X-ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: implications for inhibitor selectivity

Crohn's Disease: Basic Characteristics of the Disease, Diagnostic Methods, the Role of Biomarkers, and Analysis of Metalloproteinases: A Review

Crohn's disease is a chronic inflammatory bowel disease that affects the ileum and/or large intestine. At the same time, it can also affect any other part of the human body, i.e., from the mouth to the anus. In Crohn's disease, the physiology and functioning of the epithelial barrier are inhibited due to the correlation of various factors, such as the environment, genetic susceptibility or intestinal microbiota. The symptoms are very troublesome and cause a significant reduction in quality of life, sometimes occurring with paralyzing permanent damage to the digestive tract, requiring enteral or parenteral nutrition throughout life. In order to make a proper and accurate diagnosis, an appropriately selected diagnostic path in a given clinical entity is necessary. Standard diagnostic methods are: laboratory examination, histopathological examination, endoscopic examination, X-ray, computed tomography, ultrasound examination and magnetic resonance imaging. Medical biology and the analysis of metalloproteinases have also proved helpful in diagnosing changes occurring as a result of Crohn's disease. Here we provide a thorough review of the latest reports on Crohn's disease and its genetic conditions, symptoms, morphology, diagnosis (including the analysis of Crohn's disease biomarkers, i.e., metalloproteinases) and treatment.

MetalProGNet: a structure-based deep graph model for metalloprotein-ligand interaction predictions

Metalloproteins play indispensable roles in various biological processes ranging from reaction catalysis to free radical scavenging, and they are also pertinent to numerous pathologies including cancer, HIV infection, neurodegeneration, and inflammation. Discovery of high-affinity ligands for metalloproteins powers the treatment of these pathologies. Extensive efforts have been made to develop in silico approaches, such as molecular docking and machine learning (ML)-based models, for fast identification of ligands binding to heterogeneous proteins, but few of them have exclusively concentrated on metalloproteins. In this study, we first compiled the largest metalloprotein-ligand complex dataset containing 3079 high-quality structures, and systematically evaluated the scoring and docking powers of three competitive docking tools (i.e., PLANTS, AutoDock Vina and Glide SP) for metalloproteins. Then, a structure-based deep graph model called MetalProGNet was developed to predict metalloprotein-ligand interactions. In the model, the coordination interactions between metal ions and protein atoms and the interactions between metal ions and ligand atoms were explicitly modelled through graph convolution. The binding features were then predicted by the informative molecular binding vector learned from a noncovalent atom-atom interaction network. The evaluation on the internal metalloprotein test set, the independent ChEMBL dataset towards 22 different metalloproteins and the virtual screening dataset indicated that MetalProGNet outperformed various baselines. Finally, a noncovalent atom-atom interaction masking technique was employed to interpret MetalProGNet, and the learned knowledge accords with our understanding of physics.

The immunomodulatory role of matrix metalloproteinases in colitis-associated cancer

Matrix metalloproteinases (MMPs) are an important class of enzymes in the body that function through the extracellular matrix (ECM). They are involved in diverse pathophysiological processes, such as tumor invasion and metastasis, cardiovascular diseases, arthritis, periodontal disease, osteogenesis imperfecta, and diseases of the central nervous system. MMPs participate in the occurrence and development of numerous cancers and are closely related to immunity. In the present study, we review the immunomodulatory role of MMPs in colitis-associated cancer (CAC) and discuss relevant clinical applications. We analyze more than 300 pharmacological studies retrieved from PubMed and the Web of Science, related to MMPs, cancer, colitis, CAC, and immunomodulation. Key MMPs that interfere with pathological processes in CAC such as MMP-2, MMP-3, MMP-7, MMP-9, MMP-10, MMP-12, and MMP-13, as well as their corresponding mechanisms are elaborated. MMPs are involved in cell proliferation, cell differentiation, angiogenesis, ECM remodeling, and the inflammatory response in CAC. They also affect the immune system by modulating differentiation and immune activity of immune cells, recruitment of macrophages, and recruitment of neutrophils. Herein we describe the immunomodulatory role of MMPs in CAC to facilitate treatment of this special type of colon cancer, which is preceded by detectable inflammatory bowel disease in clinical populations.

Coordination environment changes of the vanadium in vanadium-dependent haloperoxidase enzymes

Vanadium-dependent haloperoxidases are a class of enzymes that catalyze oxidation reactions with halides to form halogenated organic products and water. These enzymes include chloroperoxidase and bromoperoxidase, which have very different protein sequences and sizes, but regardless the coordination environment of the active sites is surprisingly constant. In this manuscript, the comparison of the coordination chemistry of V-containing-haloperoxidases of the trigonal bipyramidal geometry was done by data mining. The catalytic cycle imposes changes in the coordination geometry of the vanadium to accommodate the peroxidovanadium(V) intermediate in an environment we describe as a distorted square pyramidal geometry. During the catalytic cycle, this intermediate converts to a trigonal bipyramidal intermediate before losing the halogen and forming a tetrahedral vanadium-protein intermediate. Importantly, the catalysis is facilitated by a proton-relay system supplied by the second sphere coordination environment and the changes in the coordination environment of the vanadium(V) making this process unique among protein catalyzed processes. The analysis of the coordination chemistry shows that the active site is very tightly regulated with only minor changes in the coordination geometry. The coordination geometry in the protein structures deviates from that found for both small molecules crystalized in the absence of protein and the reported functional small molecule model compounds. At this time there are no examples reported of a structurally similar small molecule with the geometry observed for the peroxidovanadium(V) in the active site of the vanadium-containing haloperoxidases.

