Matrix Metalloproteinase Target Family Landscape: A Chemometrical Approach to Ligand Selectivity Based on Protein Binding Site Analysis

Matrix Metalloproteinases (MMPs) in Targeted Drug Delivery: Synthesis of a Potent and Highly Selective Inhibitor against Matrix Metalloproteinase- 7

BACKGROUND

Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases that play a key role in both physiological and pathological tissue degradation. MMPs have reportedly shown great potentials in the degradation of the Extracellular Matrix (ECM), have shown great potentials in targeting bioactive and imaging agents in cancer treatment. MMPs could provoke Epithelial to Mesenchymal Transition (EMT) of cancer cells and manipulate their signaling, adhesion, migration and invasion to promote cancer cell aggressiveness. Therefore, targeting and particularly inhibiting MMPs within the tumor microenvironment is an effective strategy for cancer treatment. Based on this idea, different MMP inhibitors (MMPIs) have been developed to manipulate the tumor microenvironment towards conditions appropriate for the actions of antitumor agents. Studies are ongoing to improve the selectivity and specificity of MMPIs. Structural optimization has facilitated the discovery of selective inhibitors of the MMPs. However, so far no selective inhibitor for MMP-7 has been proposed.

AIMS

This study aims to comprehensively review the potentials and advances in applications of MMPs particularly MMP-7 in targeted cancer treatment approaches with the main focus on targeted drug delivery. Different targeting strategies for manipulating and inhibiting MMPs for the treatment of cancer are discussed. MMPs are upregulated at all stages of expression in cancers. Different MMP subtypes have shown significant targeting applicability at the genetic, protein, and activity levels in both physiological and pathophysiological conditions in a variety of cancers. The expression of MMPs significantly increases at advanced cancer stages, which can be used for controlled release in cancers in advance stages.

METHODS

Moreover, this study presents the synthesis and characteristics of a new and highly selective inhibitor against MMP-7 and discusses its applications in targeted drug delivery systems for therapeutics and diagnostics modalities.

RESULTS

Our findings showed that the structure of the inhibitor P3' side chains play the crucial role in developing an optimized MMP-7 inhibitor with high selectivity and significant degradation activities against ECM.

CONCLUSION

Optimized NDC can serve as a highly potent and selective inhibitor against MMP-7 following screening and optimization of the P3' side chains, with a Ki of 38.6 nM and an inhibitory selectivity of 575 of MMP-7 over MMP-1.

Enzymatic inhibitory activity of iridoid glycosides from Picrorrhiza kurroa against matrix metalloproteinases: Correlating in vitro targeted screening and docking

One specific group of MMPs; gelatinases A (MMP-2) and B (MMP-9) are of precise interest in view of the development and progression of cancer. In the current work, an attempt was made to investigate the enzymatic inhibitory activity of Kutkin (KT), Kutkoside (KS), and Picroside I (PS) by inhibition assay and to further check the downregulation of the expression of mRNA levels of MMP-2 and -9. Further in silico docking studies were performed to investigate the interaction of KT, KS and PS with MMP-2 and MMP-9. The results revealed a dose dependent cytotoxic activity of the compounds under investigation and showed a significant inhibition of MMP-9 in comparison to the activity against MMP-2. In addition, a considerable decrease in expression of mRNA levels (MMP-9) was observed in KT, KS, and PS-treated MDA-MB-231 and MDA-MB-435 cancer cells as was detected by reverse transcriptase polymerase chain reaction (semi-quantitative RT-PCR). The molecular docking studies between KT, KS, PS with MMPs revealed that KT, KS, PS occupied the active site of MMP-9 and showed better binding interactions in comparison to MMP-2. The binding energies of the complexes were -7.4, -7.1 and -7.2 kJ/mol for KT, KS and PS with MMP-9, respectively and -8.9, -8.0 and -8.0 kJ/mol for KT, KS and PS with MMP-2, respectively. The findings from the in vitro studies revealed that KT, KS and PS exhibited significant anti-proliferative effects on both MDA-MB-231 and MDA-MB-435 breast cancer cells. In addition, the results of inhibition assay showed that MMP-9 activity was significantly inhibited by KT, KS and PS and the results were consistent with in silico assay.

