Structural basis for induced formation of the inflammatory mediator prostaglandin E2

Pancreatic Cancer Cells Isolated from Muc1-Null Tumors Favor the Generation of a Mature Less Suppressive MDSC Population

Mucin 1 (MUC1) is a transmembrane mucin glycoprotein that is over-expressed and aberrantly glycosylated in >80% of human pancreatic ductal adenocarcinoma (PDA) and is associated with poor prognosis. To understand the role of MUC1 in PDA, we have recently developed two mouse models of spontaneous PDA, one that expresses full-length human MUC1 transgene (KCM mice) and one that is null for MUC1 (KCKO mice). We have previously reported that KCM mice express high levels of myeloid derived suppressor cells (MDSCs) in their tumors and develop highly aggressive PDA. To further understand the underlying mechanism for high MDSC levels in KCM-tumors, we generated primary cell lines from KCM and KCKO-tumors. In this study, we report that MDSCs derived using KCM cells express significantly higher levels of arginase 1 and inducible nitric oxide synthase (markers associated with immune suppression) and lower levels of CD115 (a marker associated with maturation of myeloid cells) as compared to KCKO-derived MDSCs. Functionally, KCM-derived MDSCs secrete significantly higher levels of urea and nitric oxide (NO) when co-cultured with normal splenic cells as compared to KCKO-derived MDSCs. Data indicates that KCM-derived MDSCs remain immature and are more suppressive as compared to KCKO-derived MDSCs. This was further corroborated in vivo where MDSCs isolated from KCM-tumor-bearing mice retained their immature state and were highly suppressive as compared to MDSCs derived from KCKO-tumor-bearing mice. Finally, we show that KCM cells secrete significantly higher levels of prostaglandin E2 (PGE₂), a COX-2 metabolite and a known driver of suppressive MDSCs as compared to KCKO cells. Thus, inhibiting PGE₂ with a specific COX-2 inhibitor reverses the immunosuppressive and immature phenotype of KCM-derived MDSCs. This is the first report that clearly suggests a functional role of pancreatic tumor-associated MUC1 in the development of functional MDSCs.

The Concise Guide to PHARMACOLOGY 2013/14: enzymes

The Concise Guide to PHARMACOLOGY 2013/14 provides concise overviews of the key properties of over 2000 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.12444/full. Enzymes are one of the seven major pharmacological targets into which the Guide is divided, with the others being G protein-coupled receptors, ligand-gated ion channels, ion channels, nuclear hormone receptors, catalytic receptors and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in previous Guides to Receptors and Channels. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and the Guide to Receptors and Channels, providing a permanent, citable, point-in-time record that will survive database updates.

Trial and error: investigational drug induced liver injury, a case series report

This is a case report series of four patients who exhibited signs and symptoms of acute liver dysfunction during participation in a Phase I trial of a novel non-steroidal anti-inflammatory drug (NSAID) designed to inhibit microsomal prostaglandin synthase 1 (MPGES1). Within one month of trial initiation, all four patients presented with epigastric pain, fatigue, nausea, and increasing liver function tests (LFTs). Two out of four patients required hospitalization, underwent liver biopsies, and were treated with N-acetylcysteine. The remaining two patients were managed as outpatients. Liver biopsies were consistent with drug induced liver injury (DILI). Within three months of stopping the investigational drug, symptoms subsided and LFTs normalized in all patients. This case report series signifies the importance of NSAIDs and novel drug agents in general as potentially hepatotoxic substances, the need for a high level of suspicion of DILI when considering possible etiologies of acute liver failure, and the need for prompt withdrawal of the causative agent in management of patients presenting with DILI.

Potent inhibition of human 5-lipoxygenase and microsomal prostaglandin E₂ synthase-1 by the anti-carcinogenic and anti-inflammatory agent embelin

Embelin (2,5-dihydroxy-3-undecyl-1,4-benzoquinone) possesses anti-inflammatory and anti-carcinogenic properties in vivo, and these features have been related to interference with multiple targets including XIAPs, NFκB, STAT-3, Akt and mTOR. However, interference with these proteins requires relatively high concentrations of embelin (IC₅₀>4 μM) and cannot fully explain its bioactivity observed in several functional studies. Here we reveal human 5-lipoxygenase (5-LO) and microsomal prostaglandin E₂ synthase (mPGES)-1 as direct molecular targets of embelin. Thus, embelin potently suppressed the biosynthesis of eicosanoids by selective inhibition of 5-LO and mPGES-1 with IC₅₀=0.06 and 0.2 μM, respectively. In intact human polymorphonuclear leukocytes and monocytes, embelin consistently blocked the biosynthesis of various 5-LO products regardless of the stimulus (fMLP or A23187) with IC₅₀=0.8-2 μM. Neither the related human 12- and 15-LO nor the cyclooxygenases-1 and -2 or cytosolic phospholipase A₂ were significantly affected by 10 μM embelin. Inhibition of 5-LO and mPGES-1 by embelin was (I) essentially reversible after wash-out, (II) not impaired at higher substrate concentrations, (III) unaffected by inclusion of Triton X-100, and (IV) did not correlate to its proposed antioxidant properties. Docking simulations suggest concrete binding poses in the active sites of both 5-LO and mPGES-1. Because 5-LO- and mPGES-1-derived eicosanoids play roles in inflammation and cancer, the interference of embelin with these enzymes may contribute to its biological effects and suggests embelin as novel chemotype for development of dual 5-LO/mPGES-1 inhibitors.

