Lethal Mutagenesis of RNA Viruses and Approved Drugs with Antiviral Mutagenic Activity

Abstract

In RNA viruses, a small increase in their mutation rates can be sufficient to exceed their threshold of viability. Lethal mutagenesis is a therapeutic strategy based on the use of mutagens, driving viral populations to extinction. Extinction catastrophe can be experimentally induced by promutagenic nucleosides in cell culture models. The loss of HIV infectivity has been observed after passage in 5-hydroxydeoxycytidine or 5,6-dihydro-5-aza-2'-deoxycytidine while producing a two-fold increase in the viral mutation frequency. Among approved nucleoside analogs, experiments with polioviruses and other RNA viruses suggested that ribavirin can be mutagenic, although its mechanism of action is not clear. Favipiravir and molnupiravir exert an antiviral effect through lethal mutagenesis. Both drugs are broad-spectrum antiviral agents active against RNA viruses. Favipiravir incorporates into viral RNA, affecting the G→A and C→U transition rates. Molnupiravir (a prodrug of β-d-N⁴-hydroxycytidine) has been recently approved for the treatment of SARS-CoV-2 infection. Its triphosphate derivative can be incorporated into viral RNA and extended by the coronavirus RNA polymerase. Incorrect base pairing and inefficient extension by the polymerase promote mutagenesis by increasing the G→A and C→U transition frequencies. Despite having remarkable antiviral action and resilience to drug resistance, carcinogenic risks and genotoxicity are important concerns limiting their extended use in antiviral therapy.

Keywords: HIV; RNA polymerase; SARS-CoV-2; error catastrophe; favipiravir; lethal mutagenesis; molnupiravir; nucleoside analogs; ribavirin.

Figure 3

Poliovirus (A) and foot-and-mouth disease virus (B) RdRp structures showing the location of motifs A–D and residues relevant for ribavirin binding and resistance. Locations of motifs A, B, C, and D are shown in orange, yellow, blue, and magenta, respectively [34,121]. Spheres are used to represent the location of relevant amino acid substitutions. Crystal structures were taken from PDB files 2ILY (poliovirus RdRp) and 1U09 (foot-and-mouth disease virus RdRp).

Figure 4

Proposed model for the antiviral mechanism of molnupiravir based on β-d-N⁴-hydroxycytidine (NHC)-induced mutagenesis and the inhibition of RNA synthesis. Tautomeric forms and the base pairing of NHC are shown in the lower-left panel. Illustration based on the experimental data reported by Gordon et al. [136] and Kabinger et al. [137], and adapted from ref. [146].

Figure 1

Chemical structures of mutagenic base and nucleoside analogs and prodrugs used in lethal mutagenesis experiments. KP-1461 is a prodrug of KP-1212.

Figure 2

Chemical structures of approved drugs inducing mutagenesis in viral replication assays. Molnupiravir is the isopropylester prodrug of β-d-N⁴-hydroxycytidine. The isopropylester moiety is shown in red.