Rilpivirine and Doravirine Have Complementary Efficacies Against NNRTI-Resistant HIV-1 Mutants

Steven J. Smith, PhD; Gary T. Pauly, PhD; Aamir Akram, MS; Kevin Melody, MS; Zandrea Ambrose, PhD; Joel P. Schneider, PhD; Stephen H. Hughes, PhD


J Acquir Immune Defic Syndr. 2016;72(5):485-491. 

In This Article

Abstract and Introduction


Background: Rilpivirine (RPV) is the latest non-nucleoside reverse transcriptase inhibitor (NNRTI) to be approved by Food and Drug Administration to combat HIV-1 infections. NNRTIs inhibit the chemical step in viral DNA synthesis by binding to an allosteric site located about 10 Å from the polymerase active site of reverse transcriptase (RT). Although NNRTIs potently inhibit the replication of wild-type HIV-1, the binding site is not conserved, and mutations arise in the binding pocket. Doravirine (DOR) is a new NNRTI in phase III clinical trials.

Methods: Using a single round HIV-1 infection assay, we tested RPV and DOR against a broad panel of NNRTI-resistant mutants to determine their respective activities. We also used molecular modeling to determine if the susceptibility profile of each compound was related to how they bind RT.

Results: Several mutants displayed decreased susceptibility to DOR. However, with the exception of E138K, our data suggest that the mutations that reduce the potency of DOR and RPV are non-overlapping. Thus, these 2 NNRTIs have the potential to be used together in combination therapy. We also show that the location at which DOR and RPV bind with the NNRTI binding pocket of RT correlates with the differences in their respective susceptibility to the panel of NNRTI-resistance mutations.

Conclusions: This shows that (1) DOR is susceptible to a number of well-known NNRTI resistance mutations and (2) an understanding of the mutational susceptibilities and binding interactions of NNRTIs with RT could be used to develop pairs of compounds with non-overlapping mutational susceptibilities.


There are 2 classes of drugs that block reverse transcription, nucleoside analogs, nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). NRTIs are analogs of the deoxynucleosides that are used to synthesize DNA. The NRTIs used to treat HIV-1 infection lack the 3'–OH.[1,2] If an NRTI is incorporated into the growing viral DNA strand, reverse transcriptase (RT) will not be able to add the next nucleotide, blocking DNA elongation. The 5 approved NNRTIs all bind in a hydrophobic pocket ~10 Å from the polymerase active site called the NNRTI binding pocket. Once an NNRTI binds within the pocket, structural changes perturb the portion of RT that underlies the nucleic acid substrate, affecting the alignment of the primer terminus and the polymerase active site, inhibiting the chemical step of DNA synthesis.[3–5] NNRTIs potently inhibit the replication of wild-type HIV-1; however, because the polymerase activity of RT does not directly involve residues within the NNRTI binding pocket, changes in the NNRTI binding pocket can arise that undermine the effectiveness of these compounds. There are 5 NNRTIs that have been approved for the treatment of HIV-1 infection: nevirapine (Viramune), delavirdine (Rescriptor), efavirenz (Sustiva), etravirine (ETR, Intelence), and RPV (Edurant).

Although there are significant differences in the structures of the first generation NNRTIs (nevirapine, delavirdine, and efavirenz), they all bind in the same hydrophobic pocket of RT.[5–8] Resistance mutations that are selected by one NNRTI often reduce the susceptibility of RT to other first generation NNRTIs, without having a large effect on viral replication capacity.[1,2] A partial list of NNRTI resistance mutations include L100I, K103N, V106A, E138K, Y181C, Y188L, and H221Y; these mutations can occur singly, or in combinations.[2] Recently, a shift in NNRTI design from more bulky and structurally restricted bi- and tri-cyclic ring compounds to more structurally adaptable compounds has led to the development of the second generation NNRTIs ETR and RPV (Supp. Fig. 1), which are relatively effective against WT HIV-1 and mutants that carry many of the well-known NNRTI resistance mutations.[8–10] However, in clinical trials, individuals on an ETR-containing regimen, who experienced virological failure, were infected with viruses that had a combination of RT mutations including V90I, A98G, L100I, K101E/P, V106I, V179D/F, Y181C/I/V, and G190A/S.[11] In clinical trials that involved RPV and 2 NRTIs, the RT resistance mutations E138K and M184I/V were selected.[12–15] In addition, viruses that grew out in an in vitro selection with RPV or a compound closely related to RPV had the RT mutations K101E or E40K, D67E, V111A, E138K, Y181C, and M230I, respectively. Thus, it would be useful to develop new NNRTIs that could block the replication of a broader spectrum of resistant variants.

Figure 1.

Antiviral activity of DOR and RPV against HIV-1 vectors that carry well-known NNRTI resistance mutations. A, The IC50 values of DOR against WT HIV-1 and several NNRTI-resistant mutants represented in different colors were measured using a single round infection assay. B, The IC50 values of RPV and DOR against WT HIV-1 and several other well-characterized NNRTI resistant mutants, represented in different colors, were measured using a single round infection assay. The IC50 value of DOR against the M230L, K103N/P225H, and V106A/G190A/F227L resistant mutants were .100 nM. Error bars represent the standard deviations of independent experiments, (n = 4). The RPV susceptibility data were also used as a control in experiments testing the efficacy of a series of RPV analogs (21).

Doravirine (DOR) (Supp. Fig. 1) is being developed by Merck and is currently in Phase III clinical trials.[16,17] DOR can effectively inhibit the replication of viruses that carry several prevalent NNRTI resistance mutations; however, DOR selected mutations in RT that confer reduced susceptibility in experiments done in cultured cells. Mutations that reduced the susceptibility of RT to DOR did not, in general, confer a decrease in susceptibility to RPV and vice-versa, suggesting this difference would make DOR a useful new drug.[17] However, in this initial study, only a limited number of mutants were tested. We tested the ability of DOR and RPV to inhibit the replication of WT HIV-1 and a large number of well-characterized NNRTI-resistant mutants. DOR loses potency against a number of NNRTI-resistant mutants; however, DOR is generally effective against mutants that reduce the potency of RPV, although DOR did lose some potency against E138K. Based on these results, it seems likely that, if DOR was used as the only NNRTI in a regimen, there could be problems with resistance. We suggest an alternative strategy in which DOR would be used in combination with RPV; this would in some sense be similar to strategies in which 2 NRTIs that select non-overlapping mutations (eg, Emtricitabine (FTC) and tenofovir) are used together in combination antiretroviral therapy (cART). Using DOR and RPV together should be effective against HIV-1s that encode most of the well-characterized NNRTI resistance mutations. It also appears that the difference in the susceptibility of the mutants to DOR and RPV is a result of differences in the way the 2 compounds bind to RT; this information might be useful in the design of other complementary pairs of NNRTIs.