A pipeline for comprehensive and automated processing of electron diffraction data in IPLT

Electron crystallography of two-dimensional crystals allows the structural study of membrane proteins in their native environment, the lipid bilayer. Determining the structure of a membrane protein at near-atomic resolution by electron crystallography remains, however, a very labor-intense and time-consuming task. To simplify and accelerate the data processing aspect of electron crystallography, we implemented a pipeline for the processing of electron diffraction data using the Image Processing Library and Toolbox (IPLT), which provides a modular, flexible, integrated, and extendable cross-platform, open-source framework for image processing. The diffraction data processing pipeline is organized as several independent modules implemented in Python. The modules can be accessed either from a graphical user interface or through a command line interface, thus meeting the needs of both novice and expert users. The low-level image processing algorithms are implemented in C++ to achieve optimal processing performance, and their interface is exported to Python using a wrapper. For enhanced performance, the Python processing modules are complemented with a central data managing facility that provides a caching infrastructure. The validity of our data processing algorithms was verified by processing a set of aquaporin-0 diffraction patterns with the IPLT pipeline and comparing the resulting merged data set with that obtained by processing the same diffraction patterns with the classical set of MRC programs.

Influences of membrane mimetic environments on membrane protein structures

The number of membrane protein structures in the Protein Data Bank is becoming significant and growing. Here, the transmembrane domain structures of the helical membrane proteins are evaluated to assess the influences of the membrane mimetic environments. Toward this goal, many of the biophysical properties of membranes are discussed and contrasted with those of the membrane mimetics commonly used for structure determination. Although the mimetic environments can perturb the protein structures to an extent that potentially gives rise to misinterpretation of functional mechanisms, there are also many structures that have a native-like appearance. From this assessment, an initial set of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structures. With experimental techniques for validation and computational methods for refinement and quality assessment and enhancement, there are good prospects for achieving native-like structures for these very important proteins.

Inhibition of microsomal prostaglandin E synthase-1 by aminothiazoles decreases prostaglandin E2 synthesis in vitro and ameliorates experimental periodontitis in vivo

The potent inflammatory mediator prostaglandin E2 (PGE2) is implicated in the pathogenesis of several chronic inflammatory conditions, including periodontitis. The inducible enzyme microsomal prostaglandin E synthase-1 (mPGES-1), catalyzing the terminal step of PGE2 biosynthesis, is an attractive target for selective PGE2 inhibition. To identify mPGES-1 inhibitors, we investigated the effect of aminothiazoles on inflammation-induced PGE2 synthesis in vitro, using human gingival fibroblasts stimulated with the cytokine IL-1β and a cell-free mPGES-1 activity assay, as well as on inflammation-induced bone resorption in vivo, using ligature-induced experimental periodontitis in Sprague-Dawley rats. Aminothiazoles 4-([4-(2-naphthyl)-1,3-thiazol-2-yl]amino)phenol (TH-848) and 4-(3-fluoro-4-methoxyphenyl)-N-(4-phenoxyphenyl)-1,3-thiazol-2-amine (TH-644) reduced IL-1β-induced PGE2 production in fibroblasts (IC50 1.1 and 1.5 μM, respectively) as well as recombinant mPGES-1 activity, without affecting activity or expression of the upstream enzyme cyclooxygenase-2. In ligature-induced experimental periodontitis, alveolar bone loss, assessed by X-ray imaging, was reduced by 46% by local treatment with TH-848, compared to vehicle, without any systemic effects on PGE2, 6-keto PGF1α, LTB4 or cytokine levels. In summary, these results demonstrate that the aminothiazoles represent novel mPGES-1 inhibitors for inhibition of PGE2 production and reduction of bone resorption in experimental periodontitis, and may be used as potential anti-inflammatory drugs for treatment of chronic inflammatory diseases, including periodontitis.

