Structural basis for matrix metalloproteinase 1-catalyzed collagenolysis

The proteolysis of collagen triple-helical structure (collagenolysis) is a poorly understood yet critical physiological process. Presently, matrix metalloproteinase 1 (MMP-1) and collagen triple-helical peptide models have been utilized to characterize the events and calculate the energetics of collagenolysis via NMR spectroscopic analysis of 12 enzyme-substrate complexes. The triple-helix is bound initially by the MMP-1 hemopexin-like (HPX) domain via a four amino acid stretch (analogous to type I collagen residues 782-785). The triple-helix is then presented to the MMP-1 catalytic (CAT) domain in a distinct orientation. The HPX and CAT domains are rotated with respect to one another compared with the X-ray "closed" conformation of MMP-1. Back-rotation of the CAT and HPX domains to the X-ray closed conformation releases one chain out of the triple-helix, and this chain is properly positioned in the CAT domain active site for subsequent hydrolysis. The aforementioned steps provide a detailed, experimentally derived, and energetically favorable collagenolytic mechanism, as well as significant insight into the roles of distinct domains in extracellular protease function.     

From the X-ray compact structure to the elongated form of the full-length MMP-2 enzyme in solution: a molecular dynamics study

Current understanding on the collagenolytic activity performed by the MMPs assumes some degree of relative motion between the catalytic and the hemopexin-like domains of the enzyme. However, all the crystal structures available for the full-length enzymes display a compact arrangement of the protein domains. Herein, we employ Molecular Dynamics simulations to investigate the structure of the full-length MMP-2 enzyme in aqueous solution. This simulation, together with previous experimental results that have been obtained very recently for the MMP-9 and MMP-12 enzymes, gives strong support to the hypothesis that the interdomain dynamics of the MMP enzymes in solution can result in a manifold of conformations including some structures with a large interdomain separation. The simulation of MMP-2 provides also a detailed molecular picture of the structures involved in the transition from the compact X-ray arrangement to the extended form in solution. Such information could be helpful in future studies of the regulation and/or the collagenolytic activity of these important enzymes.     

Catalytic mechanism of matrix metalloproteinases: two-layered ONIOM study

The two-layered ONIOM(B3LYP:MNDO) method has been used to investigate the hydrolytical mechanism of matrix metalloproteinases (MMPs), a large family of zinc-dependent endopeptidases capable of degrading a wide range of macromolecules of the extracellular matrix. Human stromelysin-1 (MMP-3) was chosen as a physiologically important member of the MMP family. As a structural reference, X-ray data on the stromelysin-1 catalytic domain (SCD) complexed to the transition state analogue diphenyl piperidine sulfonamide inhibitor was used. The backbone spacer of 11 residues (201-211) was included in the final model, spanning the catalytic Glu202 residue and the three structural His201,205,211 zinc ligands. The polypeptide framework incorporated, partly accounting for the protein rigidity, reduces the activation free energy slightly by 1.6 kcal/mol. Essentially a single-step catalytic mechanism was obtained, generally following a classical proposal for MMPs. Glu202 here acts as a base, abstracting a proton from the metal-bound reactant water and delivering this proton to the peptide nitrogen. An auxiliary water molecule is suggested to be of crucial importance acting as an electrophilic agent to the carbonyl oxygen of the substrate. The direct inclusion of the auxiliary water molecule decreases the activation free energy by about 5 kcal/mol via donation of a strong hydrogen bond. The calculated activation barrier of 13.1 kcal/mol agrees well with experimental rates.     

Structural basis for the highly selective inhibition of MMP-13

Inhibitors for matrix metalloproteinases (MMPs) are under investigation for the treatment of cancer, arthritis, and cardiovascular disease. Here, we report a class of highly selective MMP-13 inhibitors (pyrimidine dicarboxamides) that exhibit no detectable activity against other MMPs. The high-resolution X-ray structures of three molecules of this series bound to MMP-13 reveal a novel binding mode characterized by the absence of interactions between the inhibitors and the catalytic zinc. The inhibitors bind in the S1' pocket and extend into an additional S1' side pocket, which is unique to MMP-13. We analyze the determinants for selectivity and describe the rational design of improved compounds with low nanomolar affinity.     

