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


Current cART regimens use combinations of at least 3 drugs to fully suppress HIV-1 replication. In some cases, drugs in the same class can be used together if they select for non-overlapping resistance mutations such as the NRTIs tenofovir and FTC.[23] One issue with NNRTIs is their considerable cross-resistance. A new NNRTI, DOR, which is in phase III clinical trials, has potent antiviral activity against WT HIV-1 and some of the well-characterized NNRTI-resistant mutants. Based on the analysis of the mutations in RT that were selected by DOR in cell culture, it was suggested that DOR and RPV select for different resistance mutations and that DOR could be a useful new NNRTI.[17] However, when we analyzed a large panel of NNRTI-resistance mutations, we found that several well-known NNRTI-resistance mutations, either singly or in combination, caused a considerable loss of DOR potency against HIV-1.

The tripartite structure of RPV is a key to its ability to inhibit a wide range of NNRTI-resistant HIV-1 mutants. The relatively long linker that joins the cyanovinyl group to the pyrimidine scaffold (11.1 Å) allows the cyanovinyl group of RPV to be flexible in response to mutations that change the structure of the binding pocket, allowing the drug to make new contacts with other residues, maintaining its ability to inhibit RT. Increasing the length of the linker groups that join the functional moieties to the pharmacophore is becoming a common theme in the design of HIV-1 inhibitors. Dolutegravir (DTG) is an integrase inhibitor that has a long linker joining its benzyl moiety and tri-cyclic scaffold;[24,25] this allows DTG to maintain an interaction between the benzyl moiety and penultimate cytosine of the incoming viral DNA.[24] Thus DTG is able to inhibit integration even when resistance mutations alter the structure of the integrase active site. The distances between the pyridone scaffold of DOR and its cyano and triazolone moieties, (Supp. Fig. 2) are 7.75 and 6.35 Å, respectively, which are considerably shorter than the linkers that join RPV's cyanovinyl (11.1 Å) and benzonitrile moieties (8.3 Å). This suggests DOR may be more limited in its ability to adapt to the changes in the NNRTI binding pocket caused by some mutations and to overcome resistance. Importantly, classical NNRTI mutants, for example Y188L, caused a substantial drop in DOR susceptibility, and other classical NNRTI mutants including K103N and K103N/Y181C caused more modest drops in susceptibility to DOR. Based on the resistance data we present here, we question whether DOR has significant advantages relative to the available NNRTIs. However, it might be possible to develop cART regimens in which DOR was combined with RPV; however, as previously mentioned, E138K mutation could pose a problem for this combined strategy. Although DOR apparently did not select for the E138K mutation in cell culture, we found that this mutation did reduce the susceptibility of HIV-1 to DOR by about 20-fold. As has already been reported, the E138K mutation does not cause a significant reduction in susceptibility to RPV in cell culture assays (including ours). The complication is that, in HIV-infected individuals, RPV selects for the E138K mutation.[12,13] This apparent paradox has been noted before, by us[20] and by others.[10,15] However, it is possible that DOR would not be effective in suppressing the selection and replication of E138K mutants that arise during RPV-containing cART.

We superimposed the structures of HIV-1 RT with RPV or DOR to determine if differences in the binding of the compounds can explain the differences in their resistance susceptibility profiles. Based on the structure of RPV bound to RT, it is not surprising that the K101P caused a substantial decrease in susceptibility to RPV. K101P would appear to cause a steric clash with RPV in the binding pocket and the interaction of E138 with K101 would be lost.[21] Mutating these residues likely affects the rates of association/dissociation of RPV within the NNRTI binding pocket. The K101P/V179I mutant caused a large decrease in RPV susceptibility, because it affects both the contacts between the amine linkers and pyrimidine core with the residues of the binding pocket by introducing steric clash through the branched isoleucine and the cyclic proline. The Y181I mutant also displayed a decrease in susceptibility to RPV, unlike the other mutant at this position, Y181C, likely because of the unavoidable steric clash from beta-branched isoleucine that prevents RPV from recruiting Y183 toward the NNRTI binding pocket to compensate for the loss of interaction between Y181 and its phenyl moiety.[22] However, RPV did not lose efficacy against viruses with mutations in the upper portion of the NNRTI binding pocket (including the DOR-associated mutations), suggesting that residues on the rim of the NNRTI binding pocket are much more important for the binding of RPV. Conversely, DOR interacts primarily with residues in the upper portion of the NNRTI binding pocket, making important contacts with K103, V106, Y188, and P236. Mutations at V106, with or without additional secondary mutations (F227L, L234I, and F227L/L234I), caused substantial decreases in susceptibility to DOR. The branched, hydrophobic side chain of V106 interacts with the pyridone core of DOR; in the presence of the V106A mutation, this important contact is lost. The Y188L mutation causes the loss of the [pi]-[pi] stacking interaction, which in turn reduces the potency of DOR inhibition, whereas the lack of interaction with Y181 explains the fact that the Y181C and Y181I mutants are susceptible to DOR. The P236L mutation causes a modest decrease in DOR susceptibility by introducing clash and preventing the CH-[pi] interaction between the triazolone of DOR and P236. Interestingly, the E138K mutant caused a 20-fold drop in susceptibility to DOR. Although the E138 residue does not make any direct contacts with DOR, the binding of DOR within the pocket caused the position of this residue to shift substantially, which could prevent the interaction between E138K of the p51 subunit and K101 of the p66 subunit.

We suggest that there might be advantages to a 4 drug regimen that would include one or 2 NRTIs or an NRTI and an integrase inhibitor, in combination with 2 NNRTIs. If the NNRTIs are carefully chosen, it should be difficult for the virus to develop resistance, and the low toxicity of the NNRTIs would be an advantage for patients.[26,27] Whether DOR and RPV represent a clinically useful pair of NNRTIs that could be used together in cART remains to be seen; however, it would be useful to find additional pairs of NNRTIs whose resistance profiles do not overlap. Thus there is a need to develop new NNRTIs that are broadly effective against known NNRTI-resistant mutants, and the development of new NNRTIs should make use of the available structural data, in relation to the resistance susceptibility profiles of the compounds, as a guide to develop compounds (or combinations of compounds) that can overcome known NNRTI-resistant mutants.