Crystal structure of microsomal prostaglandin E2 synthase provides insight into diversity in the MAPEG superfamily

Prostaglandin E2 (PGE2) is a key mediator in inflammatory response. The main source of inducible PGE2, microsomal PGE2 synthase-1 (mPGES-1), has emerged as an interesting drug target for treatment of pain. To support inhibitor design, we have determined the crystal structure of human mPGES-1 to 1.2 Å resolution. The structure reveals three well-defined active site cavities within the membrane-spanning region in each monomer interface of the trimeric structure. An important determinant of the active site cavity is a small cytosolic domain inserted between transmembrane helices I and II. This extra domain is not observed in other structures of proteins within the MAPEG (Membrane-Associated Proteins involved in Eicosanoid and Glutathione metabolism) superfamily but is likely to be present also in microsomal GST-1 based on sequence similarity. An unexpected feature of the structure is a 16-Å-deep cone-shaped cavity extending from the cytosolic side into the membrane-spanning region. We suggest a potential role for this cavity in substrate access. Based on the structure of the active site, we propose a catalytic mechanism in which serine 127 plays a key role. We have also determined the structure of mPGES-1 in complex with a glutathione-based analog, providing insight into mPGES-1 flexibility and potential for structure-based drug design.

Introduction to electron crystallography

From the earliest work on regular arrays in negative stain, electron crystallography has contributed greatly to our understanding of the structure and function of biological macromolecules. The development of electron cryo-microscopy (cryo-EM) then lead to the first groundbreaking atomic models of the membrane proteins bacteriorhodopsin and light harvesting complex II within lipid bilayers. Key contributions towards cryo-EM and electron crystallography methods included specimen preparation and vitrification, liquid-helium cooling, data collection, and image processing. These methods are now applied almost routinely to both membrane and soluble proteins. Here we outline the advances and the breakthroughs that paved the way towards high-resolution structures by electron crystallography, both in terms of methods development and biological milestones.

Grid preparation for cryo-electron microscopy

Once 2D crystals suitable for electron crystallography have been obtained, grid preparation for cryo-EM is a critical step in obtaining high-resolution structural information. Specimens have to be prepared in a manner that prevents dehydration and disruption of the crystals in the vacuum of the electron microscope. Sugar embedding is an effective way to preserve specimens in the native and hydrated state. Preparation of almost perfectly flat specimens is another prerequisite. Imperfect specimen flatness is a crucial problem in the recording of images and diffraction patterns at higher tilt angles because it causes the blurring of spots perpendicular to the tilt axis. In this chapter, we describe the protocols of preparing 2D crystal specimen for electron crystallographical data collection. These protocols cover preparation of a flat carbon support film by sparkless carbon evaporation, sugar embedding using back injection, and the recently developed carbon sandwich technique.

Discovery of depsides and depsidones from lichen as potent inhibitors of microsomal prostaglandin E2 synthase-1 using pharmacophore models

Nature in silico: Virtual screening using validated pharmacophore models identified lichen depsides and depsidones as potential inhibitors of mPGES-1, an emerging target for NSAIDs. Evaluation of the virtual hits in a cell-free assay revealed physodic acid and perlatolic acid as potent inhibitors of mPGES-1 (IC(50) = 0.4 and 0.43 μM, respectively), indicating that these natural products have potential as novel anti-inflammatory agents.

High-Precision, Room Temperature Screening Assay for Inhibitors of Microsomal Prostaglandin E Synthase-1

Microsomal prostaglandin E synthase-1 (mPGES-1) is the major enzyme catalyzing the isomerization of prostaglandin (PG) H2 to PGE2. Here we report the development of a robust and practical automated assay in a 384-well format for room temperature screening of mPGES-1 inhibitors with high precision and low reagent consumption. The assay should enable precise structure-activity relationship development. It uses acetonitrile as solvent for PGH2, FeCl2/citrate as stop reagent, and a short reaction time. Combined with high-precision liquid transfer and extensive mixing after addition of reactants, these properties let the assay reach Z′ > 0.7 and high reproducibility of inhibitor IC50 values. Thorough investigation of the quality of mixing in all liquid transfer steps proved crucial for reaching high-precision performance.

