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1.
Eur J Med Chem ; 201: 112420, 2020 Sep 01.
Article in English | MEDLINE | ID: mdl-32526553

ABSTRACT

Targeting energy metabolism in Mycobacterium tuberculosis (Mtb) is a new paradigm in the search for innovative anti-TB drugs. NADH:menaquinone oxidoreductase is a non-proton translocating type II NADH dehydrogenase (NDH-2) that is an essential enzyme in the respiratory chain of Mtb and is not found in mammalian mitochondria. Phenothiazines (PTZs) represent one of the most known class of NDH-2 inhibitors, but their use as anti-TB drugs is currently limited by the wide range of potentially serious off-target effects. In this work, we designed and synthesized a series of new PTZs by decorating the scaffold in an unconventional way, introducing various halogen atoms. By replacing the sulfur atom with selenium, a dibromophenoselenazine 20 was also synthesized. Among the synthesized poly-halogenated PTZs (HPTZs), dibromo and tetrachloro derivatives 9 and 11, along with the phenoselenazine 20, emerged with a better anti-TB profile than the therapeutic thioridazine (TZ). They targeted non-replicating Mtb, were bactericidal, and synergized with rifampin and bedaquiline. Moreover, their anti-TB activity was found to be related to the NDH-2 inhibition. Most important, they showed a markedly reduced affinity to dopaminergic and serotonergic receptors respect to the TZ. From this work emerged, for the first time, as the poly-halogenation of the PTZ core, while permitting to maintain good anti-TB profile could conceivably lead to fewer CNS side-effects risk, making more tangible the use of PTZs for this alternative therapeutic application.


Subject(s)
Antitubercular Agents/pharmacology , Organoselenium Compounds/pharmacology , Phenothiazines/pharmacology , Animals , Antitubercular Agents/chemical synthesis , Antitubercular Agents/metabolism , Antitubercular Agents/toxicity , Chlorocebus aethiops , Drug Synergism , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/toxicity , HEK293 Cells , Humans , Microsomes, Liver/metabolism , Molecular Structure , Mycobacterium smegmatis/drug effects , Mycobacterium tuberculosis/drug effects , NADH Dehydrogenase/antagonists & inhibitors , Organoselenium Compounds/chemical synthesis , Organoselenium Compounds/metabolism , Organoselenium Compounds/toxicity , Parasitic Sensitivity Tests , Phenothiazines/chemical synthesis , Phenothiazines/metabolism , Phenothiazines/toxicity , Protein Binding , Receptors, Dopamine D2/metabolism , Receptors, Serotonin/metabolism , Structure-Activity Relationship , Vero Cells
2.
mSphere ; 5(2)2020 03 18.
Article in English | MEDLINE | ID: mdl-32188750

ABSTRACT

Globally, more antimicrobials are used in food-producing animals than in humans, and the extensive use of medically important human antimicrobials poses a significant public health threat in the face of rising antimicrobial resistance (AMR). The development of novel ionophores, a class of antimicrobials used exclusively in animals, holds promise as a strategy to replace or reduce essential human antimicrobials in veterinary practice. PBT2 is a zinc ionophore with recently demonstrated antibacterial activity against several Gram-positive pathogens, although the underlying mechanism of action is unknown. Here, we investigated the bactericidal mechanism of PBT2 in the bovine mastitis-causing pathogen, Streptococcus uberis In this work, we show that PBT2 functions as a Zn2+/H+ ionophore, exchanging extracellular zinc for intracellular protons in an electroneutral process that leads to cellular zinc accumulation. Zinc accumulation occurs concomitantly with manganese depletion and the production of reactive oxygen species (ROS). PBT2 inhibits the activity of the manganese-dependent superoxide dismutase, SodA, thereby impairing oxidative stress protection. We propose that PBT2-mediated intracellular zinc toxicity in S. uberis leads to lethality through multiple bactericidal mechanisms: the production of toxic ROS and the impairment of manganese-dependent antioxidant functions. Collectively, these data show that PBT2 represents a new class of antibacterial ionophores capable of targeting bacterial metal ion homeostasis and cellular redox balance. We propose that this novel and multitarget mechanism of PBT2 makes the development of cross-resistance to medically important antimicrobials unlikely.IMPORTANCE More antimicrobials are used in food-producing animals than in humans, and the extensive use of medically important human antimicrobials poses a significant public health threat in the face of rising antimicrobial resistance. Therefore, the elimination of antimicrobial crossover between human and veterinary medicine is of great interest. Unfortunately, the development of new antimicrobials is an expensive high-risk process fraught with difficulties. The repurposing of chemical agents provides a solution to this problem, and while many have not been originally developed as antimicrobials, they have been proven safe in clinical trials. PBT2, a zinc ionophore, is an experimental therapeutic that met safety criteria but failed efficacy checkpoints against both Alzheimer's and Huntington's diseases. It was recently found that PBT2 possessed potent antimicrobial activity, although the mechanism of bacterial cell death is unresolved. In this body of work, we show that PBT2 has multiple mechanisms of antimicrobial action, making the development of PBT2 resistance unlikely.


