Human Matrix Metalloproteinase Research Articles

MOLECULAR DYNAMICS STUDIES OF FULL HUMAN MATRIX METALLOPROTEINASE 9 LIGANDED WITH N-HYDROXY-2-[(4-PHENYLPHENYL) SULFONYL-PROPAN-2-YLOXYAMINO] ACETAMIDE

The research presented in this article aimed to provide a full quarternary structure of human matrix metalloproteinase 9 (MMP9) enzyme with a ligand in the catalytic site for structure-based virtual screening. The enzyme plays an important role in wound healing of diabetic foot ulcer. By employing the primary structure of the enzyme obtained from UniProt database (UniProt:P14780), the theoretical structure of full apoenzyme of the human MMP9 (PDB:1LKG), the crystal structures of the catalytic domain (PDB:4H3X) and the hemopexin domain (PDB:1ITV) of the human MMP9, homology modeling studies have been performed. The ligand N-2-(biphenyl-4-yl-sulfonyl)-N-2-(isopropyloxy)-acetohydroxamic acid (CC27) or N-hydroxy-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxyamino]acetamide (IUPAC version) from PDB:4H3X was embedded in the catalytic site of the enzyme. The modeling made use of the modules of homology modeling in YASARA structure. Subsequently, molecular dynamics (MD) simulations in YASARA structure were performed to examine the stability of the enzyme. The homology model was found stable after 5.05 ns and the lowest energy of the model was found at the 6.40 ns of the MD production run. This lowest energy snapshot was then energetically minimized and analyzed for its applicability for virtual screening. This optimized model was then stored in Mendeley Data (DOI: 10.17632/4gsb4p75gz.1).

Thermal stability of human matrix metalloproteinases

Matrix metalloproteinases (MMP) are key players in the remodelling of the extracellular matrix under physiological and pathological conditions. Thermodynamic parameters of human recombinant metalloproteinases of the active (rMMP2, 3, 7, 8 and 9) and latent (rPro-MMP2, 3 and 9) forms were obtained by differential scanning calorimetry (DSC). Temperature by itself does not result in autocatalysis of recombinant MMP. The transitions observed by DSC correspond to structural domains of the monomeric protein. In this study, we show the domain organization of these proteins, where the thermal transition (Tm) of the main component is observed at 71.3 °C (ProMMP-2); 74.8 °C (ProMMP-8); 80.0 °C (ProMMP-3); 92.6 °C (ProMMP-9) and 98.3 °C (ProMMP-7). For MMP-3, this main Tm is related to the catalytic domain (CD). The isolated recombinant CD of MMP-3 unfolds as a single transition at Tm 83.4 °C, matching the more stable domain observed in the full-length active form of rMMP-3. The denaturation profile of rProMMP-3 shows the main transition at Tm 80 °C, a less stable domain before the propeptide domain (PD) cleavage. Our results indicate that the structural stability of MMP and particularly their CD are not substantially altered after cleavage of the PD. We propose that the thermodynamic parameters obtained by DSC are relevant for the functional study of MMP, particularly to reveal their contribution in complex biological samples in health and disease.

Practical context of enzymatic treatment for wound healing: A secreted protease approach (Review).

Skin wounds have been extensively studied as their healing represents a critical step towards achieving homeostasis following a traumatic event. Dependent on the severity of the damage, wounds are categorized as either acute or chronic. To date, chronic wounds have the highest economic impact as long term increases wound care costs. Chronic wounds affect 6.5 million patients in the United States with an annual estimated expense of $25 billion for the health care system. Among wound treatment categories, active wound care represents the fastest-growing category due to its specific actions and lower costs. Within this category, proteases from various sources have been used as successful agents in debridement wound care. The wound healing process is predominantly mediated by matrix metalloproteinases (MMPs) that, when dysregulated, result in defective wound healing. Therapeutic activity has been described for animal secretions including fish epithelial mucus, maggot secretory products and snake venom, which contain secreted proteases (SPs). No further alternatives for use, sources or types of proteases used for wound healing have been found in the literature to date. Through the present review, the context of enzymatic wound care alternatives will be discussed. In addition, substrate homology of SPs and human MMPs will be compared and contrasted. The purpose of these discussions is to identify and propose the stages of wound healing in which SPs may be used as therapeutic agents to improve the wound healing process.

Structure and Function of Human Matrix Metalloproteinases.