Matrix metalloproteinases outside vertebrates

The matrix metalloproteinase (MMP) family belongs to the metzincin clan of zinc-dependent metallopeptidases. Due to their enormous implications in physiology and disease, MMPs have mainly been studied in vertebrates. They are engaged in extracellular protein processing and degradation, and present extensive paralogy, with 23 forms in humans. One characteristic of MMPs is a ~165-residue catalytic domain (CD), which has been structurally studied for 14 MMPs from human, mouse, rat, pig and the oral-microbiome bacterium Tannerella forsythia. These studies revealed close overall coincidence and characteristic structural features, which distinguish MMPs from other metzincins and give rise to a sequence pattern for their identification. Here, we reviewed the literature available on MMPs outside vertebrates and performed database searches for potential MMP CDs in invertebrates, plants, fungi, viruses, protists, archaea and bacteria. These and previous results revealed that MMPs are widely present in several copies in Eumetazoa and higher plants (Tracheophyta), but have just token presence in eukaryotic algae. A few dozen sequences were found in Ascomycota (within fungi) and in double-stranded DNA viruses infecting invertebrates (within viruses). In contrast, a few hundred sequences were found in archaea and >1000 in bacteria, with several copies for some species. Most of the archaeal and bacterial phyla containing potential MMPs are present in human oral and gut microbiomes. Overall, MMP-like sequences are present across all kingdoms of life, but their asymmetric distribution contradicts the vertical descent model from a eubacterial or archaeal ancestor. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.

Structural Studies of Matrix Metalloproteinase by X-Ray Diffraction

Matrix Metalloproteinases (MMPs) are a family of proteolytic enzymes whose endopeptidase activity is dependent on the presence of specific metal ions. MT1-MMP (or MMP-14), which has been implicated in tumor progression and cellular invasion, contains a membrane-spanning region located C-terminal to a hemopexin-like domain and an N-terminal catalytic domain. We recombinantly expressed the catalytic domain of human MT1-MMP in E. coli and purified it from inclusion bodies using a refolding protocol that yielded significant quantities of active protein. Crystals of MT1-MMP were obtained using the vapour diffusion method. Here, we describe the protocols used for crystallization and the data analysis together with the resulting diffraction pattern.

Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of membrane type 1 matrix metalloproteinase

Membrane type 1 matrix metalloproteinase (MT1-MMP) belongs to the large family of zinc-dependent endopeptidases termed MMPs that are located in the extracellular matrix. MT1-MMP was crystallized at 277 K using the vapour-diffusion method with PEG as a precipitating agent. Data sets for MT1-MMP were collected to 2.24 Å resolution at 100 K. The crystals belonged to space group P4(3)2(1)2, with unit-cell parameters a = 62.99, c = 122.60 Å. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (VM) of 2.90 Å(3) Da(-1); the solvent content is estimated to be 57.6%.

Cardiac matrix: a clue for future therapy

Cardiac muscle is unique because it contracts ceaselessly throughout the life and is highly resistant to fatigue. The marvelous nature of the cardiac muscle is attributed to its matrix that maintains structural and functional integrity and provides ambient micro-environment required for mechanical, cellular and molecular activities in the heart. Cardiac matrix dictates the endothelium myocyte (EM) coupling and contractility of cardiomyocytes. The matrix metalloproteinases (MMPs) and their tissue inhibitor of metalloproteinases (TIMPs) regulate matrix degradation that determines cardiac fibrosis and myocardial performance. We have shown that MMP-9 regulates differential expression of micro RNAs (miRNAs), calcium cycling and contractility of cardiomyocytes. The differential expression of miRNAs is associated with angiogenesis, hypertrophy and fibrosis in the heart. MMP-9, which is involved in the degradation of cardiac matrix and induction of fibrosis, is also implicated in inhibition of survival and differentiation of cardiac stem cells (CSC). Cardiac matrix is distinct because it renders mechanical properties and provides a framework essential for differentiation of cardiac progenitor cells (CPC) into specific lineage. Cardiac matrix regulates myocyte contractility by EM coupling and calcium transients and also directs miRNAs required for precise regulation of continuous and synchronized beating of cardiomyocytes that is indispensible for survival. Alteration in the matrix homeostasis due to induction of MMPs, altered expression of specific miRNAs or impaired signaling for contractility of cardiomyocytes leads to catastrophic effects. This review describes the mechanisms by which cardiac matrix regulates myocardial performance and suggests future directions for the development of treatment strategies in cardiovascular diseases.

Mechanism of the binding of Z-L-tryptophan and Z-L-phenylalanine to thermolysin and stromelysin-1 in aqueous solutions

The chemical shift of the carboxylate carbon of Z-tryptophan is increased from 179.85 to 182.82 ppm and 182.87 ppm on binding to thermolysin and stromelysin-1 respectively. The chemical shift of Z-phenylalanine is also increased from 179.5 ppm to 182.9 ppm on binding to thermolysin. From pH studies we conclude that the pK(a) of the inhibitor carboxylate group is lowered by at least 1.5 pK(a) units when it binds to either enzyme. The signal at ~183 ppm is no longer observed when the active site zinc atom of thermolysin or stromelysin-1 is replaced by cobalt. We estimate that the distance of the carboxylate carbon of Z-[1-(13)C]-L-tryptophan is ≤3.71Å from the active site cobalt atom of thermolysin. We conclude that the side chain of Z-[1-(13)C]-L-tryptophan is not bound in the S(2)' subsite of thermolysin. As the chemical shifts of the carboxylate carbons of the bound inhibitors are all ~183 ppm we conclude that they are all bound in a similar way most probably with the inhibitor carboxylate group directly coordinated to the active site zinc atom. Our spectrophotometric results confirm that the active site zinc atom is tetrahedrally coordinated when the inhibitors Z-tryptophan or Z-phenylalanine are bound to thermolysin.

