Development of an Assay Suitable for High-Throughput Screening to Measure Matrix Metalloprotease Activity

MMPs, part of a family of enzymes with >35 known members, play an important role in tissue remodeling and repair, in the biology of neoplasia, and during development. Hydroxamic and carboxylic acid inhibitors of these proteases have long been available, but their specificities are poor and there still exists a desire to find novel chemical structures, which could be modified to optimize specificity and biocompatibility. Established methods for measuring MMP activity are based on the cleavage of MCA-PLGL-A2pr(DNP)-AR, which provides a prompt fluorescent signal when cleaved; however, its absorption/emission properties (325/400 nm) are not best suited for HTS assays. We describe an HTS-compatible method using the peptide substrate PLGLAARK, labeled at N- and C-termini with CyDye fluors Cy3 and Cy5Q, respectively, which is cleavable by MMP-1, -2, -3, -7, -9, and -13. HTS assays for MMP-13 and MMP-9 inhibitors were set up in approximately 20 microl in 384-well plates as a prompt fluorescence readout (excitation/emission = 540/570 nm) using the LEADseeker homogenous imaging system. These assays yielded IC(50) values comparable to standard methods, but with a faster, very sensitive, and normalized readout, thus conserving compound, enzyme (approximately 1.5 ng/well), and time (20 s read/plate). Data quality (Z' approximately 0.9) was such that hit-picking to -25% change in primary screening could be performed with confidence, and the subsequent rate of confirmation and validation in IC(50) determinations of the picked compounds was >60%. Parallel screening of related proteases also permitted immediate specificity comparisons, including evaluation of inactive or weakly active compounds.

Structural aspects of the metzincin clan of metalloendopeptidases

Metalloendopeptidases are present across all kingdoms of living organisms; they are ubiquitous and widely involved in metabolism regulation through their ability either to extensively degrade proteins or to selectively hydrolyze specific peptide bonds. They must be subjected to exquisite spatial and temporal control to prevent this vast potential from becoming destructive. These enzymes are mostly zinc-dependent and the majority of them, named zincins, possess a short consensus sequence, HEXXH, with the two histidines acting as ligands of the catalytic zinc and the glutamate as the general base. A subclass of the zincins is characterized by a C-terminally elongated motif, HEXXHXXGXXH/D, with an additional strictly conserved glycine and a third zinc-binding histidine or aspartate. Currently, representative three-dimensional structures of six different proteinase families bearing this motif show, despite low sequence similarity, comparable overall topology. This includes a substrate-binding crevice, which subdivides the enzyme moiety into an upper and a lower subdomain. A common five-stranded beta-sheet and two alpha-helices are always found in the upper subdomain. The second of these helices encompasses the first half of the elongated consensus sequence and is therefore termed the active-site helix. Other shared characteristics are an invariant methionine-containing Met-turn beneath the catalytic metal and a further C-terminal helix in the lower subdomain. All these structural features identify the metzincin clan of metalloendopeptidases. This clan is reviewed from a structural point of view, based on the reported structures of representative members of the astacins, adamalysins, serralysins, matrixins, snapalysins, and leishmanolysins, and of inhibited forms, either by specific endogenous protein inhibitors or by zymogenic pro-domains. Moreover, newly available genomic sequences have unveiled novel putative metzincin families and new hypothetical members of existing ones.

Molecular cloning and sequence analysis of ussurin, a new metalloproteinases/disintegrin from Gloydius ussuriensis

The metalloproteinases/disintegrins in the snake venom act as platelet aggregation inhibitor by an antagonism against integrin on platelet through its RGD sequence and may play other important role in cell-cell fusion, cell matrix interaction and other cellular function. Ussurin is a new metalloproteinase/disintegrin that was cloned from Gloydius ussuriensis. Poly (A+) RNA was purified from the total RNA preparation from venom gland of a single G. ussuriensis using the poly (A+) tract-mRNA isolation system. A cDNA library was constructed with the SMART PCR cDNA library construction kit. The cDNA library was screened and the positive clones were selected. The full-length cDNA of Ussurin was obtained. The cDNA encoding the Ussurin precursor has a 51bp 5'-UTR, the open reading frame of Ussurin and a 490 bp 3'-UTR, the open reading frame of Ussurin cDNA nucleotide sequence is 1434 bp and codes for 478 amino acids with a predicted molecular mass of 53.2 kD and an isoelectric point of 5.37. There is no potential N-glycosylation site in the deduced sequence region. Its deduced amino acid sequence consists of four region, a signal sequence of 18 amino acid residues, a zymogen pro-peptide of 171 amino acid residues with a cysteine switch motif (PK-MCGVT) in it, a central metalloproteinase domain of 201 amino acid residues containing a conserved zinc-chelating sequence (HEXXHXXGXXH) and a methionine-turn CIM involving zinc banding also, a space sequence between metalloproteinase domain and disintegrin domain of 15 amino acid residues with a conserved T392, T397, S400, which is specific residues of the P-II snake venom metalloproteinases, a disintegrin domain of 73 amino acid residues with a characteristic RGD region and six-disulfide bonds. Ussurin belongs to P-II class. The cDNA sequence and deduced amino acid sequence of Ussurin precursor were compared with homologous sequence in the GenBank database, the result reveals high degree of homology in sequence and organization pattern of domain with metalloproteinase/disintegrin gene family of other snake species. Compared with the alignment of amino acid sequence of metalloproteinase/disintegrin member, hypervariable regions of this member were revealed, besides they share higher homologous in the zymogen domain. It suggests that the hypervariable regions are the counterparts directly suitable for interacting with different domain of receptors, different receptors or substrates.

Combinatorial Strategies for Targeting Protein Families: Application to the Proteases

Tens of thousands of proteins have been identified as a result of recent large scale genomic and proteomic efforts. With this large influx of new proteins, the formidable task of elucidating their function begins. However, this task becomes more manageable if proteins are divided into families based upon sequence homology, thereby allowing tools for their systematic study to be developed based upon their common structural and mechanistic characteristics. Combinatorial chemistry is ideally suited for the systematic study of protein families because a large amount of diversity can be readily displayed about a common scaffold designed to target a given protein family. Targeted combinatorial libraries have been particularly effective for the study of a ubiquitous family of proteins, the proteases. Substrate-specificity profiles of many proteases have been determined by using combinatorial libraries of appropriately labeled peptides. This specificity information been utilized to identify the physiological protein substrates of these enzymes and has facilitated inhibitor design efforts. Furthermore, combinatorial libraries of small molecules prepared with mechanism-based scaffolds have resulted in the identification of potent, small-molecule inhibitors of numerous proteases. Cell-permeable small-molecule inhibitors identified by these methods have served as powerful chemical tools to study protease function in vitro and in vivo and have served as leads for the development of therapeutic agents.