Abbreviations: mPGES-1 (microsomal prostaglandin E synthase-1); FRET (fluorescence resonance energy transfer); HTRF (homogeneous time-resolved fluorescence); PGH2 (prostaglandin H2); PGE2 (prostaglandin E2); SAR (structure-activity relationship); COX-2 (cyclooxygenase-2); GSH (glutathione); ALP (automated labware positioner)

Microsomal Prostaglandin E2 Synthase-1

The prostanoids and leukotrienes (LTs) formed from arachidonic acid (AA) via the cyclooxygenase (COX)-1/2 and 5-lipoxygenase (5-LO) pathway, respectively, mediate inflammatory responses, chronic tissue remodelling, cancer, asthma and autoimmune disorders, but also possess homeostatic functions in the gastrointestinal tract, uterus, brain, kidney, vasculature and host defence. Based on the manifold functions of these eicosanoids, the clinical use of non-steroidal anti-inflammatory drugs (NSAIDs), a class of drugs that block formation of all prostanoids, is hampered by severe side-effects including gastrointestinal injury, renal irritations and cardiovascular risks. Therefore, anti-inflammatory agents interfering with eicosanoid biosynthesis require a well-balanced pharmacological profile to minimize these on-target side-effects. Current anti-inflammatory research aims at identifying compounds that can suppress the massive formation of pro-inflammatory prostaglandin (PG)E2 without affecting homeostatic PGE2 and PGI2 synthesis. The inducible microsomal prostaglandin E2 synthase-1 (mPGES-1) is one promising target enzyme. We will give an overview about the structure, regulation and function of mPGES-1 and then present novel inhibitors of mPGES-1 that may possess a promising pharmacological profile.

Glycines: role in α-helical membrane protein structures and a potential indicator of native conformation

Among the growing number of membrane protein structures in the Protein Data Bank, there are many transmembrane domains that appear to be native-like; at the same time, there are others that appear to have less than complete native-like character. Hence, there is an increasing need for validation tools that distinguish native-like from non-native-like structures. Membrane mimetics used in protein structural characterizations differ in numerous physicochemical properties from native membranes and provide many opportunities for introducing non-native-like features into membrane protein structures. One possible approach for validating membrane protein structures is based on the use of glycine residues in transmembrane domains. Here, we have reviewed the membrane protein structure database and identified a set of benchmark proteins that appear to be native-like. In these structures, conserved glycine residues rarely face the lipid interstices, and many of them participate in close helix-helix packing. Glycine-based validation allowed the identification of non-native-like features in several membrane proteins and also shows the potential for verifying the native-like character for numerous other membrane protein structures.

Cardiovascular biology of microsomal prostaglandin E synthase-1

Both traditional and purpose-designed nonsteroidal anti-inflammatory drugs, selective for inhibition of cyclooxygenase (COX)-2, alleviate pain and inflammation but confer a cardiovascular hazard attributable to inhibition of COX-2-derived prostacyclin (PGI(2)). Deletion of microsomal PGE synthase-1 (mPGES-1), the dominant enzyme that converts the COX-derived intermediate product PGH(2) to PGE(2), modulates inflammatory pain in rodents. In contrast with COX-2 deletion or inhibition, PGI(2) formation is augmented in mPGES-1(-/-) mice-an effect that may confer cardiovascular benefit but may undermine the analgesic potential of inhibitors of this enzyme. This review considers the cardiovascular biology of mPGES1 and the complex challenge of developing inhibitors of this enzyme.

Ligand-based virtual screening approach using a new scoring function

In this study, we aimed to develop a new ligand-based virtual screening approach using an effective shape-overlapping procedure and a more robust scoring function (denoted by the HWZ score for convenience). The HWZ score-based virtual screening approach was tested against the compounds for 40 protein targets available in the Database of Useful Decoys (DUD; dud.docking.org/jahn/ ), and the virtual screening performance was evaluated in terms of the area under the receiver operator characteristic (ROC) curve (AUC), enrichment factor (EF), and hit rate (HR), demonstrating an improved overall performance compared to other popularly used approaches examined. In particular, the HWZ score-based virtual screening led to an average AUC value of 0.84 ± 0.02 (95% confidence interval) for the 40 targets. The average HR values at the top 1% and 10% of the active compounds for the 40 targets were 46.3% ± 6.7% and 59.2% ± 4.7%, respectively. In addition, the performance of the HWZ score-based virtual screening approach is less sensitive to the choice of the target.

Observation of two modes of inhibition of human microsomal prostaglandin E synthase 1 by the cyclopentenone 15-deoxy-Δ(12,14)-prostaglandin J(2)

Microsomal prostaglandin E synthase 1 (MPGES1) is an enzyme that produces the pro-inflammatory molecule prostaglandin E(2) (PGE(2)). Effective inhibitors of MPGES1 are of considerable pharmacological interest for the selective control of pain, fever, and inflammation. The isoprostane, 15-deoxy-Δ(12,14)-prostaglandin J(2) (15d-PGJ(2)), a naturally occurring degradation product of prostaglandin D(2), is known to have anti-inflammatory properties. In this paper, we demonstrate that 15d-PGJ(2) can inhibit MPGES1 by covalent modification of residue C59 and by noncovalent inhibition through binding at the substrate (PGH(2)) binding site. The mechanism of inhibition is dissected by analysis of the native enzyme and the MPGES1 C59A mutant in the presence of glutathione (GSH) and glutathione sulfonate. The location of inhibitor adduction and noncovalent binding was determined by triple mass spectrometry sequencing and with backbone amide H/D exchange mass spectrometry. The kinetics, regiochemistry, and stereochemistry of the spontaneous reaction of GSH with 15d-PGJ(2) were determined. The question of whether the anti-inflammatory properties of 15d-PGJ(2) are due to inhibition of MPGES1 is discussed.