Matrix metalloproteinases

Remodeling of extracellular matrix is crucial for many physiological (cell migration, proliferation, growth, and development) and pathological (remodeling of heart, carcinogenesis, metastasis, etc.) events. Thus, the interaction between cells and extracellular matrix plays a key role in normal development and differentiation of organism and many pathological states as well. Changes in extracellular matrix are regulated by a system of proteolytic enzymes that are responsible for proteolysis of huge quantity of extracellular matrix components. Matrix metalloproteinases (MMPs) represent the main group of regulating proteases in ECM. Ability of matrix metalloproteinases to modify the structural integrity of tissues is essential for certain aspects of normal physiology and pathology. The ability to process molecules such as growth factors, receptors, adhesion molecules, other proteinases, and proteinase inhibitors makes MMPs potent controllers of physiological and pathological events in the cell microenvironment. Overactivation of MMPs has been implicated in numerous disease states.

THEORETICAL STUDY ON POTENCY AND SELECTIVITY OF NOVEL NONPEPTIDE INHIBITORS OF MATRIX METALLOPROTEINASES MMP-2 AND MMP-9

Two novel matrix metalloproteinase (MMP) inhibitors, myricetin (m) and kaempferol (k), were found and the inhibitory activity is both in decreased order towards MMP-2 and MMP-9. To understand the mechanism during the processes when inhibitors bind to MMP-2 and MMP-9, molecular modeling, docking, and density functional theory (DFT) calculations were performed. The calculated results indicated that the hydroxyls on benzene ring of the inhibitors control the binding modes between inhibitors and MMPs, thus play an important role on the potency and selectivity. Besides coordinating with the N atoms of three His residues, Zn also interacts with a hydroxyl group of inhibitors by O – Zn distances of 2.66–2.78 Å in all of the docked complexes, so that the hydroxyl acts as a weak zinc binding group (ZBG). The DFT calculated results support the above analysis. The binding affinity calculations between inhibitors and MMPs present the total interaction energies in the m-MMP < k-MMP order and the solvation energy of myricetin is less than that of kaempferol, which reflect the experimental inhibitory activity.

A multidisciplinary approach to probing enthalpy-entropy compensation and the interfacial mobility model

In recent years, interfacial mobility has gained popularity as a model with which to rationalize both affinity in ligand binding and the often observed phenomenon of enthalpy-entropy compensation. While protein contraction and reduced mobility, as demonstrated by computational and NMR techniques respectively, have been correlated to entropies of binding for a variety of systems, to our knowledge, Raman difference spectroscopy has never been included in these analyses. Here, nonresonance Raman difference spectroscopy, isothermal titration calorimetry, and X-ray crystallography were utilized to correlate protein contraction, as demonstrated by an increase in protein interior packing and decreased residual protein movement, with trends of enthalpy-entropy compensation. These results are in accord with the interfacial mobility model and lend additional credence to this view of protein activity.

POVME: an algorithm for measuring binding-pocket volumes

Researchers engaged in computer-aided drug design often wish to measure the volume of a ligand-binding pocket in order to predict pharmacology. We have recently developed a simple algorithm, called POVME (POcket Volume MEasurer), for this purpose. POVME is Python implemented, fast, and freely available. To demonstrate its utility, we use the new algorithm to study three members of the matrix-metalloproteinase family of proteins. Despite the structural similarity of these proteins, differences in binding-pocket dynamics are easily identified.

Molecular modeling and biological effects of peptidomimetic inhibitors of TACE activity

We investigated the molecular basis of specificity for the interaction between tumor necrosis factor-alpha converting enzyme (TACE) and peptidomimetic inhibitors. Four novel peptidomimetic TACE inhibitors (8a-d) were designed and synthesized by introducing a substituted sulfur group and a hydrophobic group to a novel matrix metalloprotease (MMP) inhibitor. Inhibition was determined by in vitro lipopolysaccharide (LPS) cytotoxicity tests in HL-60 cell lines and by measuring the expression of mTNF-alpha using FCM techniques and immunohistochemistry in vivo. We simulated the interaction of the inhibitors with the 3D structure of the TACE active site in the Brookhaven Protein Database (PDB). The four inhibitors (8a-d) inhibited activity by 9.1%, 54.5%, 27.3%, and 54.5%, respectively. 8b and 8d showed significant in vitro inhibition in cytotoxicity tests, which corresponded to the molecular docking results. 8d also showed inhibitory activity in vivo. We explored the interface between enzyme and substrate by combining bioinformatics with experimental observations to further the development of specific TACE inhibitors to reduce inflammatory responses.

Inhibitory effect of quercetin on matrix metalloproteinase 9 activity molecular mechanism and structure-activity relationship of the flavonoid-enzyme interaction

Epidemiological studies have demonstrated an inverse association between the consumption of flavonoid-rich diets and the risk of atherosclerosis. In addition, an increased activity of the matrix metalloproteinase 9 (MMP-9) has been implicated in the development and progression of atherosclerotic lesions. Even though the relationship between flavonoid chemical structure and the inhibitory property on MMP activity has been established, the molecular mechanisms of this inhibition are still unknown. Herein, we first evaluated the inhibitory effect of quercetin on MMP-9 activity by zymography and a fluorescent gelatin dequenching assay, secondly we determined the most probable sites and modes of quercetin interaction with the MMP-9 catalytic domain by using molecular modelling techniques, and finally, we investigated the structure-activity relationship of the inhibitory effect of flavonoids on MMP-9 activity. We show that quercetin inhibited MMP-9 activity with an IC(50) value of 22 microM. By using docking and molecular dynamics simulations, it was shown that quercetin interacted in the S1' subsite of the MMP-9 active site. Moreover, the structure-activity relationship analysis demonstrated that flavonoid R(3)(')-OH and R(4)(')-OH substitutions were relevant to the inhibitory property against MMP-9 activity. In conclusion, our data constitute the first evidence about the quercetin and MMP-9 interaction, suggesting a mechanism to explain the inhibitory effect of the flavonoid on the enzymatic activity of MMP-9, which provides an additional molecular target for the cardioprotective activity of quercetin.

