Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design

Abstract

The successful development of a number of HIV-1 protease (PR) inhibitors for the treatment of AIDS has validated the utilization of retroviral PRs as drug targets and necessitated their detailed structural study. Here we report the structure of a complex of human T cell leukemia virus type 1 (HTLV-1) PR with a substrate-based inhibitor bound in subsites P5 through P5'. Although HTLV-1 PR exhibits an overall fold similar to other retroviral PRs, significant structural differences are present in several loop areas, which include the functionally important flaps, previously considered to be structurally highly conserved. Potential key residues responsible for the resistance of HTLV-1 PR to anti-HIV drugs are identified. We expect that the knowledge accumulated during the development of anti-HIV drugs, particularly in overcoming drug resistance, will help in designing a novel class of antileukemia drugs targeting HTLV-1 PR and in predicting their drug-resistance profile. The structure presented here can be used as a starting point for the development of such anticancer therapies.

Fig. 1.

The structure of HTLV-1 PR and a comparison with other retroviral PRs. (A) Overall view of a dimer of HTLV-PR. Helices are shown in red and β strands in pale green. The inhibitor and the catalytic aspartates are shown in stick representation. (B) Superposition of seven retroviral PRs shown in ribbon representation. HTLV-1 PR is colored blue; HIV-1 PR, green; HIV-2 PR, dark blue; SIV PR, gray; RSV PR, magenta; EIAV PR, yellow; and FIV PR, red. The numbers indicate residues within regions in HTLV-1 PR, with the most pronounced structural differences as compared with other retroviral enzymes.

Fig. 2.

Structure-based sequence alignment of the retroviral PRs with known structures. The color of the background indicates the secondary structure elements, with cyan denoting β strands; red, α helices; magenta, 3₁₀ helices; and gray, loops and irregular structure. Conserved residues are bold and white, and residues similar to those in HTLV-1 PR are bold and brown, whereas the remaining residues are black. Residues that were either not present in the constructs used to solve the structures (HTLV-1 PR) or not visible in the electron density maps (FIV PR) are italicized.

Fig. 3.

The flaps of retroviral PRs. (A) Superposition of the flaps in HTLV-1 (blue) and HIV-1 (tan) PRs. The distances between the corresponding pairs of atoms on the leading and trailing edges of the flaps are indicated. (B) Superposition of the flaps of the seven retroviral PRs (colored as in Fig. 1B) shown in ribbon representation, in stereo. The inhibitor bound to HTLV-1 PR is shown for reference in stick representation.

Fig. 4.

Stereoview showing the binding of the inhibitor I (blue, with O atoms red and N, dark blue) to the AB dimer of HTLV-1 PR (green, with O atoms red; N, blue; and S, yellow). The conserved water located between the flaps and the inhibitor is shown as a red sphere.

Fig. 5.

Stereoview of the overlay of the inhibitor bound to HTLV-1 PR with the clinical inhibitors of HIV-1 PR. The alignment is based on the superposition of the Cα atoms of the proteins. Amprenavir is shown in blue, ritonavir in green, nelfinavir in pink, saquinavir in black, and indinavir in red. Selected residues of HTLV-1 PR that interfere with drug binding are shown in thick lines.