Advances in structural and functional analysis of membrane proteins by electron crystallography

Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.

Role of basic science in the development of new medicines: examples from the eicosanoid field

The role of basic science in the development of health care has received more and more attention. In my own area of research involving the so-called eicosanoids, there are many examples of how studies of structure and function of small molecules, as well as proteins and genes, have led to new therapeutic agents for treatment of a variety of diseases. In most of the cases, the discoveries have resulted in the recognition of novel therapeutic targets amenable to modulation by small molecules. However, there are also examples in which the molecular mechanisms of actions of drugs, discovered by phenotypic screening, have been elucidated. The majority of the examples in this article consist of approved drugs; however, in some cases, ongoing developments of potential therapeutics are cited.

Identification and development of mPGES-1 inhibitors: where we are at?

Microsomal prostaglandin E synthase-1 (mPGES-1) is the terminal synthase responsible for the synthesis of the pro-tumorigenic prostaglandin E(2) (PGE(2)). mPGES-1 is overexpressed in a wide variety of cancers. Since its discovery in 1997 by Bengt Samuelsson and collaborators, the enzyme has been the object of over 200 peer-reviewed articles. Although today mPGES-1 is considered a validated and promising therapeutic target for anticancer drug discovery, challenges in inhibitor design and selectivity are such that up to this date there are only a few published records of small-molecule inhibitors targeting the enzyme and exhibiting some in vivo anticancer activity. This review summarizes the structures, and the in vitro and in vivo activities of these novel mPGES-1 inhibitors. Challenges that have been encountered are also discussed.

Pre-steady-state kinetic characterization of thiolate anion formation in human leukotriene C₄ synthase

Human leukotriene C₄ synthase (hLTC4S) is an integral membrane protein that catalyzes the committed step in the biosynthesis of cysteinyl-leukotrienes, i.e., formation of leukotriene C₄ (LTC₄). This molecule, together with its metabolites LTD₄ and LTE₄, induces inflammatory responses, particularly in asthma, and thus, the enzyme is an attractive drug target. During the catalytic cycle, glutathione (GSH) is activated by hLTC4S that forms a nucleophilic thiolate anion that will attack LTA₄, presumably according to an S(N)2 reaction to form LTC₄. We observed that GSH thiolate anion formation is rapid and occurs at all three monomers of the homotrimer and is concomitant with stoichiometric release of protons to the medium. The pK(a) (5.9) for enzyme-bound GSH thiol and the rate of thiolate formation were determined (k(obs) = 200 s⁻¹). Taking advantage of a strong competitive inhibitor, glutathionesulfonic acid, shown here by crystallography to bind in the same location as GSH, we determined the overall dissociation constant (K(d((GS) = 14.3 μM). The release of the thiolate was assessed using a GSH release experiment (1.3 s⁻¹). Taken together, these data establish that thiolate anion formation in hLTC4S is not the rate-limiting step for the overall reaction of LTC₄ production (k(cat) = 26 s⁻¹), and compared to the related microsomal glutathione transferase 1, which displays very slow GSH thiolate anion formation and one-third of the sites reactivity, hLTC4S has evolved a different catalytic mechanism.

Molecular docking and competitive binding study discovered different binding modes of microsomal prostaglandin E synthase-1 inhibitors

Microsomal prostaglandin E synthase-1 (mPGES-1) is a newly recognized therapeutic target for the treatment of inflammation, pain, cancer, atherosclerosis, and stroke. Many mPGES-1 inhibitors have been discovered. However, as the structure of the binding site is not well-characterized, none of these inhibitors was designed based on the mPGES-1 structure, and their inhibition mechanism remains to be fully disclosed. Recently, we built a new structural model of mPGES-1 which was well supported by experimental data. Based on this model, molecular docking and competition experiments were used to investigate the binding modes of four representive mPGES-1 inhibitors. As the inhibitor binding sites predicted by docking overlapped with both the substrate and the cofactor binding sites, mPGES-1 inhibitors might act as dual-site inhibitors. This inhibitory mechanism was further verified by inhibitor-cofactor and inhibitor-substrate competition experiments. To investigate the potency-binding site relationships of mPGES-1 inhibitors, we also carried out molecular docking studies for another series of compounds. The docking results correlated well with the different inhibitory effects observed experimentally. Our data revealed that mPGES-1 inhibitors could bind to the substrate and the cofactor binding sites simultaneously, and this dual-site binding mode improved their potency. Future rational design and optimization of mPGES-1 inhibitors can be carried out based on this binding mechanism.