Synthesis and SAR of 2-phenyl-1-sulfonylaminocyclopropane carboxylates as ADAMTS-5 (Aggrecanase-2) inhibitors

A series of 1-sulfonylaminocyclopropanecarboxylates was synthesized as ADAMTS-5 (Aggrecanase-2) inhibitors. After an intensive investigation of the central cyclopropane core including its absolute stereochemistry and substituents, we found compound 22 with an Agg-2 IC50=7.4 nM, the most potent ADAMTS-5 inhibitor reported so far.

Evolution of binding sites for zinc and calcium ions playing structural roles

The geometry of metal coordination by proteins is well understood, but the evolution of metal binding sites has been less studied. Here we present a study on a small number of well-documented structural calcium and zinc binding sites, concerning how the geometry diverges between relatives, how often nonrelatives converge towards the same structure, and how often these metal binding sites are lost in the course of evolution. Both calcium and zinc binding site structure is observed to be conserved; structural differences between those atoms directly involved in metal binding in related proteins are typically less than 0.5 A root mean square deviation, even in distant relatives. Structural templates representing these conserved calcium and zinc binding sites were used to search the Protein Data Bank for cases where unrelated proteins have converged upon the same residue selection and geometry for metal binding. This allowed us to identify six "archetypal" metal binding site structures: two archetypal zinc binding sites, both of which had independently evolved on a large number of occasions, and four diverse archetypal calcium binding sites, where each had evolved independently on only a handful of occasions. We found that it was common for distant relatives of metal-binding proteins to lack metal-binding capacity. This occurred for 13 of the 18 metal binding sites we studied, even though in some of these cases the original metal had been classified as "essential for protein folding." For most of the calcium binding sites studied (seven out of eleven cases), the lack of metal binding in relatives was due to point mutation of the metal-binding residues, whilst for zinc binding sites, lack of metal binding in relatives always involved more extensive changes, with loss of secondary structural elements or loops around the binding site.

Synthesis and evaluation of novel heterocyclic MMP inhibitors

A variety of novel heterocyclic compounds were synthesized and evaluated for MMP inhibition. Broad spectrum inhibition of MMPs 1, 2, 9, and 12 was found with pyridinone-based compounds while N-heterocyclic triazoles and tetrazoles were largely ineffective. A highly selective tetrazole inhibitor for MMP-2 was discovered.

Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering

We have investigated the influence of post-filtering virtual screening results, with pharmacophoric features generated from an X-ray structure, on enrichment rates. This was performed using three docking softwares, zdock+, Surflex and FRED, as virtual screening tools and pharmacophores generated in UNITY from co-crystallized complexes. Sets of known actives along with 9997 pharmaceutically relevant decoy compounds were docked against six chemically diverse protein targets namely CDK2, COX2, ERalpha, fXa, MMP3, and NA. To try to overcome the inherent limitations of the well-known docking problem, we generated multiple poses for each compound. The compounds were first ranked according to their scores alone and enrichment rates were calculated using only the top scoring pose of each compound. Subsequently, all poses for each compound were passed through the different pharmacophores generated from co-crystallized complexes and the enrichment factors were re-calculated based on the top-scoring passing pose of each compound. Post-filtering with a pharmacophore generated from only one X-ray complex was shown to increase enrichment rates in all investigated targets compared to docking alone. This indicates that this is a general method, which works for diverse targets and different docking softwares.

Discovery and Characterization of a Novel Inhibitor of Matrix Metalloprotease-13 That Reduces Cartilage Damage in Vivo without Joint Fibroplasia Side Effects

Matrix metalloproteinase-13 (MMP13) is a Zn(2+)-dependent protease that catalyzes the cleavage of type II collagen, the main structural protein in articular cartilage. Excess MMP13 activity causes cartilage degradation in osteoarthritis, making this protease an attractive therapeutic target. However, clinically tested MMP inhibitors have been associated with a painful, joint-stiffening musculoskeletal side effect that may be due to their lack of selectivity. In our efforts to develop a disease-modifying osteoarthritis drug, we have discovered MMP13 inhibitors that differ greatly from previous MMP inhibitors; they do not bind to the catalytic zinc ion, they are noncompetitive with respect to substrate binding, and they show extreme selectivity for inhibiting MMP13. By structure-based drug design, we generated an orally active MMP13 inhibitor that effectively reduces cartilage damage in vivo and does not induce joint fibroplasias in a rat model of musculoskeletal syndrome side effects. Thus, highly selective inhibition of MMP13 in patients may overcome the major safety and efficacy challenges that have limited previously tested non-selective MMP inhibitors. MMP13 inhibitors such as the ones described here will help further define the role of this protease in arthritis and other diseases and may soon lead to drugs that safely halt cartilage damage in patients.