Synthesis of N-H Bearing Imidazolidinones and Dihydroimidazolones Using Aza-Heck Cyclizations

The synthesis of unsaturated, unprotected imidazolidinones via an aza-Heck reaction is described. This palladium-catalyzed process allows for the cyclization of N-phenoxy ureas onto pendant alkenes. The reaction has broad functional group tolerance, can be applied to complex ring topologies, and can be used to directly prepare mono- and bis-unprotected imidazolidinones. By addition of Bu4 NI, dihydroimidazolones can be accessed from the same starting materials. Improved conditions for preparing unsaturated, unprotected lactams are also reported.

Prediction of MMP-9 inhibitory activity of N-hydroxy-α-phenylsulfonylacetamide derivatives by pharmacophore based modeling and 3-D QSAR studies

Matrix metalloproteinase-9 (MMP-9), also known as gelatinase B, is a MMP that is strongly associated with multiple cellular processes including proliferation, angiogenesis, and metastasis. Various studies have shown that N-hydroxy-α-phenylsulfonylacetamide (HPSAs) derivatives are promising and selective for the MMP-9 inhibition. In the present study, we have selected and reported 80 HPSAs derivatives as inhibitors of MMP-9 and performed structure-based 3-dimensional quantitative structure-activity relationship (3D-QSAR) studies to elucidate the important structural elements responsible for binding affinity. Developed pharmacophore models; QSAR model I contains 2 hydrogen-bond acceptors (A), 2 hydrogen-bond donors (D), and 1 aromatic ring (R) and QSAR model II contains 3 hydrogen-bond acceptors (A), 1 positive ionic (P), and 1 aromatic ring (R). The statistical results of QSAR models (I and II) such as good correlation coefficient (0.61 for I and 0.63 for II), good predictive power (0.84 and 0.77 for I and II, respectively) with low standard deviation (SD\0.3 for both) strongly suggest that the developed models are virtuous for the future prediction of MMP-9 inhibitory activity of HPSAs derivatives. The geometry and features of pharmacophore were expected to be useful for further design and development of selective MMP-9 inhibitors.

Scrutinizing human MHC polymorphism: Supertype analysis using Poisson-Boltzmann electrostatics and clustering

Peptide-binding MHC proteins are thought the most variable across the human population; the extreme MHC polymorphism observed is functionally important and results from constrained divergent evolution. MHCs have vital functions in immunology and homeostasis: cell surface MHC class I molecules report cell status to CD8+ T cells, NKT cells and NK cells, thus playing key roles in pathogen defence, as well as mediating smell recognition, mate choice, Adverse Drug Reactions, and transplantation rejection. MHC peptide specificity falls into several supertypes exhibiting commonality of binding. It seems likely that other supertypes exist relevant to other functions. Since comprehensive experimental characterization is intractable, structure-based bioinformatics is the only viable solution. We modelled functional MHC proteins by homology and used calculated Poisson-Boltzmann electrostatics projected from the top surface of the MHC as multi-dimensional descriptors, analysing them using state-of-the-art dimensionality reduction techniques and clustering algorithms. We were able to recover the 3 MHC loci as separate clusters and identify clear sub-groups within them, vindicating unequivocally our choice of both data representation and clustering strategy. We expect this approach to make a profound contribution to the study of MHC polymorphism and its functional consequences, and, by extension, other burgeoning structural systems, such as GPCRs.

Nitro-based selective inhibitors against matrix metalloproteinase-7 over matrix metalloproteinase-1

A series of nitro-based dipeptidic compounds were synthesized and evaluated as matrix metalloproteinase (MMP) inhibitors, with improved selectivity for the inhibition of MMP-7 over MMP-1.

Synthesis, Structure, and SAR of Tetrahydropyran-Based LpxC Inhibitors

In the search for novel Gram-negative agents, we performed a comprehensive search of the AstraZeneca collection and identified a tetrahydropyran-based matrix metalloprotease (MMP) inhibitor that demonstrated nanomolar inhibition of UDP-3-O-(acyl)-N-acetylglucosamine deacetylase (LpxC). Crystallographic studies in Aquifex aeolicus LpxC indicated the tetrahydropyran engaged in the same hydrogen bonds and van der Waals interactions as other known inhibitors. Systematic optimization of three locales on the scaffold provided compounds with improved Gram-negative activity. However, the optimization of LpxC activity was not accompanied by reduced inhibition of MMPs. Comparison of the crystal structure of the native product, UDP-3-O-(acyl)-glucosamine, in Aquifex aeolicus to the structure of a tetrahydropyran-based inhibitor indicates pathways for future optimization.