The extracellular matrix (ECM) is a macromolecules network, in which the most abundant molecule is collagen. This protein in triple helical conformation is highly resistant to proteinases degradation, the only enzymes capable of degrading the collagen are matrix metalloproteinases (MMPs). This resistance and maintenance of collagen, and consequently of ECM, is involved in several biological processes and it must be strictly regulated by endogenous inhibitors (TIMPs). The deregulation of MMPs activity leads to development of numerous diseases. This review shows MMPs complexity.

Matrix Metalloproteinases: How Much Can They Do?

Zinc-dependent matrix metalloproteinases (MMPs) belong to metzincins that comprise not only 23 human MMPs but also other metalloproteinases, such as 21 human ADAMs (a disintegrin and metalloproteinase domain) and 19 secreted ADAMTSs (a disintegrin and metalloproteinase thrombospondin domain). The many setbacks from the clinical trials of broad-spectrum MMP inhibitors for cancer indications in the late 1990s emphasized the extreme complexity of the participation of these proteolytic enzymes in biology. This editorial mini-review summarizes the Special Issue, which includes four review articles and 10 original articles that highlight the versatile roles of MMPs, ADAMs, and ADAMTSs, in normal physiology as well as in neoplastic and destructive processes in tissue. In addition, we briefly discuss the unambiguous involvement of MMPs in wound healing.

Kinetic and Computational Investigations into the Origin of Metal‐Ion Specificity in Matrix Metalloproteinase‐1

Matrix Metalloproteinases (MMPs) are a family of Zn‐dependent proteases responsible for cleaving peptide bonds. MMPs have essential roles in cell proliferation, differentiation, immune responses, among many others. Human MMPs have been implicated in a number of diseases including cancer and arthritis and as such have been the focus of studies related to their roles. We are interested in exploring the high specificity for the Zn2+ ion by MMP‐1 using kinetic assays and computational modeling. Human MMP‐1 contains a classical HEXXHXXGXXH Zn‐binding domain. Both the Zn2+ and second sphere Glu219 residue are involved in the first step of catalysis – deprotonating a Zn‐coordinated water. Interestingly, the Volvox species has a proteinase (VMP3) with a modified QEXXHXXGXXH metal‐binding domain that displays enhanced activity with Cu2+ and is much less active with Zn2+. In our study, a variety of metal‐substituted samples of MMP‐1 were prepared using dialysis to remove the Zn2+ ion. Kinetic assays using a FRET substrate demonstrate less than 5% activity in all cases when Cu2+ is substituted for Zn2+. To further explore these results, we developed a series of computational models of the MMP‐1 active site substituting either Zn2+ or Cu2+ into the active site. Density Functional Theory (DFT) as implemented in the ORCA program was used to develop these models, simulating the protein environment using either solvation models or by directly including second sphere residues as part of the quantum mechanics (QM) calculation. Models were validated by comparison to experimental results, including the kinetic data and spectroscopy data in the case of the Cu2+ models. Our work shows two effects at play. First, the first sphere geometry in MMP‐1 is primed to support a tetrahedral coordination environment, which is preferred by Zn2+ whereas Cu2+ prefers a square planar coordination environment. Second, the positioning of the Zn2+‐OH2 unit in the active site positions the water for deprotonation by Glu219. In the Cu2+ models, the distortion of the Cu2+‐OH2 unit due to the less stable coordination species increases the energy associated with proton transfer. This work provides a clear example of how first and second sphere active site residues are finely tuned to maximize enzyme activity.Support or Funding InformationWentworth Institute of Technology

Effect of prostaglandin analogs: Latanoprost, bimatoprost, and unoprostone on matrix metalloproteinases and their inhibitors in human trabecular meshwork endothelial cells

Bimatoprost, latanoprost, and unoprostone are prostaglandin F2α analogs (PGAs) and are used to lower intraocular pressure. We investigated the free acid effects of these three prostaglandin analogs: bimatoprost, latanoprost, and unoprostone on human matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMP) in the trabecular meshwork (TM) cells. Immunoblot results show that all three PGAs generally increased MMPs-1,9 and TIMPs-4. Additionally, bimatoprost and latanoprost both increased MMP-3 and TIMP-2, while unoprostone had an indeterminate effect on both. Zymography results show that all three PGAs except unoprostone increased intermediate MMP-1 activity while bimatoprost and latanoprost increased MMP-9 activity. Together, these data suggest that the balance between MMPs and TIMPs correlate to the relative intraocular pressure lowering effectiveness observed in clinical studies of these PGAs.

