5′,6′‐Nucleoside Phosphonate Analogues Architecture: Synthesis and Comparative Evaluation towards Metabolic Enzymes

Abstract

Nucleoside phosphonates have been designed as stable 5'-mononucleotide mimics and are nowadays considered a potent class of antiviral agents. Within cells, they must be metabolised to the corresponding diphosphate to exert their biological activity. In this process, the first phosphorylation step, catalysed by nucleoside monophosphate kinases (NMP kinases), has been proposed as a bottleneck. Herein, we report the synthesis of a series of ribonucleoside phosphonate derivatives isosteric to 5'-mononucleotides, with different degrees of flexibility within the 5',6'-C-C bond, as well as different polarities, through the introduction of hydroxy groups. The influence of these modifications on the capacity of the compounds to act as substrates for appropriate human NMP kinases, involved in nucleic acids metabolism, has been investigated. Low flexibility, as well as an absence of hydroxy groups within the ribose-phosphorus architecture, is critical for efficient phosphotransfer. Among the series of pyrimidine analogues, one derivative was shown to be phosphorylated by human UMP-CMP kinase, with rates similar to those of dUMP and even better than dCMP.

Identification of metabolically stable 5′-phosphate analogs that support single-stranded siRNA activity

“…Similarly 5′-deoxy-5′-( Z )-vinyl(dimethylphosphonate)-2′- O -(2-methoxyethyl)-thymidine-3′-phosphoramidite 55 was also synthesized (Figure 12 and Supplementary data) ( 28 ). We also synthesized 5′-deoxy-( E )-5′-fluorovinyl(dimethylphosphonate)-2′- O -(2-methoxyethyl)-thymidine-3′-phosphoramidite 56 (Figure 12 and Supplementary data) ( 34 , 35 ) and 5′-deoxy-( Z )-5′-fluorovinyl(dimethylphosphonate)-2′- O -(2-methyl)-thymidine-3′-phosphoramidite 57 (Figure 12 and Supplementary data) using reported methods ( 36 , 37 ).…”

Structural Insights into the Inhibition of Cytosolic 5′-Nucleotidase II (cN-II) by Ribonucleoside 5′-Monophosphate Analogues

“…The uracil series of ribonucleoside phosphonate analogues (Figure 1) were synthesized as previously described [35], [36], [37] starting from uridine (Carbosynth, UK). This nucleosidic strategy has lead to derivatives 1 – 11 , 24 and 25 (see Figure 1).…”

Squaramide‐Based 5’‐Phosphate Replacements Bind to the DNA Repair Exonuclease SNM1A

“…Phosphate bioisosteres such as phosphonates, phosphorothioates, boranophosphates and squaramides, are commonly used to overcome these problems and have been the subject of several reviews . Mononucleotide analogues with isosteres at the 5’‐position are being investigated as antiviral agents, as the introduction of the mimic overcomes the rate limiting phosphorylation of the nucleoside drug . The activity of siRNA depends on 5’‐terminal phosphorylation by kinases, which limits chemical modifications of siRNA as extensive modification can compromise recognition by kinases .…”