthetic oligonucleotides have been prepared in the last few decades and it has been shown that proper chemical modifications to either the nucleobase, the ribofuranose unit or the phosphate backbone can protect the nucleic acids from degradation, enable efficient cellular uptake and target localization ensuring the efficiency of the oligonucleotide-based therapy. In this review, we present a summary of structure and properties of artificial nucleic acids containing nucleobase, sugar or backbone modifications, and provide an overview of the structure and mechanism of action of approved oligonucleotide drugs including gene silencing agents, aptamers and mRNA vaccines.

Specificity of oligonucleotide gene therapy (OGT) agents

“…The OGT agents, subjects of this review, are antisense oligonucleotides (ASO agents), small interfering RNA (siRNA), ribozymes (Rz), deoxyribozymes (Dz) and CRISPR/Cas. To date, the global pharmaceutical market offers ten ASO agents and four siRNAs for the treatment of genetic disorders and the cytomegalovirus infection [3][4][5][6]. However, despite significant progress in pre-clinical and clinical studies, not a single anti-cancer OGT agent has been approved for clinical use [5][6][7].…”

“…To date, the global pharmaceutical market offers ten ASO agents and four siRNAs for the treatment of genetic disorders and the cytomegalovirus infection [3][4][5][6]. However, despite significant progress in pre-clinical and clinical studies, not a single anti-cancer OGT agent has been approved for clinical use [5][6][7]. The major problems in OGT development include inefficient intracellular delivery, lower efficiency, and high cost [2,3].…”

“…The issue of interaction with TLRs can be solved by using extra additional Dz agents as controls. These controls are designed to bear single-nucleotide mutations in the 15-nt 10-23 catalytic domain (i.e., 5'-GGC TAG 6 CTA CAA CGA-3', G 6 >C 6 ), which render the Dz inactive in cleaving but near identical in all other aspects. Another way to improve specificity is to test for TLR9/NF-kB activation alongside reference oligonucleotides [143].…”

N‐Fluoroalkylated Morpholinos – a New Class of Nucleoside Analogues

“…The morpholine motif is obtained from the corresponding ribonucleoside derivative by oxidation to 2′,3′‐secodialdehyde followed by a reductive amination‐cyclisation reaction with ammonia [2] or alkylamines [1,3] . Phosphorodiamidate morpholino oligomers (PMOs) [2] built up of morpholino monomers are valuable agents in gene silencing therapy, four of the eleven approved antisense oligonucleotide drugs – eteplirsen, golodirsen, viltolarsen, casimersen ‐ have a PMO structure and are used to treat Duchenne muscular dystrophy [4] . PMOs are also effective gene silencing agents against viruses [5] …”

“…Therefore, fluorination of bioactive molecules, including nucleosides, is an important strategy in the design and discovery of novel drug candidates [9,10] . Currently, many fluorinated nucleoside analogues, for example 5‐fluoro‐2’‐deoxyuridine, gemcitabine, trifluorothymidine, emtricitabine, fludarabine, capecitabine, clofarabine, are approved for the treatment of viral infections and cancer, [11,12] moreover, 2’‐deoxy‐2’‐fluorinated ribonucleosides are common building blocks of small interfering RNA‐based gene silencing drugs [4,12] . However, to the best of our knowledge, fluorine‐containing morpholino derivatives have not yet been produced.…”