Protective Effect of Diphlorethohydroxycarmalol Isolated from Ishige okamurae Against Particulate Matter-Induced Skin Damage by Regulation of NF-κB, AP-1, and MAPKs Signaling Pathways In Vitro in Human Dermal Fibroblasts.

Particulate matters (PM), the main contributor to air pollution, have become a serious issue that threatens human’s health. Skin is the largest organ in humans, as well as the primary organ exposed to PM. Overexposure of PM induces skin damage. Diphlorethohydroxycarmalol (DPHC), an algal polyphenol with the potential of skin protection, has been isolated from the edible brown seaweed Ishige okamurae. The purpose of the present study is to investigate the protective effect of DPHC against PM (ERM-CZ100)-induced skin damage in human dermal fibroblasts (HDF) cells. The results indicated that DPHC significantly and dose-dependently reduced intracellular reactive oxygen species generation in HDF cells. In addition, DPHC significantly induced collagen synthesis and inhibited collagenase activity in ERM-CZ100-stimulated HDF cells. Further study demonstrated that DPHC remarkably reduced the expression of human matrix metalloproteinases through regulation of nuclear factor kappa B, activator protein 1, and mitogen-activated protein kinases signaling pathways in ERM-CZ100-stimulated HDF cells. This study suggested that DPHC is a potential candidate to protect skins against PM-induced damage, and it could be used as an ingredient in pharmaceutical and cosmeceutical industries.

Molecular Docking Analysis of Triazole Analogues as Inhibitors of Human Neutrophil Elastase (HNE), Matrix Metalloproteinase (MMP 2 and MMP 9) and Tyrosinase

Triazole analogues are well known to have desirable properties for medicinal chemistry such as hydrogen bonding capability, moderate dipole character, rigidity and stability under in vivo conditions etc. This prompts us to carry out the present study, we have selected 20 triazole analogues and evaluated on the docking behavior of four targeted enzymes such as HNE, MMP 2, MMP 9 and tyrosinase. The molecular physicochemical analysis revealed that all the tested ligands (expect ligand 5 and 18) showed nil violation and complied well with the Lipinski's rule of five. ADME analysis showed that ligand 15 alone predicated to have low gastrointestinal (GI) absorption effect. Docking studies revealed that ligand 18 [2-(2,4-difluorophenyl)-1-(4-((1-(4-ethylbenzyl)-1H-1,2,3-triazol-4-yl)methyl)piperazin-1-yl)-3-(1H-1,2,4-triazol-1-yl)propan-2-ol] had exhibited the maximum binding energy for three target enzymes such as HNE, MMP 2 and MMP 9. The present study has paved a new insight in understanding 20 triazole analogues as potential inhibitors against HNE, MMP 2, MMP 9 and tyrosinase.

Sequencing analysis of matrix metalloproteinase 7-induced genetic changes in Schwann cells.

Previous research revealed the positive activity of matrix metalloproteinase 7 (MMP7) on migration and myelin regeneration of Schwann cells (SCs). However, understanding of the molecular changes and biological activities induced by increased amounts of MMP7 in SCs remains limited. To better understand the underlying molecular events, primary SCs were isolated from the sciatic nerve stump of newborn rats and cultured with 10 nM human MMP7 for 24 hours. The results of genetic testing were analyzed at a relatively relaxed threshold value (fold change ≥ 1.5 and P-value < 0.05). Upon MMP7 exposure, 149 genes were found to be upregulated in SCs, whereas 133 genes were downregulated. Gene Ontology analysis suggested that many differentially expressed molecules were related to cellular processes, single-organism processes, and metabolic processes. Kyoto Enrichment of Genes and Genomes pathway analysis further indicated the critical involvement of cell signaling and metabolism in MMP7-induced molecular regulation of SCs. Results of Ingenuity Pathway Analysis (IPA) also revealed that MMP7 regulates biological processes, molecular functions, cellular components, diseases and functions, biosynthesis, material metabolism, cell movement, and axon guidance. The outcomes of further analysis will deepen our comprehension of MMP7-induced biological changes in SCs. This study was approved by the Laboratory Animal Ethics Committee of Nantong University, China (approval No. 20190225-004) on February 27, 2019.

Recombinant human MMP-2 associated with monoolein improves bone repair.