Activity of anchored human matrix metalloproteinase-1 catalytic domain on Au (111) surfaces monitored by ESI-MS

Matrix metalloproteinases (MMPs) are a family of Zn-dependent endo-peptidases known for their ability to cleave several components of the extracellular matrix, but which can also cleave many non-matrix proteins. There are many evidences that MMPs are involved in physiological and pathological processes, and a huge effort has been put in the development of possible inhibitors that could reduce the activity of MMPs, as it is clear that the ability to monitor and control such activity plays a pivotal role in the search for potential drugs aimed at finding a cure for several diseases such as pulmonary emphysema, rheumatoid arthritis, fibrotic disorders and cancer.A powerful method currently available to study enzyme-inhibitor interactions is based on the use of the surface plasmon resonance (SPR) technique. When MMP interactions are studied, a procedure by which inhibitors are normally anchored on sensor chips and SPR technique is used in order to study their interaction with MMPs molecules is usually followed. This is because it is currently believed that MMPs cannot be anchored on the sensor-chip surface without losing their activity. However, this approach gives rise to problems, as the anchoring of low-molecular-weight inhibitors on gold surfaces easily affects their ability to interact with MMPs. For this reason, the anchoring of MMPs is highly desirable.A new experimental protocol that couples the Fourier transform-SPR (FT-SPR) technique with electrospray ionization-mass spectroscopy (ESI-MS) is described here for the evaluation of the activity of MMP-1 catalytic domain (cdMMP-1) anchored on gold surfaces. The cdMMP-1 surface coverage is calculated by using FT-SPR and the enzyme activity is estimated by ESI-MS. The proposed method is label-free.     

Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases

X-ray analyses of matrix metalloproteinases (MMPs) have shown that the catalytic zinc ion (Zn1) can bind to one to three water molecules in addition to three conserved histidine residues. To estimate the relative stability of the possible Zn1 coordination structures in the active site of the MMPs, we carry out computational analyses on the coordination environment of the Zn1 ion in the gelatinase A enzyme (or matrix metalloproteinase 2; MMP-2). Four-, five-, and six-coordinated complexes representative of the Zn1 site are fully characterized by means of quantum mechanical (QM) methodologies. On one hand, B3LYP/LACVP* minimizations of various cluster models of the MMP-2 active site show that the trigonal bipyramidal geometry is energetically favored in the gas phase and that continuum solvent effects stabilize preferentially the tetrahedral complexes. On the other hand, B3LYP/OPLS-AA hybrid QM/molecular mechanical calculations in the solvated catalytic domain of the MMP-2 enzyme complemented with electrostatic Poisson-Boltzmann calculations show that the mature enzyme presents most likely a Zn1 ion coordinated by three histidine residues and two water molecules, while the active site glutamic acid is negatively charged. In consonance with X-ray diffraction data, other possible Zn1 configurations, a six-coordinated structure with Zn1-water as well as four- and five-coordinated complexes with a Zn1-bound hydroxide, are predicted to be very close in energy.     

基质金属蛋白酶活性中心肽段的合成及纯化

基质金属蛋白酶(MMPs)是一类生物活性依赖于钙锌离子,能降解细胞外基质(extracellar matrix,ECM)的酶家族.目前已发现26个成员,越来越多的研究表明,MMPs在肿瘤侵袭转移中起着重要作用,此作用不仅仅限于它有利于细胞外基质的降解,还对肿瘤微环境的维持和促进肿瘤生长起着重要作用[1].     

