Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is the major target of antiretroviral drug treatments. RT inhibitors constitute the largest class of HIV-1 drugs and are grouped in two separate categories. The first category consists of the nucleos(t)ide RT inhibitors (NRTIs), which are analogs of the natural nucleosides. Most NRTIs lack a 3’-OH and act as chain terminators by blocking DNA polymerization [1–8]. The other group includes the nonnucleoside RT inhibitors (NNRTIs), which are non-competitive RT inhibitors with respect to either dNTP or nucleic acid substrates and block DNA synthesis by binding to a hydrophobic pocket of RT [9–15]. Highly Active Antiretroviral Therapies (HAART) are based on combinations of antiretrovirals and have helped extend the lives of HIV-1 patients. However, the efficacy of combination therapies is being challenged by the selection of drug-resistant variants of HIV-1.
There are two major mechanisms of NRTI resistance [16, 17]. The first is the discrimination mechanism, which is based on decreased incorporation of the nucleotide analog into the elongating DNA over the canonical dNTP substrate [16, 18–21]. An example of this type of resistance is conferred by the M184V mutation, which decreases HIV susceptibility to lamivudine (3TC) and emtricitabine (FTC) [20–24]. The second mechanism is the excision mechanism, which is based on the enhanced ability of the mutant RT to remove the chain-terminating inhibitor from the DNA terminus [25–28] through a phosphorolytic reaction that uses primarily adenosine triphosphate (ATP) as a substrate. Upon removal of the inhibitor DNA synthesis resumes. The excision reaction is facilitated by Excision Enhancement Mutations (EEMs), typically M41L, D67N, K70R, T215Y/F, L210W, and K219E/Q, which are also known as Thymidine Associated Mutations (TAMs) because they were historically linked to resistance to thymidine analogs AZT and d4T [29, 30].
Tenofovir disoproxil fumarate (TDF) is one of the most prescribed anti-HIV drugs, and is described as a key component of all first-line regimens in the DHHS HIV guidelines (http://aidsinfo.nih.gov/contentfiles/lvguidelines/adultandadolescentgl.pdf). The K65R mutation in HIV-1 RT is the signature mutation selected during tenofovir-based therapy. Viruses carrying K65R have reduced susceptibility to tenofovir and other NRTIs, but remain susceptible to zidovudine (AZT) [31–36]. This mutation has also been associated with a reduction in viral replication capacity, NRTI excision, NRTI incorporation, and dNTP incorporation [37–43]. Recent crystallographic data suggest that the K65R mutation disrupts the interaction between the side chains of 65R and 72R resulting in structural changes that lead to NRTI resistance .
We have previously shown that a series of NRTIs with 4’-substitutions and a 3’-OH group are very potent inhibitors of WT and multi-drug resistant HIV-1. The most effective of these compounds is the adenosine analog 4’-ethynyl-2-fluoro-2’-deoxyadenosine (EFdA) [45, 46]. We have demonstrated that EFdA acts in a DNA-sequence specific manner, primarily inhibiting DNA synthesis as an immediate chain terminator, but less often, at some DNA sequences can also act as a delayed chain terminator . Compounds that exhibit this novel mechanism of inhibition have been dubbed Translocation Defective Reverse Transcriptase Inhibitors (TDRTIs) .
In an effort to investigate the effect of EFdA against drug-resistant strains of HIV-1 we found that RT mutation K65R confers hypersusceptibility to EFdA. We carried out a series of biochemical experiments to elucidate the mechanism of this phenomenon and we propose here that K65R increases the susceptibility to EFdA mainly by suppressing the ATP- or PPi-dependent repair of EFdA-MP-terminated DNA. Understanding the molecular basis of K65R hypersusceptibility to EFdA may lead to new and more effective combination therapies.