The main objective of the present study was to investigate the possible osteostimulatory action of recombinant human matrix metalloproteinase-2 (rhMMP-2) implanted in a bone defect made in calvaria of rats, bounded to the monoolein as carrier. Forty-four adult male Wistar rats (about 600 g body weight) underwent surgery in order to create a spherical defect in parietal bone on the right side of the median sagittal suture by using 4 mm diameter of a trephine drill. Animals were divided into three groups: no treatment (control, C), treatment with rhMMP-2 diluted in monoolein liquid crystal (rhMMP-2) and negative control with monoolein (M). The groups were divided into two experimental times, 2- and 4-weeks of experimental time. The rate of new-formed bone, estimated by the number of points on new-formed cancellous bone, was in enhanced rhMMP-2 group in both periods in comparison to C or M groups. There was no difference in bone neoformation between second to fourth week within groups. In the present study, monoolein alone had a negative role in the post-operative surgery, but monoolein associated with +rhMMP-2 had a positive role on releasing rhMMP-2 and enhance the rate of new-formed bone (Tab. 1, Fig. 5, Ref. 71).

The luciferase reporter system of the MMP12 endogenous promoter for investigating transcriptional regulation of the human MMP12 gene

Background: Matrix metalloproteinase 12 (MMP12), a member of MMPs, can take lots of roles including extracellular matrix component degradation, viral infection, inflammation, tissue remodeling and tumorigenesis. To explore the transcriptional regulation of MMP12 gene, a sensitive luciferase reporter HEK293 cell line for endogenous MMP12 promoter was generated by CRISPR/Cas9 technology. Results: The HEK293-MMP12-T2A-luciferase-KI cell line was successfully established by CRISPR/Cas9 technology. The sequencing results indicated that one allele of the genome was proven to have a site-directed insertion of luciferase gene and another allele of the genome was confirmed to have additional 48 bp insertion in this cell line. The cell line was further demonstrated to be a sensitive reporter of the endogenous MMP12 promoter by applying transcription factors STAT3, AP-1 and SP-1 to the cell line. The reporter cell line was then screened with bioactive small molecule library, and a small molecule Tanshinone I was found to significantly inhibit the transcriptional activity of MMP12 gene in HEK293-MMP12-T2A-luciferase-KI cell line by luciferase activity assay, which was further confirmed to inhibit the expression of MMP12 mRNA in wild-type HEK293 cells. Conclusions: This novel luciferase knock-in reporter system will be helpful for investigating the transcriptional regulation of MMP12 gene and screening the drugs targeting MMP12 gene. Normal 0 false false false ES-CL X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:Tabla normal; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri,sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Times New Roman; mso-bidi-theme-font:minor-bidi; mso-ansi-language:ES-CL;}

Development of anti-matrix metalloproteinase-2 (MMP-2) nanobodies as potential therapeutic and diagnostic tools

Matrix metalloproteinase-2 (MMP-2) is an endopeptidase involved in cardiovascular disease and cancer. To date, no highly selective MMP-2 inhibitors have been identified for potential use in humans. Aim of our work was to apply the nanobody technology to the generation of highly selective inhibitors of human MMP-2 and to assess their effects on platelet function and their applicability as conjugated nanobodies. We constructed a nanobody library after immunising an alpaca with human active MMP-2 and identified, after phage display and screening, one MMP-2 inhibitory nanobody (VHH-29), able to hinder the effects of MMP-2 on platelet activation, and one nanobody not inhibiting MMP-2 activity (VHH-136) which, chemically conjugated to a fluorescent probe, allowed the detection of human MMP-2 by flow-cytometry and immune-cytochemistry. In conclusion, we have generated and characterized two new nanotechnological molecular tools for human MMP-2 which represent promising agents for the study of MMP-2 in cardiovascular pathophysiology.

Design of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations

Pseudolysin (PLN) is a metalloproteinase secreted from bacteria that degrades extracellular proteins to produce bacterial nutrition. It is thus expected that inhibitors against PLN can suppress the growth of bacteria and their pandemic spread. In addition, since these inhibitors do not attack to bacteria directly, there is a reduced risk for producing drug-resistant bacteria. On the other hand, as PLN has large structural similarity in the active sites with human matrix-metalloproteinases (MMPs), there is a possibility that the inhibitors for PLN also inhibit MMP activity, resulting in a loss of necessary nutrients to be produced by MMPs. Therefore, it is required the agents inhibiting the activity of only PLN not MMPs. In the present study, we employed a hydroxamate compound galardin, which has a significant inhibition effect against PLN and MMP, and investigated its specific interactions with PLN/MMP at atomic and electronic levels, by use of ab initio molecular simulations. Based on the results, we proposed several derivatives of galardin and elucidated which derivatives that can bind more strongly to PLN and be putative antimicrobial agents capable of inhibiting the PLN activity.Communicated by Ramaswamy H. Sarma

Conformation and Domain Movement Analysis of Human Matrix Metalloproteinase-2: Role of Associated Zn2+ and Ca2+ Ions.