Predictive in silico off-target profiling in drug discovery

Drug action can be rationalized as interaction of a molecule with proteins in a regulatory network of targets from a specific biological system. Both drug and side effects are often governed by interaction of the drug molecule with many, often unrelated, targets. Accordingly, arrays of protein–ligand interaction data from numerous in vitro profiling assays today provide growing evidence of polypharmacological drug interactions, even for marketed drugs. In vitro off-target profiling has therefore become an important tool in early drug discovery to learn about potential off-target liabilities, which are sometimes beneficial, but more often safety relevant. The rapidly developing field of in silico profiling approaches is complementing in vitro profiling. These approaches capitalize from large amounts of biochemical data from multiple sources to be exploited for optimizing undesirable side effects in pharmaceutical research. Therefore, current in silico profiling models are nowadays perceived as valuable tools in drug discovery, and promise a platform to support optimally informed decisions.

Enhanced hit-to-lead process using bioanalogous lead evolution and chemogenomics: application in designing selective matrix metalloprotease inhibitors

The authors describe an innovative approach for designing novel inhibitors. This approach effectively integrates the emerging chemogenomics concept of target-family-based drug discovery with bioanalogous design strategies, including privileged structures, molecular frameworks as well as bioisosteric and bioanalogous/isofunctional modifications. The authors applied this method in the design of selective inhibitors of matrix metalloproteases (MMPs), also referred to as matrixins, on the basis of a unique analysis of the ligand-target knowledge base, the 'matrixinome'. For this analysis, the authors created an annotated MMP database containing ∼ 300 inhibitors with their published activity profile. The ligand space was then arranged into a lead evolution tree, where the substructural transformations in each virtual step led to marked changes in the activity pattern. This allowed subtype-specific privileged fragments to be extracted as well as modifications, which improve activity and/or selectivity. Furthermore, the compounds with the preferred activity profile were correlated with sequence homology as well as binding site similarity within the target family, thereby leading to the identification of substructural modifications that turn non-selective, biohomologous structures into selective inhibitors. The matrixinomic application of the authors' approach, therefore, provides an example of how the combination of ligand space knowledge with sequence-related data can radically improve the outcome of the lead optimisation process to achieve higher selectivity within a given target family.

The influence of flavonoid compounds on the in vitro inhibition study of a human fibroblast collagenase catalytic domain expressed in E. coli

The human fibroblast collagenase catalytic domain (MMP1ca) that is considered a prototype for all interstitial collagenase and plays an important role in the turnover of collagen fibrils in the matrix was expressed as an inclusion body in the Escherichia coli. The purified enzyme displayed activity with substrate Dnp-Pro-Leu-Ala-Leu-Trp-Ala-Arg-OH with a K(m) value of 26.61±1.42 μM. The inhibition activity of the nine flavonoid compounds and gallic acid against MMP1ca was examined. Among the compounds tested, the IC(50) of seven flavonoid compounds were determined and ranged from 14.13 to 339.21 μM. Epigallocatechin gallate (EGCG) showed the highest inhibition toward MMP1ca with IC(50) values of 14.13±0.49 μM. EGCG showed a competitive inhibition pattern with a K(i) value of 10.47±0.51 μM. The free binding energy of EGCG against MMP1ca was -13.07 kcal mol(-1), which was calculated by using Autodock 3.0.5 software and showed numerous hydrophobic and hydrogen bond interactions. The galloyl group of EGCG, gallocatechin gallate and epicatechin gallate was determined to be important for inhibitory activity against MMP1ca.