Fragment-based phase extension for three-dimensional structure determination of membrane proteins by electron crystallography

In electron crystallography, membrane protein structure is determined from two-dimensional crystals where the protein is embedded in a membrane. Once large and well-ordered 2D crystals are grown, one of the bottlenecks in electron crystallography is the collection of image data to directly provide experimental phases to high resolution. Here, we describe an approach to bypass this bottleneck, eliminating the need for high-resolution imaging. We use the strengths of electron crystallography in rapidly obtaining accurate experimental phase information from low-resolution images and accurate high-resolution amplitude information from electron diffraction. The low-resolution experimental phases were used for the placement of α helix fragments and extended to high resolution using phases from the fragments. Phases were further improved by density modifications followed by fragment expansion and structure refinement against the high-resolution diffraction data. Using this approach, structures of three membrane proteins were determined rapidly and accurately to atomic resolution without high-resolution image data.

Microsomal prostaglandin E synthase-1 exhibits one-third-of-the-sites reactivity

mPGES-1 (microsomal prostaglandin E synthase-1) is a newly recognized target for the treatment of inflammatory diseases. As the terminal enzyme of the prostaglandin production pathway, mPGES-1 inhibition may have a low risk of side effects. Inhibitors of mPGES-1 have attracted considerable attention as next-generation anti-inflammatory drugs. However, as mPGES-1 is a membrane protein, its enzymatic mechanism remains to be disclosed fully. We used MD (molecular dynamics) simulations, mutation analysis, hybrid experiments and co-IP (co-immunoprecipitation) to investigate the conformation transitions of mPGES-1 during catalysis. mPGES-1 forms a homotrimer with three substrate-binding sites (pockets). In the MD simulation, only one substrate molecule could bind to one of the pockets and form the active complex, suggesting that the mPGES-1 trimer has only one pocket active at any given time. This one-third-of-the-sites reactivity enzyme mechanism was verified further by hybridization experiments and MD simulations. The results of the present study revealed for the first time a novel one-third-of-the-sites reactivity enzyme mechanism for mPGES-1, and the unique substrate-binding pocket in our model constituted an active conformation that was suitable for further enzymatic mechanism study and structural-based drug design against mPGES-1.

Novel human mPGES-1 inhibitors identified through structure-based virtual screening

Microsomal prostaglandin E synthase-1 (mPGES-1) is an inducible prostaglandin E synthase after exposure to pro-inflammatory stimuli and, therefore, represents a novel target for therapeutic treatment of acute and chronic inflammatory disorders. It is essential to identify mPGES-1 inhibitors with novel scaffolds as new leads or hits for the purpose of drug design and discovery that aim to develop the next-generation anti-inflammatory drugs. Herein we report novel mPGES-1 inhibitors identified through a combination of large-scale structure-based virtual screening, flexible docking, molecular dynamics simulations, binding free energy calculations, and in vitro assays on the actual inhibitory activity of the computationally selected compounds. The computational studies are based on our recently developed three-dimensional (3D) structural model of mPGES-1 in its open state. The combined computational and experimental studies have led to identification of new mPGES-1 inhibitors with new scaffolds. In particular, (Z)-5-benzylidene-2-iminothiazolidin-4-one is a promising novel scaffold for the further rational design and discovery of new mPGES-1 inhibitors. To our best knowledge, this is the first time a 3D structural model of the open state mPGES-1 is used in structure-based virtual screening of a large library of available compounds for the mPGES-1 inhibitor identification. The positive experimental results suggest that our recently modeled trimeric structure of mPGES-1 in its open state is ready for the structure-based drug design and discovery.

Investigation into potent inflammation inhibitors from traditional Chinese medicine

Microsomal prostaglandin E synthase-1 (mPGES-1) is the key enzyme for prostaglandin E2 (PGE2) generation during inflammation and is a potential target for designing anti-inflammatory drugs. Potential inhibitors of m-PGES-1 were selected from traditional Chinese medicine (TCM Database@Taiwan) based on the pharmacophore map generated by the top HypoGen hypothesis and validated using structure- and ligand-based analysis. Key features for potential m-PGES-1 inhibitors include pi-interactions and H-bond donors. TCM compounds, shanciol B, shanciol A, castilliferol, and aurantiamide acetate, contoured to the quantitative structure-activity relationship pharmacophore and exhibited high docking scores and binding stability with m-PGES-1. Bioactivity models multiple linear regression (MLR) and support vector machine also supported activity predictions for the candidate compounds. Our results indicate that the investigated TCM compounds could be of use for development into mPGES-1 inhibitors.