Modeling of enzyme–substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10

The matrix metalloproteases (MMPs) and the ADAMs (A Disintegrin And Metalloprotease domain) are proteolytic enzyme families containing a catalytic zinc ion, that are implicated in a variety of normal and pathological processes involving tissue remodeling and cancer. Synthetic MMP inhibitors have been designed for applications in pathological situations. However, a greater understanding of substrate binding and the catalytic mechanism is required so that more effective and selective inhibitors may be developed for both experimental and clinical purposes. By modeling a natural substrate spanning P4-P4' in complex with the catalytic domains, we aim to compare substrate-specificities between Stromelysin-1 (MMP-3), ADAM-9 and ADAM-10, with the aid of molecular dynamics simulations. Our results show that the substrate retains a favourable antiparallel beta-sheet conformation on the P-side in addition to the well-known orientation of the P'-region of the scissile bond, and that the primary substrate selectivity is dominated by the sidechains in the S1' pocket and the S2/S3 region. ADAM-9 has a hydrophobic residue as the central determinant in the S1' pocket, while ADAM-10 has an amphiphilic residue, which suggests a different primary specificity. The S2/S3 pocket is largely hydrophobic in all three enzymes. Inspired by our molecular dynamics calculations and supported by a large body of literature, we propose a novel, hypothetical, catalytic mechanism where the Zn-ion polarizes the oxygens from the catalytic glutamate to form a nucleophile, leading to a tetrahedral oxyanion anhydride transition state.     

Enzymatic inhibitory activity of Ficus deltoidea leaf extract on matrix metalloproteinase-2, 8 and 9

Dysregulation of matrix metalloproteinases (MMPs) activity is known in many pathological conditions with which most of the conditions are related to elevate MMPs activities. Ficus deltoidea (FD) is a plant known for its therapeutic properties. In order to evaluate the therapeutic potential of FD leaf extract, we study the enzymatic inhibition properties of FD leaf extract and its major bioactive compounds (vitexin and isovitexin) on a panel of MMPs (MMP-2, MMP-8 and MMP-9) using experimental and computational approaches. FD leaf extract and its major bioactive compounds showed pronounced inhibition activity towards the MMPs tested. Computational docking analysis revealed that vitexin and isovitexin bind to the active site of the three tested MMPs. We also evaluated the cytotoxicity and cell migration inhibition activity of FD leaf extract in the endothelial EA.hy 926 cell line. Conclusively, this study provided additional information on the potential of FD leaf extract for therapeutical application.     

A new methodology for monitoring the activity of cdMMP-12 anchored and freeze-dried on Au (111)

Matrix metalloproteinases (MMPs) are cell-secreted soluble and membrane-tethered enzymes that are capable of degrading extracellular matrix proteins, but also can process a number of bioactive molecules. They are involved in the cleavage of cell surface receptors, but are also thought to play a major role on cell behaviors as well as in diverse physiological and pathological processes, including embryonic development, wound repair, inflammatory diseases, and cancer. For these reasons, it is obvious that a control over MMPs activity is highly desirable. Consequently, the frantic search for new inhibitors has been coupled to the development of high-throughput methods able to rapidly screen the effect of possible MMP inhibitors on the activity of these enzymes. In this scenario, solid-state—based methods play a major role because of their compatibility with array formats that are able to extract more information from smaller sample volumes and offer some important advantages that are not available in the standard solution assays. In this work, the catalytic domain of MMP-12 was immobilized on a gold substrate and the surface coverage was measured by FT-SPR experiments. A new experimental procedure was developed to freeze-dry the anchored molecules and their activity was measured by ESI-MS. The kinetics parameters obtained for the immobilized enzyme are in good accordance with those reported for similar systems in solution. Inhibition of the immobilized molecules was also carried out, demonstrating the applicability of the method for rapid screening of MMP inhibitors.     

Triple-helical transition state analogues: a new class of selective matrix metalloproteinase inhibitors

Alterations in activities of one family of proteases, the matrix metalloproteinases (MMPs), have been implicated in primary and metastatic tumor growth, angiogenesis, and pathological degradation of extracellular matrix (ECM) components, such as collagen and laminin. Since hydrolysis of the collagen triple-helix is one of the committed steps in ECM turnover, we envisioned modulation of collagenolytic activity as a strategy for creating selective MMP inhibitors. In the present study, a phosphinate transition state analogue has been incorporated within a triple-helical peptide template. The template sequence was based on the alpha1(V)436-450 collagen region, which is hydrolyzed at the Gly(439)-Val(440) bond selectively by MMP-2 and MMP-9. The phosphinate acts as a tetrahedral transition state analogue, which mimics the water-bound peptide bond of a protein substrate during hydrolysis. The phosphinate replaced the amide bond between Gly-Val in the P1-P1' subsites of the triple-helical peptide. Inhibition studies revealed Ki values in the low nanomolar range for MMP-2 and MMP-9 and low to middle micromolar range for MMP-8 and MMP-13. MMP-1, MMP-3, and MT1-MMP/MMP-14 were not inhibited effectively. Melting of the triple-helix resulted in a decrease in inhibitor affinity for MMP-2. The phosphinate triple-helical transition state analogue has high affinity and selectivity for the gelatinases (MMP-2 and MMP-9) and represents a new class of protease inhibitors that maximizes potential selectivity via interactions with both prime and nonprime active site subsites as well as with secondary binding sites (exosites).     