A new class of highly potent matrix metalloproteinase inhibitors based on triazole-substituted hydroxamates: (radio)synthesis and in vitro and first in vivo evaluation

In vivo imaging of MMPs is of great (pre)clinical interest and can potentially be realized with modern three-dimensional and noninvasive in vivo molecular imaging techniques such as positron emission tomography (PET). Consequently, MMP inhibitors (MMPIs) radiolabeled with positron emitting nuclides (e.g., (18)F) represent a suitable tool for the visualization of activated MMPs with PET. On the basis of our previous work and results regarding radiolabeled and unlabeled derivatives of the nonselective MMPIs, we discovered a new class of fluorinated MMPIs with a triazole-substituted hydroxamate substructure. These novel MMPIs are characterized by an increased hydrophilicity compared with the lead structures and excellent MMP inhibition potencies for MMP-2, MMP-8, MMP-9, and MMP-13 (IC(50) = 0.006-107 nM). Therefore, one promising fluorinated triazole-substituted hydroxamate (30b) was selected and resynthesised as its (18)F-labeled version to yield the potential PET radioligand [(18)F]30b. The biodistribution behavior of this novel compound was investigated with small animal PET.

The significance of the C(α) substituent in the selective inhibition of matrix metalloproteinases 1 and 9

Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing C(α) substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC(50) value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the C(α) substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand's morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P(1)' and P(2)' may confer selectivity among MMPs and may aid in the search for novel lead compounds.

The significance of the C(α) substituent in the selective inhibition of matrix metalloproteinases 1 and 9

Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing C(α) substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC(50) value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the C(α) substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand's morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P(1)' and P(2)' may confer selectivity among MMPs and may aid in the search for novel lead compounds.

Stictamides A-C, MMP12 inhibitors containing 4-amino-3-hydroxy-5-phenylpentanoic acid subunits

An extensive study of the secondary metabolites produced by a new Sticta sp. of lichen has led to the isolation of three new compounds containing the 4-amino-3-hydroxy-5-phenylpentanoic acid residue (Ahppa). The structures of stictamides A-C (1-3) were assigned by 2D NMR spectroscopic and chemical methods. Due to extensive epimerization of the Ahppa residue observed after acid hydrolysis, the configuration of this unit was deduced through conversion of 1 to an appropriate derivative and application of our recently developed statine NMR database. Evaluation of stictamide A against a panel of disease-relevant proteases showed that it inhibited MMP12 at 2.3 μM and significantly reduced invasion in the human glioma cell line U87MG. Docking studies suggest that stictamide A inhibits MMP12 by a non-zinc-binding mechanism.

Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

Proteochemometric modeling is founded on the principles of QSAR but is able to benefit from additional information in model training due to the inclusion of target information.

Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering

Background

Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge.

Results

We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands.

Conclusions

The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S₁' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often CMC produced more informative and more easy interpretable dendrograms. Finally, CMC was successful for standard pairwise analysis (i.e., Smith-Waterman algorithm) of protein sequences and was used to convincingly explain the complementarity existing between the molecular shapes of the co-crystallised ligand molecules and the accessible MMP void volumes.

Matrix metalloproteinase inhibitors: a critical appraisal of design principles and proposed therapeutic utility

Matrix metalloproteinases (MMPs) play an important role in tissue remodelling associated with various physiological and pathological processes, such as morphogenesis, angiogenesis, tissue repair, arthritis, chronic heart failure, chronic obstructive pulmonary disease, chronic inflammation and cancer metastasis. As a result, MMPs are considered to be viable drug targets in the therapy of these diseases. Despite the high therapeutic potential of MMP inhibitors (MMPIs), all clinical trials have failed to date, except for doxycycline for periodontal disease. This can be attributed to (i) poor selectivity of the MMPIs, (ii) poor target validation for the targeted therapy and (iii) poorly defined predictive preclinical animal models for safety and efficacy. Lessons from previous failures, such as recent discoveries of oxidative/nitrosative activation and phosphorylation of MMPs, as well as novel non-matrix related intra- and extracellular targets of MMP, give new hope for MMPI development for both chronic and acute diseases. In this article we critically review the major structural determinants of the selectivity and the milestones of past design efforts of MMPIs where 2-/3-dimensional structure-based methods were intensively applied. We also analyse the in vitro screening and preclinical/clinical pharmacology approaches, with particular emphasis on drawing conclusions on how to overcome efficacy and safety problems through better target validation and design of preclinical studies.

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.

