Saquinavir is a widely used HIV-1 protease inhibitor
drug for AIDS therapy. Its effectiveness, however, has
been hindered by the emergence of resistant mutations,
a common problem for inhibitor drugs that target HIV-1
viral enzymes. Three HIV-1 protease mutant species, G48V,
L90M, and G48V/L90M double mutant, are associated in vivo
with saquinavir resistance by the enzyme (Jacobsen et al.,
1996). Kinetic studies on these mutants demonstrate a 13.5-,
3-, and 419-fold increase in Ki
values, respectively, compared to the wild-type enzyme (Ermolieff
J, Lin X, Tang J, 1997, Biochemistry 36:12364–12370).
To gain an understanding of how these mutations modulate
inhibitor binding, we have solved the HIV-1 protease crystal
structure of the G48V/L90M double mutant in complex with
saquinavir at 2.6 Å resolution. This mutant complex
is compared with that of the wild-type enzyme bound to
the same inhibitor (Krohn A, Redshaw S, Richie JC, Graves
BJ, Hatada MH, 1991, J Med Chem 34:3340–3342).
Our analysis shows that to accommodate a valine side chain
at position 48, the inhibitor moves away from the protease,
resulting in the formation of larger gaps between the inhibitor
P3 subsite and the flap region of the enzyme. Other subsites
also demonstrate reduced inhibitor interaction due to an
overall change of inhibitor conformation. The new methionine
side chain at position 90 has van der Waals interactions
with main-chain atoms of the active site residues resulting
in a decrease in the volume and the structural flexibility
of S1/S1′ substrate binding pockets. Indirect interactions
between the mutant methionine side chain and the substrate
scissile bond or the isostere part of the inhibitor may
differ from those of the wild-type enzyme and therefore
may facilitate catalysis by the resistant mutant.