Subject(s)
Anti-Bacterial Agents/pharmacology , Clioquinol/analogs & derivatives , Ionophores/pharmacology , Streptococcus/drug effects , Zinc/metabolism , Animals , Cattle , Clioquinol/pharmacology , Female , Mastitis, Bovine/microbiology , Oxidative Stress/drug effects , Reactive Oxygen Species/metabolism , Superoxide Dismutase/antagonists & inhibitors
3.
J Bacteriol ; 202(7)2020 03 11.
Article in English | MEDLINE | ID: mdl-31988080

ABSTRACT

Exoelectrogens are able to transfer electrons extracellularly, enabling them to respire on insoluble terminal electron acceptors. Extensively studied exoelectrogens, such as Geobacter sulfurreducens and Shewanella oneidensis, are Gram negative. More recently, it has been reported that Gram-positive bacteria, such as Listeria monocytogenes and Enterococcus faecalis, also exhibit the ability to transfer electrons extracellularly, although it is still unclear whether this has a function in respiration or in redox control of the environment, for instance, by reducing ferric iron for iron uptake. In this issue of Journal of Bacteriology, Hederstedt and colleagues report on experiments that directly compare extracellular electron transfer (EET) pathways for ferric iron reduction and respiration and find a clear difference (L. Hederstedt, L. Gorton, and G. Pankratova, J Bacteriol 202:e00725-19, 2020, https://doi.org/10.1128/JB.00725-19), providing further insights and new questions into the function and metabolic pathways of EET in Gram-positive bacteria.


Subject(s)
Enterococcus faecalis , Shewanella , Electron Transport , Electrons , Geobacter , Homeostasis , Nutrients , Oxidation-Reduction
4.
J Am Chem Soc ; 142(3): 1311-1320, 2020 01 22.
Article in English | MEDLINE | ID: mdl-31880924

ABSTRACT

Type II NADH:quinone oxidoreductase (NDH-2) plays a crucial role in the respiratory chains of many organisms. Its absence in mammalian cells makes NDH-2 an attractive new target for developing antimicrobials and antiprotozoal agents. We established a novel bioelectrochemical platform to characterize the catalytic behavior of NDH-2 from Caldalkalibacillus thermarum and Listeria monocytogenes strain EGD-e while bound to native-like lipid membranes. Catalysis of both NADH oxidation and lipophilic quinone reduction by membrane-bound NDH-2 followed the Michaelis-Menten model; however, the maximum turnover was only achieved when a high concentration of quinone (>3 mM) was present in the membrane, suggesting that quinone availability regulates NADH-coupled respiration activity. The quinone analogue 2-heptyl-4-hydroxyquinoline-N-oxide inhibited C. thermarum NDH-2 activity, and its potency is higher in a membrane environment compared to assays performed with water-soluble quinone analogues, demonstrating the importance of testing compounds under physiologically relevant conditions. Furthermore, when phenothiazines, one of the most commonly identified NDH-2 inhibitors, were tested, they did not inhibit membrane-bound NDH-2. Instead, our assay platform unexpectedly suggests a novel mode of phenothiazine action where chlorpromazine, a promising antitubercular agent and key medicine used to treat psychotic disorders, is able to disrupt pH gradients across bacterial membranes.


