The human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is a DNA polymerase that converts the viral RNA genome into a proviral DNA precursor. Emergence of resistance to current classes of drugs targeting HIV-1 RT (the nucleoside or nucleotide reverse transcriptase inhibitors (NRTIs) and the non-nucleoside reverse transcriptase inhibitors (NNRTIs)) means new drugs are required, which are effective against these resistant viral strains to treat the HIV infected.  

A screen was conducted using a library of fragments and saturation transfer difference (STD) nuclear magnetic resonance (NMR), to identify new binding sites in RT for the design of novel inhibitors, which led to the identification of four fragment inhibitors of HIV-1 RT. These hits were characterised using an in vitro reverse transcriptase inhibition assay. Steady state kinetic assays showed that two of these fragments, V89 and 2C4, compete with the dNTP substrate and a third, 4A2, competes with DNA substrate. These fragments were tested for inhibitory activity against common drug resistant mutants of HIV-1 RT, K103N, Y181C, G190A as well as against murine moloney leukemia virus (MMLV) RT and klenow DNA polymerase. In an RNase H activity assay, fragment 4A2 was also shown to inhibit RNase H activity of HIV-1 RT. Fragment 4A2 is also an active inhibitor when tested in anti-HIV assay using TZMbl cells with an EC50 of 18.3 μM ± 3.75 SEM.

These fragments, with distinct mechanisms of actions from currently available drugs, are promising leads for the development of novel HIV-1 RT inhibitors.