Matrix metalloproteinase–inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors

We structurally characterized the adducts of the catalytic domain of matrix metalloproteinase-3 (MMP3) with three different nonpeptidic inhibitors by solving the solution structure of one adduct [MMP3-N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid] and then by calculating structural models of the other two adducts using a reduced set of experimental NMR data, following a recently proposed procedure (Bertini et al. in J. Med. Chem. 48:7544-7559, 2005). The inhibitors were selected with the criteria of maintaining in all of them the same zinc-coordinating moiety and of selectively changing the substituents and/or the functional groups. The backbone dynamics on various time scales have been characterized as well. The comparison among these structures and with others previously reported allowed us to elucidate fine details of inhibitor-receptor interactions and to develop some criteria, which could guide in optimizing the design of selective inhibitors.

Identification of hot spots within druggable binding regions by computational solvent mapping of proteins

Here we apply the computational solvent mapping (CS-Map) algorithm toward the in silico identification of hot spots, that is, regions of protein binding sites that are major contributors to the binding energy and, hence, are prime targets in drug design. The CS-Map algorithm, developed for binding site characterization, moves small organic functional groups around the protein surface and determines their most energetically favorable binding positions. The utility of CS-Map algorithm toward the prediction of hot spot regions in druggable binding pockets is illustrated by three test systems: (1) renin aspartic protease, (2) a set of previously characterized druggable proteins, and (3) E. coli ketopantoate reductase. In each of the three studies, existing literature was used to verify our results. Based on our analyses, we conclude that the information provided by CS-Map can contribute substantially to the identification of hot spots, a necessary predecessor of fragment-based drug discovery efforts.

Imaging probes targeting matrix metalloproteinases

During the past few years, several imaging probes targeting matrix metalloproteinases (MMPs) have been developed. Most of these probes have been validated in animal models. Overall, results derived from most of these studies have been disappointing. Whether or not this relates to shortcomings of the imaging probes used or to the set-up of the reported studies is currently unclear. Firstly, MMPs targeted in these studies, MMP-1, -2 and -9, are cell secreted and their expression is known to vary extensively within one tumor type, depending on the stage of development of the tumor and on the presence of naturally occurring TIMPs. Given the lack of data on the levels of MMP expression by incoculated tumor tissue at the time of imaging in most studies reported, it cannot be excluded that the negative results reported are, in fact, false-negative imaging results. Secondly, given that most of the agents used for imaging are intrinsically broad-spectrum agents, their higher affinity for specific subsets of MMPs does not necessarily imply that a positive imaging result also corresponds to overexpression of specific subsets of MMPs, as suggested in some papers published. Accordingly, well-characterized tumor models need to be developed for the purpose of validating currently available, as well as future, MMP-imaging probes. So far, only 111In-DTPA-N-TIMP-2 has been injected in patients, respectively suffering from Kaposi Sarcoma. Imaging results obtained with this agent proved disappointing. Imaging results obtained with other MMP-targeting probes in patients are awaited.

Prediction of interaction mode between a typical ACE inhibitor and MMP-9 active site

To characterize the inhibitory specificity of angiotensin converting enzyme (ACE) inhibitors for matrix metalloproteinase 9 (MMP-9) activity, molecular modeling of these complex was performed referring the recent X-ray structure analyses using lisinopril as an ACE inhibitor. Two interaction modes differing in the orientation of the inhibitor on the active site were identified. Lisinopril was effectively stabilized by specific hydrogen bonds and hydrophobic interactions in the active site of MMP-9, and its hydrophobic group appeared to interact preferentially with the S1 site compared with the S1' site. These findings showed that ACE inhibitors could become important seeds for cardiovascular protection and the development of MMP inhibitors.

α-Biphenylsulfonylamino 2-methylpropyl phosphonates: Enantioselective synthesis and selective inhibition of MMPs

(R)-alpha-Biphenylsulfonylamino 2-methylpropyl phosphonates attain nM potency against several MMPs and are the most effective inhibitors based on phosphonate as zinc binding group. Since their preparation by direct N-acylation of expensive, enantiopure, alpha-aminophosphonic acids proceeds in low yields, we devised and evaluated a stereoselective and straightforward method of synthesis that avoids the unfavourable step of N-acylation. The key intermediate (R)-4-bromophenylsulfonylamino 2-methylpropyl phosphonate 9 was obtained by highly stereoselective addition of dibenzylphosphite to the enantiopure (S)-N-isobutylidene-p-bromobenzenesulfinamide 3, followed by oxidation with m-CPBA. Suzuki coupling of 9 with the desired arylboronic acids, gave the expected biphenylsulfonylamino derivatives in satisfactory yields. Liberation of the phosphonic group by hydrogenolysis led to the desired (R)-alpha-biphenylsulfonylamino 2-methylpropyl phosphonates 14a-i. Screening of the new compounds on MMP-1, -2, -3, -7, -8, -9, -13 and -14 showed IC(50) in the range of nM in most cases.

Comparison of properties of tumor necrosis factor-α converting enzyme (TACE) and some matrix metalloproteases (MMPs) in catalytic domains

The crystal structural data of TACE, MMP-1, MMP-2, MMP-3 and MMP-9 were obtained from PDB database, and then their catalytic domains' properties including conformation, molecular surface hydrophobicity and electrostatic potential were analyzed and compared by using Insight II molecular modeling software. It was found that the conformation and molecular surface hydrophobicity of catalytic domains of TACE and MMPs were not obviously different, but the molecular surface electrostatic potential of catalytic domain of TACE and MMPs had obvious differences. The findings are helpful in the Rational Drug Design of TACE selective inhibitor.

