Towards third generation matrix metalloproteinase inhibitors for cancer therapy

Abstract

The failure of matrix metalloproteinase (MMP) inhibitor drug clinical trials in cancer was partly due to the inadvertent inhibition of MMP antitargets that counterbalanced the benefits of MMP target inhibition. We explore how MMP inhibitor drugs might be developed to achieve potent selectivity for validated MMP targets yet therapeutically spare MMP antitargets that are critical in host protection.

Figure 1

Sequence alignment of every human MMP active site. (A) The amino-acid sequences of MMP catalytic domain regions containing the S₁′ subsite forming residues (red frame) and S₂ essential residues (blue frame) were aligned using T-Coffee (Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205–217) and annotated using ESPrint (Gouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15: 305–308). The secondary structure and numbering is based on MMP1 Protein Data bank (PDB) #1HFC. (B) Structural representation of antitarget MMPs. The catalytic domains of MMP3 (PDB:1CIZ), MMP8 (PDB: 1KBC), MMP9 (PDB:1GKD) and MMP12 (PDB: 1Y93) were structurally aligned and superimposed. The empty voids of the catalytic pockets were calculated using CASTp (Liang J, Edelsbrunner H, Woodward C (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 7: 1884–1897) and visualised using Pymol (DeLano Scientific LLC, San Francisco, CA, USA http://www.pymol.org/) and its CATSp plugin. The S₁′ pocket voids are in yellow, the essential S₂ pocket residues at position 227 are shown in blue, and the S₁′ specificity loop is shown in orange-red. The original structures contained a bound inhibitor in the active site, which was removed prior to calculation. Therefore, the S₁′ voids include any structural adaptations in the molecule that were needed to accommodate the inhibitor. Although, these adaptations occurred upon binding of different inhibitors, the character of the void spaces is quite similar (data not shown).

Figure 2

The structures of zinc binding groups, their inhibitory constants, and calculated free energy for interaction with MMP catalytic zinc. The lower free energy (ΔG) for interaction with MMP catalytic zinc of hydroxamate-based inhibitors is well correlated with their superior inhibitory constants relative to other common zinc-binding groups. This attribute of hydroxamate-based inhibitors conceals the contribution of other groups in the inhibitor structure, and therefore reduces their selectivity.