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rapidly selects viral strains containing drug-resistance mutations [9,24,25]. HIV-1 viral variants are
known whose RT is resistant to all of the currently available drugs/inhibitors (see reviews
[5,9,11,12,26,27]). In some cases, drug-resistant variants can be selected in very short periods of time
[9], a consequence of the high viral load and rapid turnover of viral populations in infected individuals
[28–30]. A better understanding of how these viral variants confer resistance should provide insight into
the limitations of their genetic flexibility. In the past few years, substantial progress has been made in
understanding the three-dimensional structure of HIV-1 RT. This paper will discuss the recent
biochemical, genetic, and clinical data of HIV-1 RT in the context of the crystal structure of HIV-1 RT
and prospects for development of more effective inhibitors of HIV-1 replication.
II. Three-Dimensional Structures of HIV-1 RT
Three-dimensional crystal structures of HIV-1 RT have been determined both for the unliganded form of
the protein and for complexes with either template-primer substrate or nonnucleoside inhibitors (Figure
2 and Table 1). Structures of HIV-1 RT have been determined in complexes with a series of NNRTIs,
including nevirapine [31–33], 1051U91 (a nevirapine analog) [33], α-APA R95845 [34], α-APA
R90385 [33], HEPT [33], 8-Cl TIBO (R86183) [35], and 9-Cl TIBO (R82913) [36,37]. The structure of
HIV-1 RT in a ternary complex with a 19-mer/18-mer double-stranded DNA (dsDNA) template-primer
and an antibody Fab fragment has been described [38]. In addition, structures of unliganded HIV-1 RT
have also been solved in multiple crystal forms [39–43]. The structure of a polypeptide corresponding to
the fingers and palm subdomains of the HIV-1 RT polymerase domain has also been determined [44].
HIV-1 RT is an asymmetric heterodimer consisting of the p66 (66 kDa) and p51 (51 kDa) subunits. The
N-terminal 440 residues of the p66 subunit constitute the polymerase domain and the C-terminal 120
residues of p66 form the RNase H domain; the p51 subunit has the same amino acid sequence as the
polymerase domain of the p66 subunit [1,2]. The polymerase domain of the p66 subunit has been
likened to a human right hand. On this basis the subdomains of both p66 and p51 have been designated
as fingers, palm, thumb, and connection (Figure 2) [31,38]. In the p66 subunit, the fingers, palm, and
thumb subdomains form a large cleft that can accommodate the DNA substrate. The polymerase active
site, which contains three strictly conserved aspartic acid residues (Asp110, Asp185, and Asp186), is
located in the DNA-binding cleft and is part of the p66 palm subdomain (Figure 3) [31,38]. In the p51
subunit, however, the thumb is rotated away from the fingers and the connection subdomain is folded
over onto the palm subdomain between the fingers and thumb subdomains. As a
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