To bind zinc or not to bind zinc: an examination of innovative approaches to improved metalloproteinase inhibition

This short review highlights some recent advances in matrix metalloproteinase inhibitor (MMPi) design and development. Three distinct approaches to improved MMP inhibition are discussed: (1) the identification and investigation of novel zinc-binding groups (ZBGs), (2) the study of non-zinc-binding MMPi, and (3) mechanism-based MMPi that form covalent adducts with the protein. Each of these strategies is discussed and their respective advantages and remaining challenges are highlighted. The studies discussed here bode well for the development of ever more selective, potent, and well-tolerated MMPi for treating several important disease pathologies.

Structure-based chemogenomics: analysis of protein family landscapes

Analysis of the three-dimensional structures of protein ligand complexes provides valuable insight into both the common interaction patterns within a target family and the discriminating features between the different members of a target family. Knowledge of the common interaction patterns helps to design target family focused chemical libraries for hit finding, while the discriminating features can be exploited to optimize the selectivity profile of a lead compound against particular member of a target family. Herein, we review the computational tools which have been developed to analyze crystal structures of members of a target family.

Identification of MMP-12 inhibitors by using biosensor-based screening of a fragment library

Small inhibitors of matrix metalloproteinase 12 (MMP-12) have been identified with a biosensor-based screening strategy and a specifically designed fragment library. The interaction between fragments and three variants of the target and a reference protein with an active-site zinc ion was measured continuously by surface plasmon resonance. The developed experimental design overcame the inherent instability of MMP-12 and allowed the identification of fragments that interacted specifically with the active-site of MMP-12 but not with the reference protein. The interaction with MMP-12 for selected compounds were analyzed for concentration dependence and saturability. Compounds interacting distinctly with the target were further evaluated by an activity-based assay, verifying MMP-12 inhibition. Two effective inhibitors were identified, and the compound with highest affinity was confirmed to be a competitive inhibitor with an IC50 of 290 nM and a ligand efficiency of 0.7 kcal/mol heavy atom. This procedure integrates selectivity and binding site identification into the screening procedure and does not require structure determination.

The design of inhibitors for medicinally relevant metalloproteins

A number of metalloproteins are important medicinal targets for conditions ranging from pathogenic infections to cancer. Many but not all of these metalloproteins contain a zinc(II) ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In this review several metalloproteins of interest are discussed, including matrix metalloproteinases (MMPs), histone deacetylases (HDACs), anthrax lethal factor (LF), and others. Different strategies that have been employed to design effective inhibitors against these proteins are described, with an effort to highlight the strengths and drawbacks of each approach. An emphasis is placed on examining the bioinorganic chemistry of these metal active sites and how a better understanding of the coordination chemistry in these systems may lead to improved inhibitors. It is hoped that this review will help inspire medicinal, biological, and inorganic chemists to tackle this important problem by considering all aspects of metalloprotein inhibitor design.

Computational analysis of ligand relationships within target families

Computational tools for the large-scale analysis and prediction of ligand-target interactions and the identification of small molecules having different selectivity profiles within target protein families complement research in chemical genetics and chemogenomics. For computational analysis and design, such tasks require a departure from the traditional focus on single targets, hit identification, and lead optimization. Recently, studies have been reported that profile compounds in silico against arrays of targets or systematically map ligand-target space. In order to identify small molecular probes that are suitable for chemical genetics applications, molecular diversity needs to be viewed in a way that partly differs from principles guiding conventional library design.

Simultaneous presence of unsaturation and long alkyl chain at P1′ of Ilomastat confers selectivity for gelatinase A (MMP-2) over gelatinase B (MMP-9) inhibition as shown by molecular modelling studies

Structural analogues of Ilomastat (Galardin), containing unsaturation(s) and chain extension carrying bulky phenyl group or alkyl moieties at P'1 were synthesized and purified by centrifugal partition chromatography. They were analyzed for their inhibitory capacity towards MMP-1, MMP-2, MMP-3, MMP-9 and MMP-14, main endopeptidases involved in tumour progression. Presence of unsaturation(s) decreased the inhibitory potency of compounds but, in turn increased their selectivity for gelatinases. 2b and 2d derivatives with a phenyl group inhibited preferentially MMP-9 with IC50 equal to 45 and 38 nM, respectively, but also display activity against MMP-2 (IC50 equal to 280 and 120 nM, respectively). Molecular docking computations confirmed affinity of these substances for both gelatinases. With aims to obtain a specific gelatinase A (MMP-2) inhibitor, P'1 of Ilomastat was modified to carry one unsaturation coupled to an alkyl chain with pentylidene group. Docking studies indicated that MMP-2, but not MMP-9, could accommodate such substitution; indeed 2a proved to inhibit MMP-2 (IC50=123 nM), while displaying no inhibitory capacity towards MMP-9.