Evaluation of binary QSAR models derived from LUDI and MOE scoring functions for structure based virtual screening

In today's world of high-throughput in silico screening, the development of virtual screening methodologies to prioritize small molecules as new chemical entities (NCEs) for synthesis is of current interest. Among several approaches to virtual screening, structure-based virtual screening has been considered the most effective. However the problems associated with the ranking of potential solutions in terms of scoring functions remains one of the major bottlenecks in structure-based virtual screening technology. It has been suggested that scoring functions may be used as filters for distinguishing binders from nonbinders instead of accurately predicting their binding free energies. Subsequently, several improvements have been made in this area, which include the use of multiple rather than single scoring functions and application of either consensus or multivariate statistical methods or both to improve the discrimination between binders and nonbinders. In view of it, the discriminative ability (distinguishing binders from nonbinders) of binary QSAR models derived using LUDI and MOE scoring functions has been compared with the models derived by Jacobbsson et al. on five data sets viz. estrogen receptor alphamimics (ERalpha_mimics), estrogen receptor alphatoxins (ERalpha_toxins), matrix metalloprotease 3 inhibitors (MMP-3), factor Xa inhibitors (fXa), and acetylcholine esterase inhibitors (AChE). The overall analyses reveal that binary QSAR is comparable to the PLS discriminant analysis, rule-based, and Bayesian classification methods used by Jacobsson et al. Further the scoring functions implemented in LUDI and MOE can score a wide range of protein-ligand interactions and are comparable to the scoring functions implemented in ICM and Cscore. Thus the binary QSAR models derived using LUDI and MOE scoring functions may be useful as a preliminary screening layer in a multilayered virtual screening paradigm.

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453

Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453 have been solved at 2.01 and 2.37A resolutions, respectively. The results revealed that the binding modes for this inhibitor to MMP-3 and -13 were quite similar. However, subtle comparative differences were observed at the bottom of S1' pockets, which were occupied with the guanidinomethyl moiety of the inhibitor. A remarkable feature of the inhibitor was the deep penetration of its long aliphatic chain into the S1' pocket and exposure of the guanidinomethyl moiety to the solvent.

Structural Insight into the Stereoselective Inhibition of MMP-8 by Enantiomeric Sulfonamide Phosphonates

Potent and selective inhibitors of matrix metalloproteinases (MMPs), a family of zinc proteases that can degrade all the components of the extracellular matrix, could be useful for treatment of diseases such as cancer and arthritis. The most potent MMP inhibitors are based on hydroxamate as zinc-binding group (ZBG). alpha-Arylsulfonylamino phosphonates incorporate a particularly favorable combination of phosphonate as ZBG and arylsulfonylamino backbone so that their affinity exceptionally attains the nanomolar strength frequently observed for hydroxamate analogues. The detailed mode of binding of [1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl]phosphonate has been clarified by the crystal structures of the complexes that the R- and S-enantiomers respectively form with MMP-8. The reasons for the preferential MMP-8 inhibition by the R-phosphonate are underlined and the differences in the mode of binding of analogous alpha-arylsulfonylamino hydroxamates and carboxylates are discussed.

N-Hydroxyurea as zinc binding group in matrix metalloproteinase inhibition: mode of binding in a complex with MMP-8

The first crystallographic structure of an N-hydroxyurea inhibitor bound into the active site of a matrix metalloproteinase is reported. The ligand and three other analogues were prepared and studied as inhibitors of MMP-2, MMP-3, and MMP-8. The crystal structure of the complex with MMP-8 shows that the N-hydroxyurea, contrary to the analogous hydroxamate, binds the catalytic zinc ion in a monodentate rather than bidentate mode and with high out-of-plane distortion of the amide bonds.

Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs

Despite a deep knowledge on the 3D-structure of several catalytic domains of MMPs, the development of highly specific synthetic active-site-directed inhibitors of MMPs, able to differentiate the different members of this protease family, remains a strong challenge. Due to the flexible nature of MMP active-site, the development of specific MMP inhibitors will need to combine sophisticated theoretical and experimental approaches to decipher in each MMP the specific structural and dynamic features that can be exploited to obtain the desired selectivity.

Synthesis and evaluation of novel oxazoline MMP inhibitors

MMP inhibitors with novel oxazoline zinc binding groups have been synthesized and evaluated. Selectivity for the inhibition of MMP-9 over MMP-1, MMP-2, and MMP-12 has been achieved in several cases.

Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12

Human macrophage elastase (MMP-12) plays an important role in inflammatory processes and has been implicated in diseases such as emphysema and chronic obstructive pulmonary disease (COPD). It is therefore an attractive target for therapeutic agents. As part of a structure-based drug design programme to find new inhibitors of MMP-12, the crystal structures of the MMP-12 catalytic domain (residues 106-268) complexed to three different non-peptidic small molecule inhibitors have been determined. The structures reveal that all three ligands bind in the S1' pocket but show varying degrees of interaction with the Zn atom. The structures of the complexes with inhibitors CP-271485 and PF-00356231 reveal that their central morpholinone and thiophene rings, respectively, sit over the Zn atom at a distance of approximately 5A, locating the inhibitors halfway down the S1' pocket. In both of these structures, an acetohydroxamate anion, an artefact of the crystallisation solution, chelates the zinc atom. By contrast, the acetohydroxamate anion is displaced by the ligand in the structure of MMP-12 complexed to PD-0359601 (Bayer), a potent zinc chelating N-substituted biaryl butyric acid, used as a reference compound for crystallisation. Although a racemate was used for the crystallisation, the S enantiomer only is bound in the crystal. Important hydrophobic interactions between the inhibitors and residues from the S1' pocket are observed in all of the structures. The relative selectivity displayed by these ligands for MMP-12 over other MMP family members is discussed.

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.

