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now clear that the binding of NNRTIs provokes substantial conformational changes in both secondary
structural elements and in side chains of residues in the NNIBP. These conformational changes in the
NNIBP could directly or indirectly affect the precise geometry and/or mobility of the nearby polymerase
catalytic site, especially the highly conserved YMDD motif and/or the divalent metal ions
[31,33,34,42,68]. The binding of NNRTIs appears to lock the flexible hinge-like structure between the
palm and thumb subdomains and restrict mobility of the thumb subdomain, placing constraints on the
geometry of the DNA-binding cleft [12,31,34,43]. The “primer grip” (i.e., β12-β13-β14 sheet), which
has close interactions with the 3'-terminus of the primer strand [38], forms a part of the NNIBP and is
involved in the binding of NNRTIs. It has become apparent that binding of NNRTIs can substantially
alter the conformation of the primer grip; this could affect the precise positioning of the primer strand
relative to the polymerase active site [34,37]. Displacement of the primer grip by NNRTI binding could
lead to repositioning of the primer terminus. This could explain the observation that dNTP binding is
largely unaffected by NNRTI binding while the rate of the chemical step of DNA polymerization is
reduced [77]. Long-range distortions of the HIV-1 RT structure by NNRTI binding can potentially
account for NNRTI inhibition of polymerization [39,41,43] and alteration of RNase H cleavage
specificity [43,78]. These possible mechanisms are not mutually exclusive and the binding of inhibitors
might have multiple influences on HIV-1 RT polymerization. The exact mechanism(s) of inhibition is
still under investigation.
IX. NNRTI-Resistance Mutations
Analyses of the crystal structures of HIV-1 RT complexed with various NNRTIs have indicated that
amino acid residues whose mutations confer high levels of resistance to NNRTIs [9,11,12,26,27] are
located close to the bound inhibitors (Figure 5 and Table 2). Subunit-specific mutagenesis studies have
confirmed that mutations that confer resistance to the NNRTIs act directly through the change in the
NNIBP itself [60,79]. In these studies, recombinant HIV-1 RTs that contained amino acid substitutions
only in the p66 subunit were resistant to NNRTIs, while those containing the same amino acid
substitutions only in the p51 subunit remained susceptible to the drugs. There is one exception: the
amino acid substitution of Glu138 to Lys, which confers resistance to inhibitors only when it is present
in the p51 subunit. Amino acid residue 138 is located in the β7–β8 connecting loop of the fingers
subdomain. In the p51 subunit this residue forms a part of the NNIBP, while its counterpart in the p66
subunit is far away from the pocket [12,60].
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