Subject(s)
Electrochemical Techniques/methods , Phenothiazines/chemistry , Bacillaceae/metabolism , Binding Sites , Listeria monocytogenes/metabolism , Oxidation-Reduction , Quinones/metabolism
5.
Front Microbiol ; 10: 1421, 2019.
Article in English | MEDLINE | ID: mdl-31293551

ABSTRACT

Parapoxvirus of red deer in New Zealand (PVNZ) is a species of the Parapoxvirus genus that causes pustular dermatitis. We identified a cluster of genes in PVNZ that encode three unique chemokine-binding proteins (CBPs) namely ORF112.0, ORF112.3 and ORF112.6. Chemokines are a large family of molecules that direct cell trafficking to sites of inflammation and through lymphatic organs. The PVNZ-CBPs were analyzed by surface plasmon resonance against a broad spectrum of CXC, CC, XC and CX3C chemokines and were found to differ in their specificity and binding affinity. ORF112.0 interacted with chemokines from the CXC, CC and XC classes of chemokines with nM affinities. The ORF112.3 showed a preference for CXC chemokines, while ORF112.6 showed pM affinity binding for CC chemokines. Structural modeling analysis showed alterations in the chemokine binding sites of the CBPs, although the core structure containing two ß-sheets and three α-helices being conserved with the other parapoxvirus CBPs. Chemotaxis assays using neutrophils and monocytes revealed inhibitory impact of the CBPs on cell migration. Our results suggest that the PVNZ-CBPs are likely to have evolved through a process of gene duplication and divergence, and may have a role in suppressing inflammation and the anti-viral immune response.

6.
Open Biol ; 9(6): 190066, 2019 06 28.
Article in English | MEDLINE | ID: mdl-31238823

ABSTRACT

The crystal structure of the F1-catalytic domain of the adenosine triphosphate (ATP) synthase has been determined from the pathogenic anaerobic bacterium Fusobacterium nucleatum. The enzyme can hydrolyse ATP but is partially inhibited. The structure is similar to those of the F1-ATPases from Caldalkalibacillus thermarum, which is more strongly inhibited in ATP hydrolysis, and in Mycobacterium smegmatis, which has a very low ATP hydrolytic activity. The ßE-subunits in all three enzymes are in the conventional 'open' state, and in the case of C. thermarum and M. smegmatis, they are occupied by an ADP and phosphate (or sulfate), but in F. nucleatum, the occupancy by ADP appears to be partial. It is likely that the hydrolytic activity of the F. nucleatum enzyme is regulated by the concentration of ADP, as in mitochondria.


Subject(s)
Adenosine Diphosphate/metabolism , Fusobacterium nucleatum/enzymology , Proton-Translocating ATPases/chemistry , Proton-Translocating ATPases/metabolism , Bacterial Proteins/chemistry , Crystallography, X-Ray , Fusobacterium nucleatum/chemistry , Hydrolysis , Models, Molecular , Molecular Conformation , Protein Domains
7.
Microbiology (Reading) ; 165(4): 475-487, 2019 04.
Article in English | MEDLINE | ID: mdl-30777814