A thiazole-containing tripodal ligand: synthesis, characterization, and interactions with metal ions and matrix metalloproteinases

A new tripodal ligand, tris[2-(((2-thiazolyl)methylidene)amino)ethyl]amine (Tatren), has been synthesized and characterized by NMR, IR, and UV-visible absorbance spectroscopy and elemental analysis. Tatren forms stable complexes with transition metal ions (Zn(2+), 1; Mn(2+), 2; Co(2+), 3) and the alkaline earth metal ions (Ca(2+), 4; Mg(2+), 5). Single-crystal X-ray structures of 1, 2, and 5 revealed six-coordinate chelate complexes with formula [M(Tatren)](ClO(4))(2) in which the metal centers are coordinated by three thiazolyl N atoms and three acyclic imine N atoms. Crystals of 1, 2, and 5 are monoclinic, P2(1)/c space group. Crystals of 4 are triclinic, P space group. The Ca(2+) complex is eight-coordinate with all N atoms of Tatren and one water molecule coordinated to the metal ion. Spectrophotometric titrations show that formation constants for the chelates of metal ions are >>1 in methanol. Free Tatren inhibits the catalytic domain of matrix metalloproteinase-13 (MMP-13, collagenase-3) with K(i) = 3.5 +/- 0.6 microM. Molecular mechanics-based docking calculations suggest that one leg of Tatren coordinates to the catalytic Zn(2+) in MMPs-2, -9, and -13 with significant hydrogen bonding to backbone amide groups. High-level DFT calculations suggest that, in the absence of nonbonded interactions between Tatren and the enzyme, the most stable first coordination sphere of the catalytic Zn(2+) is achieved with three imidazolyl groups from His residues and two imine N atoms from one leg of Tatren. While complexes (1-3) do not inhibit MMP-13 to a significant extent, 4 does (K(i) = 30 +/- 10 microM). Hence, this study shows that tripodal chelating ligands of this class and their Ca(2+) complexes have potential as active-site inhibitors for MMPs.

Crystal structure of the catalytic domain of human matrix metalloproteinase 10

The catalytic domain of matrix metalloproteinase-10 (MMP-10) has been expressed in Escherichia coli and its crystal structure solved at 2.1 A resolution. The availability of this structure allowed us to critically examine the small differences existing between the catalytic domains of MMP-3 and MMP-10, which show the highest sequence identity among all MMPs. Furthermore, the binding mode of N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH), which is one of the most known commercial inhibitors of MMPs, is described for the first time.

Structural and spectroscopic studies of tripodal [MgL]2+ chelates containing only nitrogen donor atoms: alkaline earth metal complexes as potential drug delivery agents

Several tripodal diimine ligands, tris(2-(2-thiazolyl)methyliminoethyl)amine, 2-Tatren, tris(2-(4-(5-methyl)imidazolyl)methyliminoethyl)amine, 5-Me-4-Imtren, tris(2-(4-imidazolyl)methyliminoethyl)amine, 4-Imtren, tris(2-(2-imidazolyl)methyliminoethyl)amine, 2-Imtren, and their Mg(2+) complexes were prepared and characterized. X-ray diffraction studies show that the Mg(2+) ions are six-coordinate, with three acyclic imine N atoms and three imidazolyl or thiazolyl N atoms coordinated with the general formula [Mg(L)](ClO(4))(2) (L=4-Imtren (1), 2-Imtren (2), 2-Tatren (3), and 5-Me-4-Imtren (4)). These complexes are chiral with both Delta and Lambda isomers present in the unit cell. (1)H NMR titrations reveal that complexes also form in solution and that the chirality is maintained. Variable temperature (1)H NMR reveals that the Delta and Lambda isomers interconvert in the intermediate to slow time scale. The interconversion rate slows with increasing pK(a) of the ligand heterocycle, suggesting that interconversion proceeds through a partially dissociated state. These complexes undergo trans-metallation by Zn(2+), indicating that their ligands can be released in a kinetically facile manner to form more stable metal ion complexes.

A practical approach to docking of zinc metalloproteinase inhibitors

Forty zinc-dependent metalloproteinase/ligand complexes with known crystal structures were re-docked using five docking/scoring approaches (DOCK, FlexX, DrugScore, GOLD, and AutoDock). Correct geometry of the coordination bonds between the ligand's zinc binding group (ZBG) and the catalytic zinc is important for docking accuracy and scoring reliability. More than 75% of docked poses with RMSD less than 2A were found to have appropriate ZBG binding, but for poor ZBG binding, about 95% of poses failed to dock correctly. Elimination of poses with inappropriate zinc binding resulted in better binding energy predictions that were further improved by dividing the ligands into subsets according to the ZBG (carboxylates, hydroxamates, and phosphorus containing groups). After a subset re-scoring using the regression functions obtained for individual subsets, DrugScore was able to explain 77% and the consensus scoring scheme X-CSCORE even 88% of variance in binding energies. The approach combining ZBG-based pose selection and subset re-scoring improved the hit rate in virtual screening for metalloproteinase inhibitors for all tested methods by 4-16%.