Location of inhibitor binding sites in the human inducible prostaglandin E synthase, MPGES1

The inducible microsomal prostaglandin E(2) synthase 1 (MPGES1) is an integral membrane protein coexpressed with and functionally coupled to cyclooxygenase 2 (COX-2) generating the pro-inflammatory molecule PGE(2). The development of effective inhibitors of MPGES1 holds promise as a highly selective route for controlling inflammation. In this paper, we describe the use of backbone amide H/D exchange mass spectrometry to map the binding sites of different types of inhibitors of MPGES1. The results reveal the locations of specific inhibitor binding sites that include the GSH binding site and a hydrophobic cleft in the protein thought to accommodate the prostaglandin H(2) substrate. In the absence of three-dimensional crystal structures of the enzyme-bound inhibitors, the results provide clear physical evidence that three pharmacologically active inhibitors bind in a hydrophobic cleft composed of sections of transmembrane helices Ia, IIb, IIIb, and IVb at the interface of subunits in the trimer. In principle, the H/D exchange behavior of the protein can be used as a preliminary guide for optimization of inhibitor efficacy. Finally, a comparison of the structures and H/D exchange behavior of MPGES1 and the related enzyme MGST1 in the presence of glutathione and the inhibitor glutathione sulfonate confirms the unusual observation that two proteins from the same superfamily harbor GSH binding sites in different locations.

Mechanisms of induction of cytosolic and microsomal glutathione transferase (GST) genes by xenobiotics and pro-inflammatory agents

Glutathione transferase (GST) isoezymes are encoded by three separate families of genes (designated cytosolic, microsomal and mitochondrial transferases), with distinct evolutionary origins, that provide mammalian species with protection against electrophiles and oxidative stressors in the environment. Members of the cytosolic class Alpha, Mu, Pi and Theta GST, and also certain microsomal transferases (MGST2 and MGST3), are up-regulated by a diverse spectrum of foreign compounds typified by phenobarbital, 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene, pregnenolone-16α-carbonitrile, 3-methylcholanthrene, 2,3,7,8-tetrachloro-dibenzo-p-dioxin, β-naphthoflavone, butylated hydroxyanisole, ethoxyquin, oltipraz, fumaric acid, sulforaphane, coumarin, 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole, 12-O-tetradecanoylphorbol-13-acetate, dexamethasone and thiazolidinediones. Collectively, these compounds induce gene expression through the constitutive androstane receptor (CAR), the pregnane X receptor (PXR), the aryl hydrocarbon receptor (AhR), NF-E2-related factor 2 (Nrf2), peroxisome proliferator-activated receptor-γ (PPARγ) and CAATT/enhancer binding protein (C/EBP) β. The microsomal T family includes 5-lipoxygenase activating protein (FLAP), leukotriene C(4) synthase (LTC4S) and prostaglandin E(2) synthase (PGES-1), and these are up-regulated by tumour necrosis factor-α, lipopolysaccharide and transforming growth factor-β. Induction of genes encoding FLAP, LTC4S and PGES-1 is mediated by the transcription factors C/EBPα, C/EBPδ, C/EBPϵ, nuclear factor-κB and early growth response-1. In this article we have reviewed the literature describing the mechanisms by which cytosolic and microsomal GST are up-regulated by xenobiotics, drugs, cytokines and endotoxin. We discuss cross-talk between the different induction mechanisms, and have employed bioinformatics to identify cis-elements in the upstream regions of GST genes to which the various transcription factors mentioned above may be recruited.

Microsomal glutathione transferase 1: mechanism and functional roles

Microsomal glutathione transferase 1 (MGST1) belongs to a superfamily named MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism). This family is represented in all life forms, except archae. Of the six human members, three are specialized in the synthesis of leukotrienes and prostaglandin E, whereas the others (MGST1-3) have potential roles in drug metabolism. MGST1 has a well-established role in the conjugation of electrophiles and oxidative stress protection, whereas MGST2 and 3 have been less studied. Here, we review the recent advances regarding the structure, mechanism, and functional roles of MGST1. Emerging data show that the enzyme is overexpressed in certain tumors and support a role for the enzyme in protecting cells from cytostatic drugs.