ABSTRACT

Bacitracin is a cell wall targeting antimicrobial with clinical and agricultural applications. With the growing mismatch between antimicrobial resistance and development, it is essential we understand the molecular mechanisms of resistance in order to prioritize and generate new effective antimicrobials. BcrR is a unique membrane-bound one-component system that regulates high-level bacitracin resistance in Enterococcus faecalis. In the presence of bacitracin, BcrR activates transcription of the bcrABD operon conferring resistance through a putative ATP-binding cassette (ABC) transporter (BcrAB). BcrR has three putative functional domains, an N-terminal helix-turn-helix DNA-binding domain, an intermediate oligomerization domain and a C-terminal transmembrane domain. However, the molecular mechanisms of signal transduction remain unknown. Random mutagenesis of bcrR was performed to generate loss- and gain-of-function mutants using transcriptional reporters fused to the target promoter PbcrA. Fifteen unique mutants were isolated across all three proposed functional domains, comprising 14 loss-of-function and one gain-of-function mutant. The gain-of-function variant (G64D) mapped to the putative dimerization domain of BcrR, and functional analyses indicated that the G64D mutant constitutively expresses the PbcrA-luxABCDE reporter. DNA-binding and membrane insertion were not affected in the five mutants chosen for further characterization. Homology modelling revealed putative roles for two key residues (R11 and S33) in BcrR activation. Here we present a new model of BcrR activation and signal transduction, providing valuable insight into the functional characterization of membrane-bound one-component systems and how they can coordinate critical bacterial responses, such as antimicrobial resistance.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Bacitracin/metabolism , Cell Membrane/metabolism , Drug Resistance, Bacterial , Signal Transduction/physiology , ATP-Binding Cassette Transporters/chemistry , ATP-Binding Cassette Transporters/genetics , Anti-Bacterial Agents/pharmacology , Bacillus subtilis/drug effects , Bacillus subtilis/genetics , Bacitracin/pharmacology , Drug Resistance, Bacterial/genetics , Enterococcus faecalis/drug effects , Enterococcus faecalis/genetics , Gene Expression Regulation, Bacterial , Genes, Bacterial/genetics , Mutation , Operon , Promoter Regions, Genetic , Protein Binding , Protein Domains
8.
Bioorg Med Chem Lett ; 28(13): 2239-2243, 2018 07 15.
Article in English | MEDLINE | ID: mdl-29859905

ABSTRACT

Energy generation is a promising area of drug discovery for both bacterial pathogens and parasites. Type II NADH dehydrogenase (NDH-2), a vital respiratory membrane protein, has attracted attention as a target for the development of new antitubercular and antimalarial agents. To date, however, no potent, specific inhibitors have been identified. Here, we performed a site-directed screening technique, tethering-fragment based drug discovery, against wild-type and mutant forms of NDH-2 containing engineered active-site cysteines. Inhibitory fragments displayed IC50 values between 3 and 110 µM against NDH-2 mutants. Possible binding poses were investigated by in silico modelling, providing a basis for optimisation of fragment binding and improved potency against NDH-2.


Subject(s)
Bacterial Proteins/metabolism , Drug Design , Enzyme Inhibitors/metabolism , Membrane Proteins/metabolism , NADH Dehydrogenase/metabolism , Bacillaceae/enzymology , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Binding Sites , Cysteine/chemistry , Cysteine/genetics , Enzyme Inhibitors/chemistry , Membrane Proteins/antagonists & inhibitors , Membrane Proteins/chemistry , Membrane Proteins/genetics , Molecular Docking Simulation , Mutagenesis, Site-Directed , Mutation , NADH Dehydrogenase/antagonists & inhibitors , NADH Dehydrogenase/chemistry , NADH Dehydrogenase/genetics , Protein Binding
9.
Biochim Biophys Acta Bioenerg ; 1859(7): 482-490, 2018 Jul.
Article in English | MEDLINE | ID: mdl-29621505

ABSTRACT

Type II NADH:quinone oxidoreductase (NDH-2) is a proposed drug-target of major pathogenic microorganisms such as Mycobacterium tuberculosis and Plasmodium falciparum. Many NDH-2 inhibitors have been identified, but rational drug development is impeded by the lack of information regarding their mode of action and associated inhibitor-bound NDH-2 structure. We have determined the crystal structure of NDH-2 complexed with a quinolone inhibitor 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO). HQNO is nested into the slot-shaped tunnel of the Q-site, in which the quinone-head group is clamped by Q317 and I379 residues, and hydrogen-bonds to FAD. The interaction of HQNO with bacterial NDH-2 is very similar to the native substrate ubiquinone (UQ1) interactions in the yeast Ndi1-UQ1 complex structure, suggesting a conserved mechanism for quinone binding. Further, the structural analysis provided insight how modifications of quinolone scaffolds improve potency (e.g. quinolinyl pyrimidine derivatives) and suggests unexplored target space for the rational design of new NDH-2 inhibitors.