Chemogenomic approaches to rational drug design

Paradigms in drug design and discovery are changing at a significant pace. Concomitant to the sequencing of over 180 several genomes, the high-throughput miniaturization of chemical synthesis and biological evaluation of a multiple compounds on gene/protein expression and function opens the way to global drug-discovery approaches, no more focused on a single target but on an entire family of related proteins or on a full metabolic pathway. Chemogenomics is this emerging research field aimed at systematically studying the biological effect of a wide array of small molecular-weight ligands on a wide array of macromolecular targets. Since the quantity of existing data (compounds, targets and assays) and of produced information (gene/protein expression levels and binding constants) are too large for manual manipulation, information technologies play a crucial role in planning, analysing and predicting chemogenomic data. The present review will focus on predictive in silico chemogenomic approaches to foster rational drug design and derive information from the simultaneous biological evaluation of multiple compounds on multiple targets. State-of-the-art methods for navigating in either ligand or target space will be presented and concrete drug design applications will be mentioned.

The Roles of Substrate Thermal Stability and P2 and P1′ Subsite Identity on Matrix Metalloproteinase Triple-helical Peptidase Activity and Collagen Specificity

The hydrolysis of collagen (collagenolysis) is one of the committed steps in extracellular matrix turnover. Within the matrix metalloproteinase (MMP) family distinct preferences for collagen types are seen. The substrate determinants that may guide these specificities are unknown. In this study, we have utilized 12 triple-helical substrates in combination with 10 MMPs to better define the contributions of substrate sequence and thermal stability toward triple helicase activity and collagen specificity. In general, MMP-13 was found to be distinct from MMP-8 and MT1-MMP(Delta279-523), in that enhanced substrate thermal stability has only a modest effect on activity, regardless of sequence. This result correlates to the unique collagen specificity of MMP-13 compared with MMP-8 and MT1-MMP, in that MMP-13 hydrolyzes type II collagen efficiently, whereas MMP-8 and MT1-MMP are similar in their preference for type I collagen. In turn, MMP-1 was the least efficient of the collagenolytic MMPs at processing increasingly thermal stable triple helices and thus favors type III collagen, which has a relatively flexible cleavage site. Gelatinases (MMP-2 and MMP-9(Delta444-707)) appear incapable of processing more stable helices and are thus mechanistically distinct from collagenolytic MMPs. The collagen specificity of MMPs appears to be based on a combination of substrate sequence and thermal stability. Analysis of the hydrolysis of triple-helical peptides by an MMP mutant indicated that Tyr(210) functions in triple helix binding and hydrolysis, but not in processing triple helices of increasing thermal stabilities. Further exploration of MMP active sites and exosites, in combination with substrate conformation, may prove valuable for additional dissection of collagenolysis and yield information useful in the design of more selective MMP inhibitors.

Recent advances in MMP inhibitor design

The search for an MMP inhibitor with anticancer efficacy is a nearly three-decade endeavor. This inhibitor is yet to be found. The reasons for this failure include shortcomings in the chemistry of these compounds (including broad MMP sub-type selectivity, metabolic lability, and toxicity) as well as the emerging, and arguably extraordinary, complexity of MMP cell (and cancer) biology. Together these suggest that the successful anticancer inhibitor must possess MMP selectivity against the MMP subtype whose involvement is critical, yet highly temporally (with respect to metastatic progression) and mechanistically (with respect to matrix degradation) regulated. This review summarizes the progression of chemical structure and mechanistic thinking toward these objectives, with emphasis on the disappointment, the perseverance, and the resilient optimism that such an inhibitor is there to be discovered.