The The reverse transcriptase (RT; EC 2.7.7.49) of human immunodeficiency virus (HIV) is a multifunctional enzyme critical to the viral life cycle. It is also without a homologue in eukaryotic systems, and thus is an attractive target for anti-HIV therapies. Several RT inhibitors that act as DNA chainterminating analogues of the natural nucleosides have been used to control HIV infection, such as AZT, ddI, ddC, d4T and 3TC (1). However, the emergence of resistant virus populations and significant adverse reactions (2, 3) led to extensive efforts to identify new RT inhibitors.The search for novel RT inhibitors rapidly identified the nonnucleoside inhibitors (NNIs), compounds that are typically HIV-1 specific. The NNIs now comprise a very large number of chemically diverse (but largely hydrophobic) compounds, which are subdivided into groups based on their chemical structures. From early examples {e.g., 1-(2-hydroxyethoxymethyl-6-(phenylthio)thymine (HEPT) (4), tetrahydroimidazo-[4,5,l-jk][1,4]-benzodiazepin-2(1H)-one (TIBO) (5), and nevirapine (6)} to the recent example of alkenyldiarylmethanes (7), more than 30 groups of NNIs have been identified (8). These compounds can be very potent inhibitors of RT, with low toxicity and favorable pharmacokinetic properties. However, the emergence of resistant viral populations, often within days or weeks, seriously compromises their potential therapeutic efficacy. Resistance studies suggest that the NNIs share a common mode of action, binding at a single site that is distinct from the polymerase catalytic site (8). Mutations that confer resistance to one NNI often confer cross-resistance to many other inhibitors [such as the Lys-103-Asn and Tyr-181-Cys mutations (9-11)] and so interest has focused on those compounds that retain pronounced activity against mutant RTs or that have a unique resistance profile.The first structure determination for RT [in complex with the NNI nevirapine at 3.5-Ă
resolution (12)] has been followed by structures of complexes with other NNIs (13-17), a complex with double-stranded DNA (18), and structures of the unliganded . The structures we have determined to 2.2-Ă
resolution for RT in complex with NNIs (13) represent the clearest models of RT to date; hence, we use the secondary structure nomenclature of these descriptions. RT is a heterodimer, one subunit (p66) comprises 560 residues and all enzymatic activity of the heterodimer is associated with residues in this subunit. The second chain (p51) comprises the initial 440 residues of the p66 subunit. RT is composed of nine domains (12), named fingers, palm, thumb, connection, and RNase H in the p66, with the p51 containing only the first four of these. The domains of the p66 subunit form a binding groove for the polynucleotide substrate, at the bottom of which lie the aspartyl residues implicated in polymerase activity.The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U....