Therapeutically targeting RNA viruses via lethal mutagenesis

Abstract

RNA viruses exhibit increased mutation frequencies relative to other organisms. Recent work has attempted to exploit this unique feature by increasing the viral mutation frequency beyond an extinction threshold, an antiviral strategy known as lethal mutagenesis. A number of novel nucleoside analogs have been designed around this premise. Herein, we review the quasispecies nature of RNA viruses and survey the antiviral, biological and biochemical characteristics of mutagenic nucleoside analogs, including clinically-used ribavirin. Biological implications of modulating viral replication fidelity are discussed in the context of translating lethal mutagenesis into a clinically-useful antiviral strategy.

Figure 1. Lethal mutagenesis as an antiviral strategy against RNA viruses

Treatment with a nucleoside mutagen (µ) increases the number of mutations per genome, decreasing the fitness of the progeny viral population. µMP, µDP and µTP represent mono-, di- and triphosphorylated forms of the nucleoside, respectively. RdRp: RNA-dependent RNA polymerase.

Figure 2. The extinction threshold is dependent upon mutation rate and fecundity

The dotted line represents the threshold between population extinction (above) and population survival (below). The log-linear relationship indicates that large increases in fecundity are required to overcome small changes in mutation rate. Adapted from [20]

Figure 3. Ribavirin can act as an ambiguous purine analog

Rotation of the exocyclic carboxamide allows for base pairing with either uridine (top) or cytidine (bottom).

Figure 4. Analogs of ribavirin

(A) Viramidine is an aminated prodrug that is rapidly converted to ribavirin intracellularly. (B) Iodo- and (C) propynyl-substituted ribavirin analogs demonstrate efficient incorporation by poliovirus 3Dpol compared with ribavirin [63].

Figure 5. Ribonucleoside analogs with ‘universal’ nucleobases

3-nitropyrrole nucleoside (A: 3-NPN) and 5-nitroindole nucleoside (B: 5-NINDN) have promiscuous templating properties, although low efficiency of polymerase incorporation prevents their use as lethal mutagens [69,71].

Figure 6. Pyrimidine analogs with mutagenic nucleobases

(A) 5-fluorouridine and (B) 5-hydroxy-2′-deoxycytidine have been shown to act as mutagenic nucleoside analogs. Substitution of a nitro moiety at the 5-position of cytidine (C) results in a nucleotide polymerase inhibitor [77].

Figure 7. KP-1212 is a mutagenic deoxyribonucleoside analog with antiretroviral activity

Tautomerization of the nucleobase allows for alternative base pairing with either guanosine (top) or adenosine (bottom).

Figure 8. Tautomerization of nucleobase analogs allows for ambiguous base pairing

(A) Nucleoside P can base pair with either adenosine (top) or guanosine (bottom) through its two tautomers. (B) JA28 and (C) JA30 are N-6-substituted purine analogs that are efficiently and ambiguously incorporated during poliovirus and CVB3 replication [88].