Structural analysis of bengamide derivatives as inhibitors of methionine aminopeptidases

Abstract

Natural-product-derived bengamides possess potent antiproliferative activity and target human methionine aminopeptidases (MetAPs) for their cellular effects. Several derivatives were designed, synthesized, and evaluated as MetAP inhibitors. Here, we present four new X-ray structures of human MetAP1 in complex with the inhibitors. Together with the previous structures of bengamide derivatives with human MetAP2 and tubercular MtMetAP1c, analysis of the interactions of these inhibitors at the active site provides structural basis for further modification of these bengamide inhibitors for improved potency and selectivity as anticancer and antibacterial therapeutics.

Figure 1

Chemical structures of natural bengamides (1 and 2) and their synthetic derivatives reported in literature (3 and 4) and designed and synthesized in this laboratory (5-9).

Figure 2

Coordination of bengamide derivatives with the metal ions at the dinuclear catalytic site. A. Inhibitor 4 with two Co(II) ions in HsMetAP2. B. Inhibitors 5, 7-9 with two Mn(II) ions in HsMetAP1. Inhibitors and protein residues are shown as sticks, and metal ions are shown as spheres. Coordination between the metal ions and the heteroatoms of the inhibitors or protein residues is shown as dashed lines. Only metal coordinating protein residues are shown. For coloring carbon atoms, 4 is yellow, 5 is green, 7 is orange, 8 is magenta, 9 is cyan, and protein residues are grey. For coloring non-carbon atoms, oxygen is red, and nitrogen is blue. For coloring the metal ions, Co(II) is green, and Mn(II) is orange.

Figure 3

Binding of the bengamide derivatives 5, 7, 8, and 9 at the active site pocket of HsMetAP1 (A-D, respectively). The inhibitors and protein residues (sticks) and the Mn ions (spheres) are colored in the same scheme as in Fig. 2. The semi transparent surface formed by protein residues is colored grey for carbon, red for oxygen, and blue for nitrogen. F_obs-F_calc omit maps (inhibitors were omitted in the models) are shown superimposed on the refined structures as light green meshes contoured at 3 σ.

Figure 4

A flexible K132-G133-T134 loop in HsMetAP1 at the junction of the catalytic domain and the N-terminal extension. The structure of HsMetAP1 with 5 is shown as ribbon drawing (A) and as putty drawing (C) with the tube diameters proportional to B factors. For comparison, the structures of MtMetAP1c with 5 (D) and HsMetAP2 with 4 (E) are also shown as putty drawings. The active site is shown as semitransparent surfaces with the inhibitor and metal ions. The flexible loop in human MetAP1 is indicated by an arrow in A and C. The junction residues in HsMetAP2 are invisible in 1QZY and indicated by a dotted line in E. All of the structures were adjusted to similar orientations with the same color scheme as in Fig. 2. HsMetAP1 belongs to type 1 MetAP, as EcMetAP1 and MtMetAP1c, while HsMetAP2 belongs to type 2 MetAP with a typical insert for MetAP2, and their domain structures are shown in B.

Figure 5

Stereo view of the superimposed bengamide derivatives 5 (with HsMetAP1, carbon green; with MtMetAP1c, carbon grey) and 4 (with HsMetAP2, carbon yellow) at the active site with coordination to catalytic metal ions (shown as green or orange spheres). The left panel and the right panel are a stereo pair, and one was rotated six degree to the other along z axis for viewing in stereo. The inhibitors are thicker sticks, and the protein residues are thinner sticks. Only five metal coordinating residues and two catalytically important histidine residues (See Table 2) are shown.

Figure 6

Overall structures of MtMetAP1c with 5 bound (A), HsMetAP1 with 5 bound (B) and HsMetAP2 with 4 bound (C), shown as surface drawing (carbon, grey; nitrogen blue; and oxygen, red). Inhibitors are colored the same as in Fig. 5.