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p17, p9, and p7) and replicative enzymes (protease, reverse transcriptase/ RnaseH, and integrase) are
translated as either polyprotein P55-GAG, or a larger frameshift product P160-GAG-POL. In the
process of virus assembly these polyproteins are proteolytically cleaved by the protease and this
processing step, both in its timing and accuracy, is essential for the formation of infectious particles of
HIV [6]. It was also shown early on that the inactivation of HIV PR, either by chemical inhibition or
certain mutations, leads to the production of immature, noninfectious viral particles [7,8].
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Structurally HIV PR is a 99-amino-acid protein translated initially as a central part of the P160-GAG-
POL polyprotein precursor. The autocatalytic processing from the 160 kDa precursor is poorly
understood, but most likely occurs during the process of budding of pre-formed viral particles from the
host cell [9]. After release from the precursor polyprotein, HIV PR forms a homodimer and acts in trans
to correctly process GAG and GAG-POL polyproteins—a process required for formation of the viral
capsid and nucleoprotein core.
Retroviral proteases such as HIV PR are the latest additions to the wellstudied family of aspartic
proteases. This family of enzymes, which includes, among others, proteases such as pepsin, renin, and
cathepsins D and E, has been intensely studied in the past, and the knowledge gained from studies of
these enzymes allowed early inferences as to the structure and function of the dimeric HIV PR.
Moreover, the intensive effort over the past two decades to make inhibitors of human renin provided
impetus for the early design of inhibitors of HIV PR. In fact, some of the renin inhibitors have turned
out to be effective inhibitors of retroviral aspartic proteases as well and have served as the starting point
for drug design. As a result of this many early inhibitors of HIV PR were peptidyl in nature and the best
known example of such compounds is Ro31-8959, better known as saquinavir, a hydroxyethylaminecontaining
mimetic of a hexapeptide substrate [10]. This potent inhibitor of HIV PR was discovered
using a substrate-based rational approach to drug design and displays extremely high in vitro activity
against clinical isolates and laboratory strains of HIV. Saquinavir has been recently approved by the
FDA for the treatment of AIDS in combination with nucleoside inhibitors of reverse transcriptase, and
the discovery of this compound was the first breakthrough and the starting point for many other
innovative designs.
Determination of the crystal structures of HIV PR gave new impetus to the design of novel inhibitors.
One measure of the intensity with which new inhibitors were designed or discovered is the total number
of crystal structures of inhibitory complexes, currently exceeding 250, that have been determined over
the past 5 years. Very detailed crystallographic analysis combined with extensive biochemical
characterization and site-specific mutagenesis studies made HIV PR perhaps the best characterized
enzyme to date.
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