Activity-based enrichment of matrix metalloproteinases using reversible inhibitors as affinity ligands

Matrix metalloproteinases (MMPs) are zinc dependent metalloproteases characterized by the ability to cleave extracellular matrix and many other extracellular proteins. MMP activity is tightly regulated but disturbances in this regulation can contribute to various disease processes characterized by a progressive destruction of the extracellular matrix. The ability to profile classes of enzymes based on functionally related activities would greatly facilitate research about the involvement of MMPs in physiological and/or pathological states. Here we describe the characterization of an affinity sorbent using an immobilized reversible inhibitor as a stationary phase for the activity-based enrichment of MMPs from biological samples. With a ligand density of 9.8 mM and binding constant of 58 micromol/l towards MMP-12, the capturing power of the affinity sorbent was strong enough to extract MMP-12 spiked into serum with high selectivity from relatively large sample volumes. Experiments with endogenous inhibitors revealed that MMP-12 extraction is strictly activity-dependent, offering powerful means to monitor MMP activities in relation to physiological and/or pathological events by using affinity extraction as a first step in an MMP profiling method.     

Matrix metalloproteinases in lung diseases

Matrix metalloproteinases (MMPs) are a pivotal family of zinc enzymes responsible for degradation of the extracellular matrix (ECM) components including basement membrane collagen, interstitial collagen, fibronectin, and various proteoglycans, during normal remodeling and repair processes. The potent proteolytic activities of MMPs is mainly regulated by the balance with specific tissue inhibitors of Matrix metalloproteinases (TIMP). Excessive or inappropriate expression of MMP may contribute to the pathogenesis of tissue destructive processes in a wide variety of diseases including lung diseases. Although the precise mechanisms are still unknown, the contribution of individual MMPs are worth investigating in seeking the pathogenesis of various lung diseases such as lung cancer, bronchial asthma, chronic obstructive pulmonary disease, acute lung injury, pulmonary hypertension and interstitial lung diseases. In particular, the close association of each lung disease with the destructive effects of gelatinase A and B (also called MMP-2 and MMP-9) on the basement membrane in early alveolar remodeling, and that of collagenase-1 (MMP-1) on the major interstitial structural protein of ECM have received considerable attention. The interaction of MMPs with chemical mediators and inflammatory cytokines has also been reported in some recent studies. Several promising therapeutic approaches to inhibit MMPs have just started in the field of oncology, while more specific MMP inhibitors may be required for further investigation in other fields of lung diseases. In this review, the main focus is on the recent clinical and experimental findings and the contributions of MMPs and/or TIMPs in the lung diseases.     

In vitro and in vivo inhibition of skin matrix metalloproteinases by Pothomorphe umbellata root extract

Exposure to UV radiation up-regulates the synthesis of matrix metalloproteinases (MMPs), a group of matrix-degrading enzymes. MMPs are regarded as promising therapeutic targets and the development of effective inhibitors is an important research focus. The plant Pothomorphe umbellata has been shown to exert a potent antioxidant activity on the skin and to delay the onset and reduce the incidence of UVB-induced chronic skin damage. The aim of the present study was to determine the effect of P. umbellata ethanolic root extract on MMP-2 and MMP-9. The in vitro inhibition of MMP-2 and MMP-9 was measured by gelatin zymography in the presence of different concentrations of P. umbellata extract, as well as in the presence of its isolated active principle 4-nerolidylcatechol (4-NC). The inhibitory effect of the P. umbellata extract was stronger than that of 4-NC. Gelatin zymography and histological analysis revealed that P. umbellata was able to inhibit constitutive MMP-9 activity in vivo in mice sacrificed 2 h after UVB irradiation. The intensity of the MMP-2 band was unchanged. Our data contribute to the elucidation of the mechanism of prevention of photoaging by P. umbellata and may provide a rational basis for the use of this plant in prophylaxis against and treatment of skin cancer.     

