Structure-Based Design of a Novel, Potent, and Selective Inhibitor for MMP-13 Utilizing NMR Spectroscopy and Computer-Aided Molecular Design

Abstract

The high-resolution NMR solution structure of the catalytic fragment of human collagenase-3 (MMP-13) was used as a starting point for structure-based design of selective inhibitors for MMP-13. The major structural difference observed between the MMP structures is the relative size and shape of the S1′ pocket where this pocket is significantly longer for MMP-13, nearly reaching the surface of the protein. On the basis of the extended nature of the MMP-13 S1′ pocket an inhibitor potent and selective for MMP-13 was designed from an initial high throughput screening (HTS) lead. CL-82198 was identified as a weak (10 µM) inhibitor against MMP-13 while demonstrating no activity against MMP-1, MMP-9, or the related enzyme TACE. The drug-like properties of CL-82198 made it an ideal candidate for optimization of enzyme potency and selectivity. On the basis of NMR binding studies, it was shown that inhibitor CL-82198 bound within the entire S1′ pocket of MMP-13 which is the basis of its selectivity against MMP-1, MMP-9, and TACE. A strategy utilizing this information was devised for designing new inhibitors that showed enhanced selectivity toward MMP-13. Our design strategy combined the critical selectivity features of CL-82198 with the known potency features of a nonspecific MMP inhibitor (WAY-152177) to generate a potent and selective MMP-13 inhibitor (WAY-170523). WAY-170523 has an IC50 of 17 nM for MMP-13 and showed >5800-, 56-, and >500-fold selectivity against MMP-1, MMP-9, and TACE, respectively.A structure-based approach to designing potent and selective inhibitors has established itself as an important component of the drug development process (for reviews see refs 1 and 2). This is evident by the extensive structural data available for the matrix metalloproteinase (MMP) family of enzymes and the emergence of unique inhibitors based on this structural information (for reviews see refs 3-7). The MMPs are involved in the degradation of the extracellular matrix that is associated with normal tissue remodeling processes such as pregnancy, wound healing, and angiogenesis. MMP expression and activity is highly controlled because of the degradative nature of these enzymes where the apparent loss in this regulation results in the pathological destruction of connective tissue and the ensuing disease state. Thus, the MMPs are a highly active set of targets for the design of therapeutic agents for the disease areas of arthritis and oncology. The MMP family is composed of a number of enzymes where MMP-13 was recently identified on the basis of differential expression in normal breast tissues and in breast carcinoma. Recently, both an NMR and X-ray structure of inhibited MMP-13 have been reported. 8,9 The MMPs are generally categorized based on their substrate specificity, where the collagenase subfamily of MMP-1, MMP-8, and MMP-13 selectively cleaves native interstitial collagens (types I, II, and III). It is likely that only a subset of MMP enzymes will be involved in a particular disease as is evident by the overexpression o...

Matrix metalloproteinase-13 is regulated by toll-like receptor-9 in colorectal cancer cells and mediates cellular migration

“…Furthermore, CL-82198 was shown to provide an enzyme inhibition of 89% at a concentration of 10 µg/ml (25). This inhibitory ability of almost complete MMP-13 inhibition at a relatively low concentration is consistent with our observations, since we were unable to detect a further reduction of cellular migration when the concentration of CL-82198 was increased from 10 to 20 µM κ.…”

“…CL-82198 was developed in NMR studies and binds to the entire S1' pocket of MMP-13, which is the basis for its selectivity towards MMP-13 and the lack of inhibitory activities against other MMPs (25). Furthermore, CL-82198 was shown to provide an enzyme inhibition of 89% at a concentration of 10 µg/ml (25).…”

“…CL-82198 binds to the S1' pocket of MMP-13 leading to 89% enzyme inhibition at a concentration of 10 µg/ml (25). Following a 24-h incubation, migrated cells on the underside of the membrane were counted.…”

Inhibitors of Proteinases as Potential Anti-Cancer Agents

“…Among these, a new class of MMP inhibitors that do not possess a zinc-binding group and thus do not interact directly with the zinc active site ion is of special interest (Fig. 23) (Chen et al, 2000).…”

Kinetic characterization of 4,4′-biphenylsulfonamides as selective non-zinc binding MMP inhibitors

“…A way to develop more selective MMPIs is removing the ZBG and targeting directly specific pocket(s) within the catalytic site cleft. In 2000, Chen et al 7 reported a compound (CL-82198), devoid of any obvious ZBG, which was a weak inhibitor of MMP-13 ( Figure 1B). CL-82198 interacted specifically with the deep S1…”