Similarity of binding sites of human matrix metalloproteinases

Tissue components hydrolyzing matrix metalloproteinases (MMPs) exhibit a high sequence similarity (56-64% in catalytic domains) and yet a significant degree of functional specificity. The hexapeptide-binding sites of 24 known human MMPs were compared in terms of their force field interaction energies with five probes that are most frequently encountered in substrates and inhibitors. The probes moved along a grid enclosing partially flexible binding sites in rigid catalytic domains that were represented by published experimental structures and comparative models and new comparative models for nine most recently characterized MMPs. For individual MMPs, representative interaction energies were obtained as averages for all suitable experimental structures. Correlations of the representative energies for all MMP pairs were succinctly catalogued for individual probes, subsites, and correlation levels. Among the probes (neutral sp(3) carbon and sp(3) oxygen, positive sp(3) nitrogen and hydrogen, and negative carbonyl oxygen), the last probe is least distinctive. Similarities of subsites are decreasing as S1 ' > S2 > S3 ' > S1 approximately S3 > S2 '. Most interesting, occupancies of subsites in published structures of MMP-inhibitor complexes follow an almost parallel trend, alluding to overall low selectivity of known MMP inhibitors. Flexible subsite S1 ' that appears as the specificity pocket in rigid x-ray structures is actually very similar among individual MMPs. Several correlations indicated that MMPs 3, 8, and 12 have similar binding sites. Modeling results are corroborated with published experimental data on MMP inhibition and substrate specificities. The results provide numerous clues for development of specific inhibitors and substrates, as well as for selection of MMPs for testing that provides maximum information without redundant experiments.

The Intermediate S1′ Pocket of the Endometase/Matrilysin-2 Active Site Revealed by Enzyme Inhibition Kinetic Studies, Protein Sequence Analyses, and Homology Modeling

Human matrix metalloproteinase-26 (MMP-26/endometase/matrilysin-2) is a newly identified MMP and its structure has not been reported. The enzyme active site S1' pocket in MMPs is a well defined substrate P1' amino acid residue-binding site with variable depth. To explore MMP-26 active site structure-activity, a series of new potent mercaptosulfide MMP inhibitors (MMPIs) with Leu or homophenylalanine (Homophe) side chains at the P1' site were selected. The Homephe side chain is designed to probe deep S1' pocket MMPs. These inhibitors were tested against MMP-26 and several MMPs with known x-ray crystal structures to distinguish shallow, intermediate, and deep S1' pocket characteristics. MMP-26 has an inhibition profile most similar to those of MMPs with intermediate S1' pockets. Investigations with hydroxamate MMPIs, including those designed for deep pocket MMPs, also indicated the presence of an intermediate pocket. Protein sequence analysis and homology modeling further verified that MMP-26 has an intermediate S1' pocket formed by Leu-204, His-208, and Tyr-230. Moreover, residue 233 may influence the depth of an MMP S1' pocket. The residue at the equivalent position of MMP-26 residue 233 is hydrophilic in intermediate-pocket MMPs (e.g. MMP-2, -8, and -9) and hydrophobic in deep-pocket MMPs (e.g. MMP-3, -12, and -14). MMP-26 contains a His-233 that renders the S1' pocket to an intermediate size. This study suggests that MMPIs, protein sequence analyses, and molecular modeling are useful tools to understand structure-activity relationships and provides new insight for rational inhibitor design that may distinguish MMPs with deep versus intermediate S1' pockets.

Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction

Docking of metalloproteinase inhibitors remains a challenge due to the zinc multiple coordination geometries and the lack of appropriate force field parameters to model the metal/ligand interactions. In this study, we explore the docking accuracy and scoring reliability for the docking of matrix metalloproteinase (MMP) inhibitors using AutoDock 3.0. Potential problems associated with zinc ion were investigated by docking 16 matrix metalloproteinase ligands to their crystal structures. A good coordination between the zinc binding group (ZBG) and the zinc was shown to be a prerequisite for the ligand to fit the binding site. A simplex optimization of zinc parameters, including zinc radius, well depth, and zinc charges, was performed utilizing the 14 MMP complexes with good docking. The use of optimized zinc parameters (zinc radius: 0.87 A; well depth: 0.35 kcal/mol; and zinc charges: +0.95 e) shows improvement in both docking accuracy at the zinc binding site and the prediction of binding free energies. Although further improvement in the docking procedure, particularly the scoring function is needed, optimization of zinc parameters provides an efficient way to improve the performance of AutoDock as a drug discovery tool.

An assessment of protein-ligand binding site polarizability

Electronic polarizability, an important physical property of biomolecules, is currently ignored in most biomolecular calculations. Yet, it is widely believed that polarization could account for a substantial fraction of the total nonbonded energy of a system. This belief is supported by studies of small complexes in vacuum. This perception is driving the development of a new class of polarizable force fields for biomolecular calculations. However, the quantification of this term for protein-ligand complexes has never been attempted. Here we explore the polarizable nature of protein-ligand complexes in order to evaluate the importance of this effect. We introduce two indexes describing the polarizability of protein binding sites. These we apply to a large range of pharmaceutically relevant complexes. We offer a recommendation of particular complexes as test systems with which to determine the effects of polarizability and as test cases with which to test the new generation of force fields. Additionally, we provide a tabulation of the amino acid composition of these binding sites and show that composition can be specific for certain classes of proteins. We also show that the relative abundance of some amino acids is different in binding sites than elsewhere in a protein's structure.

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.

Protease inhibitors: synthesis of matrix metalloproteinase and bacterial collagenase inhibitors incorporating 5-amino-2-mercapto-1,3,4-thiadiazole zinc binding functions

Matrix metalloproteinase (MMP)/bacterial collagenase inhibitors incorporating 5-amino-2-mercapto-1,3,4-thiadiazole zinc binding functions are reported. A series of compounds was prepared by reaction of arylsulfonyl isocyanates or arylsulfonyl halides with phenylalanyl-alanine, followed by coupling with 5-amino-2-mercapto-1,3,4-thiadiazole in the presence of carbodiimides. These new compounds were assayed as inhibitors of human MMP-1, MMP-2, MMP-8 and MMP-9, and of the collagenase isolated from the anaerobe Clostridium histolyticum (ChC). The new derivatives proved to be powerful inhibitors of these metalloproteases, with activities in the low micromolar range for some of the target enzymes, depending on the substitution pattern at the arylsulfonyl(ureido) moieties.