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when metals are bound. Finally, there is no evidence to rule out the possibility that the two termini<br />

contribute to part of the active site, occlude some of it, or restrict access to it in as yet undetermined<br />

ways. For this and other obvious reasons, three-dimensional structures of larger versions of HIV-1<br />

integrase, such as IN 1–212, IN 50–288, and the full-length protein, IN 1–288, will be required.<br />

Page 110<br />

We also lack a clear picture of how the enzyme substrates, the viral DNA ends and the target DNA, bind<br />

to integrase. The DNA must at some point approach the region defined <strong>by</strong> the three conserved acidic<br />

residues so that bond cleavage and joining can occur. However, the dominant DNA binding domain is<br />

defined <strong>by</strong> residues in the C-terminus. It would be extremely valuable to determine the relative<br />

orientation of these domains in the context of a larger version of integrase. Even more revealing would<br />

be the structure of the full-length protein with bound DNA. Once we possess this information, it should<br />

be possible to rapidly progress with structure-<strong>based</strong> drug design.<br />

C. Possible Approaches to the <strong>Design</strong> of Effective Integrase Inhibitors<br />

There are a variety of approaches to the design of integrase inhibitors that are obvious and do not depend<br />

on knowing its three-dimensional structure. However, the rational implementation and refinement of<br />

these approaches will require high-resolutional structural data, much of which, as indicated above, is not<br />

yet available. It still may be useful to discuss here different classes of inhibitors that can be envisioned.<br />

Preventing DNA Binding<br />

One approach to the inhibition of integrase would be to prevent binding of the DNA substrate.<br />

Unfortunately, we do not yet know how or where DNA binds. There are likely to be several sites on the<br />

enzyme that contact DNA, including the C-terminus and the region around the active site. In the absence<br />

of the structure of an integrase-DNA complex, structures of related enzymes (RNase H, the MuA<br />

transposase, and RuvC) with their DNA substrates would be useful guides in suggesting ways in which<br />

DNA could interact with integrase. However, there is no guarantee that modes of DNA binding are<br />

conserved among members of this polynucleotidyl transferase family. The overall structure of the Cterminus<br />

fragment suggests that it should be possible to develop compounds that bind specifically in the<br />

cleft formed <strong>by</strong> dimers of IN 220–270 (see Section IV.E) which may prevent DNA binding.<br />

Inhibition at the Active Site<br />

It may be possible to inhibit integrase <strong>by</strong> preventing the binding of the required metal cofactor(s) to the<br />

active site acidic residues that are presumed to provide<br />

http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_110.html [4/5/2004 4:52:23 PM]

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