Macrophage migration inhibitory factor activates cyclooxygenase 2-prostaglandin E2 in cultured spinal microglia

In our previous study, peripheral inflammatory stimulation evoked production of macrophage migration inhibitory factor (MIF) in the spinal cord and found spinal microglia are the major source of MIF in this context. Given the contribution of the activated-microglia to the inflammatory neuropathy plus the role for upregulated COX 2 expression and PGE(2) production in the severity of clinical manifestations of these neuroinflammatory conditions, we herein tested the hypothesis that in vitro MIF stimulation to spinal microglia could result in an activation of COX 2-PGE(2) system by MIF-CD74 interaction. We found MIF played roles in evoking COX 2 mRNA and protein expression in a dose-dependent manner correspondingly in changes in PGE(2) level in the cultured rat microglia, but these changes could be inhibited by genetic deletion of CD74. Finally, MIF-induced COX 2-PGE(2) activation could be blocked by selective inhibitors of p44/p42 and p38 MAPKs. These data highlight MIF/CD74 interaction induces upregulation of COX 2 expression and PGE(2) secretion in primary rodent microglia, and further this effect is associated with downstream activation of p38 and p44/p42 signaling cascades, and favors the role of MIF as a novel pathway for microglia-associated neuroinflammation.

Photo-products of retinal pigment epithelial bisretinoids react with cellular thiols

PURPOSE

Bisretinoids such as A2E that accumulate as components of the lipofuscin of retinal pigment epithelial cells are implicated in some retinal disease processes. These compounds undergo light-induced oxidation and cleavage with the latter releasing of a mixture of aldehyde-bearing fragments, including dicarbonyl methylglyoxal. We tested for the reactivity of photooxidation and photodegradation products of A2E with thiol-containing glutathione (GSH).

METHODS

In cell-free assays, we measured the ability of photooxo-A2E to competitively inhibit the GSH-mediated reduction of the thiol reagent 5,5'-dithiobis-(2-nitrobenzoic acid). Cellular GSH was assayed colorimetrically. Products of GSH reduction and GSH-adducts were detected by electrospray ionization mass spectrometry (ESI-MS) and GSH and oxidized GSH (glutathione disulfide [GSSG]) were quantified from chromatographic peak areas.

RESULTS

We found that GSH can donate hydrogen atoms to, and form conjugates with, photooxidized forms of the bisretinoid A2E and with its photocleavage products. Reaction with non-photooxidized A2E was not observed. Chemical reduction by GSH involved the donation of a hydrogen atom from each of two GSHs. The ratio of GSH consumed to GSSG formed was consistent with GSH being used for both reduction and adduct formation. With the aid of synthesized standards, methylglyoxal-GSH adducts were identified within mixtures of GSH and photooxidized A2E; the adducts formed noncatalytically and by glutathione-S-transferase mediation.

CONCLUSIONS

Reduction and adduct formation by GSH likely limits the reactivity of bisretinoid photoproducts and may aid their elimination from the cells. These findings are significant to forms of macular degeneration associated with bisretinoid formation and maculopathy stemming from GSH synthase deficiency.

The use of trehalose in the preparation of specimens for molecular electron microscopy

Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.

Pharmacophore modeling and virtual screening for novel acidic inhibitors of microsomal prostaglandin E₂ synthase-1 (mPGES-1)

Microsomal prostaglandin E₂ synthase-1 (mPGES-1) catalyzes prostaglandin E₂ formation and is considered as a potential anti-inflammatory pharmacological target. To identify novel chemical scaffolds active on this enzyme, two pharmacophore models for acidic mPGES-1 inhibitors were developed and theoretically validated using information on mPGES-1 inhibitors from literature. The models were used to screen chemical databases supplied from the National Cancer Institute (NCI) and the Specs. Out of 29 compounds selected for biological evaluation, nine chemically diverse compounds caused concentration-dependent inhibition of mPGES-1 activity in a cell-free assay with IC₅₀ values between 0.4 and 7.9 μM, respectively. Further pharmacological characterization revealed that also 5-lipoxygenase (5-LO) was inhibited by most of these active compounds in cell-free and cell-based assays with IC₅₀ values in the low micromolar range. Together, nine novel chemical scaffolds inhibiting mPGES-1 are presented that may possess anti-inflammatory properties based on the interference with eicosanoid biosynthesis.

Detection of membrane protein two-dimensional crystals in living cells

It is notoriously difficult to grow membrane protein crystals and solve membrane protein structures. Improved detection and screening of membrane protein crystals are needed. We have shown here that second-order nonlinear optical imaging of chiral crystals based on second harmonic generation can provide sensitive and selective detection of two-dimensional protein crystalline arrays with sufficiently low background to enable crystal detection within the membranes of live cells. The method was validated using bacteriorhodopsin crystals generated in live Halobacterium halobium bacteria and confirmed by electron microscopy from the isolated crystals. Additional studies of alphavirus glycoproteins indicated the presence of localized crystalline domains associated with virus budding from mammalian cells. These results suggest that in vivo crystallization may provide a means for expediting membrane protein structure determination for proteins exhibiting propensities for two-dimensional crystal formation.