Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor

Abstract

TMC114, a newly designed human immunodeficiency virus type 1 (HIV-1) protease inhibitor, is extremely potent against both wild-type (wt) and multidrug-resistant (MDR) viruses in vitro as well as in vivo. Although chemically similar to amprenavir (APV), the potency of TMC114 is substantially greater. To examine the basis for this potency, we solved crystal structures of TMC114 complexed with wt HIV-1 protease and TMC114 and APV complexed with an MDR (L63P, V82T, and I84V) protease variant. In addition, we determined the corresponding binding thermodynamics by isothermal titration calorimetry. TMC114 binds approximately 2 orders of magnitude more tightly to the wt enzyme (K(d) = 4.5 x 10(-12) M) than APV (K(d) = 3.9 x 10(-10) M). Our X-ray data (resolution ranging from 2.2 to 1.2 A) reveal strong interactions between the bis-tetrahydrofuranyl urethane moiety of TMC114 and main-chain atoms of D29 and D30. These interactions appear largely responsible for TMC114's very favorable binding enthalpy to the wt protease (-12.1 kcal/mol). However, TMC114 binding to the MDR HIV-1 protease is reduced by a factor of 13.3, whereas the APV binding constant is reduced only by a factor of 5.1. However, even with the reduction in binding affinity to the MDR HIV protease, TMC114 still binds with an affinity that is more than 1.5 orders of magnitude tighter than the first-generation inhibitors. Both APV and TMC114 fit predominantly within the substrate envelope, a property that may be associated with decreased susceptibility to drug-resistant mutations relative to that of first-generation inhibitors. Overall, TMC114's potency against MDR viruses is likely a combination of its extremely high affinity and close fit within the substrate envelope.

FIG. 1.

The chemical structures of APV and TMC114.

FIG. 2.

Two orientations of the TMC114_3X protease complex, shown as ribbon diagrams. The two monomers of HIV protease are shown in cyan and yellow with the side chains of the sites of mutation shown, labeled, and highlighted in blue and green. TMC114 is shown in magenta (15).

FIG. 3.

Stereo pairs showing the network of hydrogen bonds between (a) the TMC114_wt complex (note that the hydrogen bonds are the same between the wt and MDR protease complexes with TMC114) (Table 2), (b) the APV_wt complex, (c) superimposition of TMC114_wt (in magenta and purple with hydrogen bonds in black) and APV_wt (in cyan and gray with hydrogen bonds in yellow), and (d) the APV_3X complex (15).

FIG. 3.

Stereo pairs showing the network of hydrogen bonds between (a) the TMC114_wt complex (note that the hydrogen bonds are the same between the wt and MDR protease complexes with TMC114) (Table 2), (b) the APV_wt complex, (c) superimposition of TMC114_wt (in magenta and purple with hydrogen bonds in black) and APV_wt (in cyan and gray with hydrogen bonds in yellow), and (d) the APV_3X complex (15).

FIG. 4.

Inhibitor interactions with residues 82 and 84 in the various protease complexes (15). (a) TMC114_wt complex showing the van der Waals interactions between TMC114 and I84. (b) APV_wt complex showing the van der Waals interactions between APV and I84. (c) TMC114_3X complex showing the van der Waals interactions between TMC114 and V84. (d) APV_3X complex showing the van der Waals interactions with V84. (e) Superposition of TMC114_wt (in gray and cyan) and TMC114_3X (in purple-yellow and magenta) complexes. Note the additional OH-π hydrogen bond made by T82. (f) Superposition of APV_wt and APV_3X complexes. Note the conformational variability of the N-isobutyl group (arrow).

FIG. 5.

Substrate envelope (35) of HIV protease shown in blue (28), superimposed on the structures of (a) TMC114 and (b) APV. The atoms of each of the inhibitors that protrude from the envelope are shown in red and labeled. HIV protease residues that are within van der Waals contact of these atoms are also labeled.