Virtual Screening And Peptides Selection Based On MMP14 Hemopexin-Like Domain

Matrix metalloproteinases (MMPs) are a family of endopeptidases degrading extracellular matrix and basement membrane. This process relies on metal ions Zn2+ According to the latest report, there are 28 members in this family, MMPs are extensively involved in the body’s normal physiological processes, such as tissue remodeling, embryonic development, angiogenesis, cell adhesion, cell proliferation, and wound healing and so on. Wrong regulation of their activities would also led to arthritis, multiple sclerosis, periodontal disease and cancer. Membrane-type matrix metalloproteinase 1 (MT1-MMP or MMP14) is a cell surface protein zymogene MMP-2 agonists, and it can also degrade a variety of ECM components directly or indirectly, and regulate adhesion molecules and angiogenesis. MMP14 is considered to be most closely related with tumor invasion among the enzyme of the family, and MMP14 inhibitor becomes a research hotspot. However, many MMP14 inhibitors inhibit MMPs widely, which becomes a barrier of their clinical application, the development of MMP14 specific inhibitors are of great significance. MMP14 hemopexin (HPX) domain is essential for the MMP14-mediated collagen type I invasion and growth. In addition, compared to the catalytic domain, MT1-MMP HPX domain has a relatively low similarity among MMPs family. Therefore HPX domain is an ideal choice as a target for MMP 14 inhibitors development.This study, for the first time, predict the chemical molecular binding site on MMP 14 HPX domain with DOCK and MVD and screen the Specs chemical database virtually with MMP 14 HPX domain as target. A group of chemical compounds have been identified and may be used for further study as lead molecules. The Comparation of our predicted ligands to the known and published chemicals showed that there are some common characteristics and differences in their chemical structures, which provides a reference for the future sub-structure based virtual screening. By multiple sequence alignment and molecular surface pocket forecast, a unique octapeptide on MMP 14 HPX domain was identified. This unique octapeptide consists a pocket on MMP 14 HPX domain and is not homology to other MMPs; on this basis, the octapeptide was synthesized, then random peptide library technology was used to screen binding phage with this unique octapeptide as target, after three rounds of screening, binding phage was acquired. This study provides a preliminary work for anti-tumor drugs, especially anti-tumor metastasis drug development.The conclusions of this study were as follows:1. The chemical molecular binding site on MMP14 HPX domain were predicted with DOCK and MVD, thus two potential binding site, clusterl, cluster3 were found;2. By DOCK virtual screening,300 chemicals were obtained whose structure and energy match MMP14 HPX domain;3. The top 20 ligands ranked by DOCK were scored and further analyzed by Autodock. The results suggest that most of the 10 best ranked ligands (8 ligands) by Autodock were those selected by DOCK with cluster 3 as active site. In this regard, cluster 3 is better than clusterl as docking site;4. By docking of the chemicals to MMP14 HPX domain, binding mode was analyzed. It was revealed that the residues on receptor interacting with ligands are mainly of MET13, MET18, ARG30, TYR161, TYR168, LYS170, TYR182, and TRP190. These residues are in the right position where cluster3 exists. The find of potential binding mode may provide reference for Pharmacophore based virtual screening;5. By comparing the chemicals (ligands) we obtained to the published MT1-MMP inhibitors, we observed some common characters and also diversities are noted. They both contain some chemical structures fragments like (?) or(?). Our chemicals tend to containing fragments(?), while peptide bond and are frequent fragments in the reported chemicals. This result suggests that chemicals containing such fragments may bind MMP14. Meanwhile, this result may provide insight into sub-structure based virtual screening;6. With the "pocket" finding function and multiple sequence alignment, a unique octapeptide KEGRGLTD in MMP14 HPX domain was identified as target for further phage display library screening;7. Biotin-streptavidin target taged techniques were applied in phage random peptide library technology. After three rounds of screening, the phage eluted titer increase for two orders of magnitude in each round thus get a better enrichment, in addtion, in each round of seelction the P/N values were increased.