α-卤代丁二酰氧肟酸类基质金属蛋白酶抑制剂的合成及活性评价

基质金属蛋白酶(MMPs)是一族Zn2+依赖的蛋白水解酶. 该族酶的过度表达与多种病理过程密切相关, 因此其抑制剂可用于这些疾病的治疗. 本文设计合成了15个α-卤代丁二酰氧肟酸类新型基质金属蛋白酶抑制剂, 经核磁共振氢谱和质谱进行了结构表征, 并以伊洛马司他(Ilomastat)为阳性对照, 分别测定了它们对基质金属蛋白酶MMP-2和MMP-9的体外抑制活性. 结果显示, 4个化合物对MMP-2的抑制活性与阳性对照相当; 5个化合物对MMP-9的抑制活性与对照药相当.     

Chip gel electrophoresis as a tool for study of matrix metalloproteinase 9 interaction with metallothionein

Matrix metalloproteinases (MMPs) play numerous roles in physiological and pathological processes including cancer. Interactions of MMPs with other zinc-binding proteins are of great interest mainly from the point of view of the participation of these proteins in carcinogenesis. The aim of this study was to utilize chip gel electrophoresis for investigation of matrix metalloproteinase 9 (gelatinase B, MMP-9) interactions with collagen. The interaction was observed and the effect of temperature was tested. We further focused on the study of activation of MMP-9 by the presence of zinc-binding proteins called metallothioneins (MT). We confirmed the basic presumption of the activation of MMP-9 by the presence of MT similar to the temperature effect. Moreover, we chose the method of differential pulse voltammetry Brdicka reaction to verify our results. It can be concluded that the activity of MMP-9 was higher in the presence of MT in comparison with the experimental collagen(type I)-MMP-9 mixture in vitro.     

Screening a Panel of Topical Ophthalmic Medications against MMP-2 and MMP-9 to Investigate Their Potential in Keratoconus Management

Keratoconus (KC) is a serious disease that can affect people of any race or nationality, although the exact etiology and pathogenic mechanism are still unknown. In this study, thirty-two FDA-approved ophthalmic drugs were exposed to virtual screening using docking studies against both the MMP-2 and MMP-9 proteins to find the most promising inhibitors as a proposed computational mechanism to treat keratoconus. Matrix metalloproteinases (MMPs) are zinc-dependent proteases, and MMP inhibitors (MMPIs) are usually designed to interact with zinc ion in the catalytic (CAT) domain, thus interfering with enzymatic activity. In our research work, the FDA-approved ophthalmic medications will be investigated as MMPIs, to explore if they can be repurposed for KC treatment. The obtained findings of the docking study suggest that atenolol and ampicillin are able to accommodate into the active sites of MMP-2 and MMP-9. Additionally, both exhibited binding modes similar to inhibitors used as references, with an ability to bind to the zinc of the CAT. Molecular dynamic simulations and the MM-GBSA binding free-energy calculations revealed their stable binding over the course of 50 ns. An additional pharmacophoric study was carried out on MMP-9 (PDB ID: 1GKC) using the co-crystallized ligand as a reference for the future design and screening of the MMP-9 inhibitors. These promising results open the door to further biological research to confirm such theoretical results.     

