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 ؋ 10 ؊12 M) than APV (K d ‫؍‬ 3.9 ؋ 10 ؊10 M). Our X-ray data (resolution ranging from 2.2 to 1.2 Å) 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.

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

“…The entropy difference between WT and MT for APV, 1-3 kJ/mol reproduces the isothermal calorimetry value of 2.5 kJ/mol. 49 The corresponding difference for DRV, 0 to -2 kJ/mol, is also reasonably close to the experimental value of -2.5 kJ/mol. Omitting, the entropy, gives a somewhat worse MUEtr, the same τ 90 , and a slightly better r 2 , but none of the differences is statistically significant at the 90% level.…”

“…The experimental affinities are shown in kJ/mol. 18,19,49 Figure 2. Illustration of the truncation approaches.…”

Absorption, Metabolism, and Excretion of Darunavir, a New Protease Inhibitor, Administered Alone and with Low-Dose Ritonavir in Healthy Subjects

“…Its molecular formula is C 27 H 37 N 3 O 7 S ⅐ C 2 H 5 OH and molecular weight is 593.73. Darunavir binds tightly to HIV protease with a dissociation constant (K d ) of 4.5 ϫ 10 Ϫ12 M (King et al, 2004) and is highly active against wild-type and resistant strains of the virus (De Meyer et al, 2005), inhibiting dimerization (Koh et al, 2007) and catalytic activity of HIV-1 protease. It selectively inhibits the cleavage of HIV-encoded gag-pol polyproteins in virus-infected cells, preventing the formation of mature infectious virus particles.…”

The Validation of Plasma Darunavir Concentrations Determined by the HPLC Method for Protease Inhibitors

“…According to in vitro experiments, DRV was active against HIV-1 with PI resistance mutations and against PI resistant clinical isolates. [1][2][3][4] This drug is expected to be effective in antiretroviral treatment-experienced patients, such as those possessing HIV-1 strains which are resistant to more than one PI. [5][6][7][8] Bouche et al recently determined plasma DRV concentrations using liquid chromatography-tandem mass spectrometry (LC/MS/MS).…”