Matrix metaloproteinase-2 (MMP-2) is an extracellular Zn2+ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed ten families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamic cross-correlation analysis indicated domain movements corresponding to the opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the molecular mechanics Poisson Boltzman surface area-interaction entropy (MMPBSA-IE) analysis method and revealed strong binding energies for the catalytic Zn2+ ion 1, Ca2+ ion 1, and Ca2+ ion 3 with significant conformational stability at the binding sites of Zn2+ ion 1 and Ca2+ ion 1. Ca2+ ion 2 diffuses freely away from its crystallographically defined binding site. Zn2+ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca2+ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain; however, the interacting residue sidechain carboxyl groups are outside of Ca2+ ion 3′s coordination sphere.

A systematic computational analysis of human matrix metalloproteinase 13 (MMP-13) crystal structures and structure-based identification of prospective drug candidates as MMP-13 inhibitors repurposable for osteoarthritis

Osteoarthritis (OA) is the most common form of arthritis with no available disease-modifying treatments, and is a major cause of disability. Matrix metalloproteinase 13 (MMP-13) is vital for OA progression and thus, inhibition of MMP-13 is an effective strategy to treat OA. Since the past few decades, drug repurposing has gained substantial popularity worldwide as a time- and cost-effective approach to find new indications for the existing drugs. Therefore, more than 40 X-ray co-crystal structures of the human MMP-13 with bound inhibitors are investigated to gain the structural insights such as conserved direct interactions with binding site residues, namely Ala-238, Thr-245 and Thr-247. Afterwards, enrichment study using active and decoy set of ligands revealed three MMP-13 structures (PDB-IDs: 1XUC, 3WV1 and 5BPA) with optimal enrichment performance. Docking-based screening of existing drugs against the three crystal structures followed by binding free-energy calculation suggested drugs namely eltrombopag, cilostazol and domperidone as potential MMP-13 inhibitors that need further experimental validation. These insights may serve as a potential starting point of further experimental validation and structure-based drug design/repurposing of MMP-13 inhibitors for the treatment of OA. Abbreviations 2D two-dimensional 3D three-dimensional FDA Food and Drug Administration MM-GBSA Molecular Mechanics Generalized Born Surface Area MMPs matrix metalloproteinases MMP-13 matrix metalloproteinase 13 NMR nuclear magnetic resonance OA osteoarthritis PDB Protein Data Bank PDB-ID Protein Data Bank ID PLIP protein–ligand interaction profiler ROC receiver operating characteristic, RMSD root mean square deviation Communicated by Ramaswamy H. Sarma

Protective Role of Matrix Metalloproteinase-2 in Allergic Bronchial Asthma.

Inflammation, reversible obstruction, and hyperresponsiveness of the airways are characteristic findings of bronchial asthma. Several evidence has demonstrated the involvement of matrix metalloproteinase-2 in allergic airway inflammation. Matrix metalloproteinase-2 may promote aberrant tissue remodeling in late stages of allergic airway inflammation. However, whether matrix metalloproteinase-2 is detrimental or protective in early stages of allergic airway inflammation remains unclear. To evaluate this here we compared the severity of allergic bronchial asthma between mice overexpressing human matrix metalloproteinase-2 and wild type mice. After sensitization and challenge with an allergen, mice overexpressing the human matrix metalloproteinase-2 showed a significant reduction in airway hyperresponsiveness and in the expression of Th2 cytokines and IgE compared to their wild type counterparts. An inhibitor of matrix metalloproteinases abolished this beneficial effect of human matrix metalloproteinase-2 overexpression. Allergen-sensitized and challenged human matrix metalloproteinase-2 transgenic mice had enhanced percentage of M1 macrophages with increased expression of inducible nitric oxide synthase and STAT1 activation in the lungs compared to their wild type counterparts. There was no difference in the percentage of regulatory T cells between mouse groups. The results of this study showed that matrix metalloproteinase-2 is protective in allergic bronchial asthma by promoting polarization of macrophages to M1 phenotype.

Changes in the Matrix Metalloproteinase 9 Point-of-Care Test Positivity According to MMP-9 Concentration and Loading Volume.