Upregulation of extracellular matrix metalloproteinase inducer (EMMPRIN) and gelatinases in human atherosclerosis infected with Chlamydia pneumoniae: the potential role of Chlamydia pneumoniae infection in the progression of atherosclerosis

Chlamydia pneumoniae infection implicated as an important etiologic factor of atherosclerosis, especially in coronary artery disease (CAD), was found in vitro to be associated with the induction of matrix metalloproteinases (MMPs). An extracellular matrix metalloproteinase inducer (EMMPRIN)/ membrane-type 1 matrix metalloproteinase (MT1-MMP) system which induces and activates MMPs, is suggested to be functional and were upregulated in the failing myocardium. However, the upstream regulation of MMPs by C. pneumoniae within atheroma itself remains unclear. We evaluated the seroepidemiologic study of C. pneumoniae infection in CAD patients (n= 391) and controls (n=97) and performed histopathological and in vitro analysis in atherosclerotic vascular tissues obtained from patients with seropositive to C. pneumoniae (n=20), by using immunochemistry for C. pneumoniae, EMMPRIN/MT1-MMP, MMP-2, and MMP-9. The seropositive rates of both anti-C. pneumoniae IgG and IgA were 56.7% in CAD group and 43.3% in control group (P=0.033). Seropositive rate was increased in subgroups of CAD patients without conventional coronary risk factors compared to those with conventional risk factors. Immunoreactivities of EMMPRIN, MT1-MMP, MMP-2, and MMP-9 were increased in the atheromatous plaque itself, predominantly in immunoreactive macrophages/mononuclear cells to C. pneumoniae. Furthermore, Western blot analysis showed that EMMPRIN and MMP-2 were detected more prominently in atherosclerotic tissues infected with C. pneumoniae compared to control tissues. Zymographic analysis revealed that activities of MMP-2 and MMP-9 were more increased in atherosclerotic tissues infected with C. pneumoniae compared to control tissues. The present study demonstrated upstream regulation of MMPs can be induced by C. pneumoniae within atheromatous plaque itself. These findings help to understand the potential role of C. pneumoniae in the progression of atherosclerosis.     

Expression Optimization and Characterization of the Catalytic Domain of Human MT3-MMP

Introduction Matrixmetalloproteinases(MMPs)areafamilyof calciumandzincrequiringendoproteinasesthattogether candegradeallthemaincomponentsoftheextra cellu larmatrixandbasementmembranes[1].MMPsarein volvedinawiderangeofproteolyticevents,innormal andpatholog…     

Iridoid glycosides-Kutkin,Picroside I,and Kutkoside from Picrorrhiza kurroa Benth inhibits the invasion and migration of MCF-7 breast cancer cells through the down regulation of matrix metalloproteinases: 1st Cancer Update

Ethnopharmacological relevanceIridoid glycosides have been associated with decreased risks of cancer, such as hepatocarcinoma. Although Picrorrhiza kurroa has shown activity against hepatocarcinogenesis, its mechanism of action is poorly understood, further the anticancer activity of iridoid glycosides present in this plant has not been tested so far.Aim of the studyHere, MCF-7 cell lines (Human breast cancer) were used to test whether P. kurroa extract (PE) and its isolated iridoid glycosides Picroside I (PS), Kutkoside (KS), and Kutkin (KT) exerts the anti-invasion activity via down-regulation of the expression of matrix metalloproteinases (MMPs). MMPs play an important role in solid tumor invasion and migration.Materials and methodsThe activity and expression of gelatinases (MMP-2 and MMP-9) and collagenases (MMP-1 and MMP-13), protein, and mRNA were detected by gelatin zymography, and RT-PCR. The migratory and invasive capacities of MCF-7 cell lines were measured by the wound scratch migration assay. The preliminary cytotoxicity testing was done by MTT assay and propidium iodide staining. Further the inhibition of inflammatory mediators was also done by quantification of nitrite inflammatory mediators.ResultsThe study showed that PE and its isolated iridoids glycosides PS, KS, and KT exhibited considerable cytotoxic potential in a dose-dependent manner. Further PE, PS, KS, and KT inhibited MCF-7 cell invasion and migration, and decreased MMP-2, 9 and MMP-1, 13 activities. Furthermore, PS, KS, and KT reduced MMPs expression at protein and mRNA levels, and suppression of the inflammatory mediators was also exhibited.ConclusionsOur results suggest that PS, KS, and KT may be the valuable anti-invasive drug candidates for cancer therapy by suppressing Collagenases and Gelatinases. PS, KS, and KT showed good results in comparison with PE. PS and KS exhibit almost comparable down regulation while KT exhibited maximum suppression of invasion, migration, and expression of MMPs.