Nucleoside analogs containing an imino-ribitol sugar exhibit a distinctive pattern of interference with RNA synthesis by the Dengue virus polymerase.

Abstract

Iminovirs are antiviral nucleoside analogs in which the naturally occurring ribose sugar is replaced by an imino-ribitol group, linked to the base by a non-native carbon-carbon bond. The prototypical iminovir is galidesivir, an adenosine analog that inhibits replication of a wide range of RNA viruses. Initial investigation of the effects of galidesivir triphosphate on RNA synthesis by the Dengue virus serotype 2 (DENV-2) polymerase showed that the analog was incorporated with reduced efficiency relative to ATP, and incorporation of the analog at consecutive sites in the nascent RNA was effectively blocked. To better understand the origin of these effects, we have extended this work, studying both galidesivir triphosphate and three closely related compounds with variations in both the base and sugar groups. We investigated the effects of these compounds on RNA synthesis using primer extension assays with varying template sequences. Quantitative analysis of the data confirms that the DENV-2 polymerase processes iminovir triphosphates less efficiently than ATP. Galidesivir, for example, is incorporated into the nascent RNA chain around thirteen times slower than adenosine, a difference that is fully ascribable to the presence of the imino-ribitol group. Furthermore, consecutive incorporation of iminovirs is strongly disfavored. Consequently, iminovir triphosphates slow the overall rate of RNA chain extension when present at high concentrations, with this effect modulated by the template sequence. However, iminovir incorporation into the nascent RNA strand does not act to terminate RNA synthesis, which suggests that antiviral activity must result from events downstream of initial incorporation.