To measure changes in the matrix metalloproteinase 9 (MMP-9) point-of-care test, InflammaDry (Rapid Pathogen Screening, Inc, Sarasota, FL) positivity, based on ocular surface MMP-9 concentrations and loading volume. Two different MMP-9 products, preform and active, were analyzed using the InflammaDry test, detecting MMP-9 levels of more than 40 ng/mL of both preform and active MMP-9. Preform MMP-9 (Natural human MMP-9 protein; Abcam, Cambridge, UK) was analyzed at different concentrations (50, 100, 500, 1000, and 1500 ng/mL) and loading volumes (5, 10, and 20 μL). Active MMP-9 (Human MMP-9 protein; Novus Biologicals, Littleton, CO) was also analyzed using the InflammaDry test at different concentrations (50 and 100 ng/mL) and loading volumes (10, 20, and 40 μL). Natural human MMP-9 protein (preform) of 50, 100, and 500 ng/mL exhibited negative results for every loading volume. At 1000 ng/mL, the 20 μL volume was positive, whereas the 5 and 10 μL volumes were negative. At 1500 ng/mL, all loading volumes were positive, but the density of positive bands varied depending on the loading volume; larger loading volumes had higher band density. Human MMP-9 protein (active) of 50 ng/mL was negative for every loading volume. In 100 ng/mL, the 20 and 40 μL volumes showed positive results with similar positive band densities. The InflammaDry test had a different detection range depending on MMP-9 formulas; higher concentrations of preform MMP-9 protein were needed to yield positive results. In addition, InflammaDry positivity varied based on the loading volumes. Clinicians should be aware of the possibility of false negatives with low tear volumes despite elevated MMP-9 concentrations.

Predictive models of protease specificity based on quantitative protease-activity profiling data

Bioinformatics-based prediction of protease substrates can help to elucidate regulatory proteolytic pathways that control a broad range of biological processes such as apoptosis and blood coagulation. The majority of published predictive models are position weight matrices (PWM) reflecting specificity of proteases toward target sequence. These models are typically derived from experimental data on positions of hydrolyzed peptide bonds and show a reasonable predictive power. New emerging techniques that not only register the cleavage position but also measure catalytic efficiency of proteolysis are expected to improve the quality of predictions or at least substantially reduce the number of tested substrates required for confident predictions. The main goal of this study was to develop new prediction models based on such data and to estimate the performance of the constructed models. We used data on catalytic efficiency of proteolysis measured for eight major human matrix metalloproteinases to construct predictive models of protease specificity using a variety of regression analysis techniques. The obtained results suggest that efficiency-based (quantitative) models show a comparable performance with conventional PWM-based algorithms, while less training data are required. The derived list of candidate cleavage sites in human secreted proteins may serve as a starting point for experimental analysis.

Circadian protein BMAL1 promotes breast cancer cell invasion and metastasis by up-regulating matrix metalloproteinase9 expression

BackgroundMetastasis is an important factor in the poor prognosis of breast cancer. As an important core clock protein, brain and muscle arnt-like 1 (BMAL1) is closely related to tumorigenesis. However, the molecular mechanisms that mediate the role of BMAL1 in invasion and metastasis remain largely unknown. In this study, we investigated the BMAL1 may take a crucial effect in the progression of breast cancer cells.MethodsBMAL1 and MMP9 expression was measured in breast cell lines. Transwell and scratch wound-healing assays were used to detect the movement of cells and MTT assays and clonal formation assays were used to assess cells’ proliferation. The effects of BMAL1 on the MMP9/NF-κB pathway were examined by western blotting, co-immunoprecipitation and mammalian two-hybrid.ResultsIn our study, it showed that cell migration and invasion were significantly enhanced when overexpressed BMAL1. Functionally, overexpression BMAL1 significantly increased the mRNA and protein level of matrix metalloproteinase9 (MMP9) and improved the activity of MMP9. Moreover, BMAL1 activated the NF-κB signaling pathway by increasing the phosphorylation of IκB and promoted human MMP9 promoter activity by interacting with NF-kB p65, leading to increased expression of MMP9. When overexpressed BMAL1, CBP (CREB binding protein) was recruited to enhance the activity of p65 and further activate the NF-κB signaling pathway to regulate the expression of its downstream target genes, including MMP9, TNFα, uPA and IL8, and then promote the invasion and metastasis of breast cancer cells.ConclusionsThis study confirmed a new mechanism by which BMAL1 up-regulated MMP9 expression to increase breast cancer metastasis, to provide research support for the prevention and treatment of breast cancer.