Subject(s)
Quinolones/chemistry , Quinone Reductases/antagonists & inhibitors , Quinone Reductases/chemistry , Bacteria/enzymology , Binding Sites , Crystallography , Drug Design , Hydrogen Bonding , Ubiquinone/chemistry
10.
Article in English | MEDLINE | ID: mdl-28971867

ABSTRACT

A screening of more than 1,500 drug-resistant strains of Mycobacterium tuberculosis revealed evolutionary patterns characteristic of positive selection for three alanine racemase (Alr) mutations. We investigated these mutations using molecular modeling, in vitro MIC testing, as well as direct measurements of enzymatic activity, which demonstrated that these mutations likely confer resistance to d-cycloserine.


Subject(s)
Alanine Racemase/genetics , Bacterial Proteins/genetics , Cycloserine/pharmacology , Drug Resistance, Bacterial/genetics , Mutation , Mycobacterium tuberculosis/genetics , Alanine Racemase/metabolism , Antibiotics, Antitubercular/pharmacology , Bacterial Proteins/metabolism , Evolution, Molecular , Gene Expression , Microbial Sensitivity Tests , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Phylogeny , Selection, Genetic
11.
Acta Crystallogr F Struct Biol Commun ; 73(Pt 10): 541-549, 2017 Oct 01.
Article in English | MEDLINE | ID: mdl-28994401

ABSTRACT

Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5 Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.


Subject(s)
Bacillus/enzymology , Quinone Reductases/chemistry , Quinone Reductases/metabolism , Binding Sites/physiology , Crystallization/methods , Protein Structure, Secondary , Protein Structure, Tertiary , X-Ray Diffraction/methods
12.
Microbiol Spectr ; 5(3)2017 06.
Article in English | MEDLINE | ID: mdl-28597820

ABSTRACT

The emergence and spread of drug-resistant pathogens, and our inability to develop new antimicrobials to combat resistance, have inspired scientists to seek out new targets for drug development. The Mycobacterium tuberculosis complex is a group of obligately aerobic bacteria that have specialized for inhabiting a wide range of intracellular and extracellular environments. Two fundamental features in this adaptation are the flexible utilization of energy sources and continued metabolism in the absence of growth. M. tuberculosis is an obligately aerobic heterotroph that depends on oxidative phosphorylation for growth and survival. However, several studies are redefining the metabolic breadth of the genus. Alternative electron donors and acceptors may provide the maintenance energy for the pathogen to maintain viability in hypoxic, nonreplicating states relevant to latent infection. This hidden metabolic flexibility may ultimately decrease the efficacy of drugs targeted against primary dehydrogenases and terminal oxidases. However, it may also open up opportunities to develop novel antimycobacterials targeting persister cells. In this review, we discuss the progress in understanding the role of energetic targets in mycobacterial physiology and pathogenesis and the opportunities for drug discovery.


Subject(s)
Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/metabolism , Oxidative Phosphorylation/drug effects , Tuberculosis/metabolism , Antitubercular Agents/pharmacology , Drug Discovery , Drug Resistance, Bacterial , Energy Metabolism/drug effects , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/growth & development , Oxidoreductases/drug effects , Oxidoreductases/metabolism , Tuberculosis/drug therapy , Tuberculosis/microbiology
13.
Mol Reprod Dev ; 84(7): 626-637, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28500669

ABSTRACT

The hypothesis that, in contrast to other transforming growth factor-beta (TGFß) superfamily ligands, the dose-response curve of Anti-Müllerian hormone (AMH) is unmodulated was tested by examining whether known TGFB superfamily modulators affect AMH signaling, using a P19/BRE luciferase reporter assay. AMHC and AMHN,C activated the reporter with an EC50 of approximately 0.5 nM. Follistatins (FS) produced concentration-dependent increases in AMHC - and AMHN,C -initiated reporter activity, with FS288 being more potent than FS315; however, the maximum bioactivity of AMH was not altered by either follistatin. Thirteen other TGFß regulators (Chordin, Chordin-like 1, Chordin-like 2, Differential screening-selected gene aberrative in neuroblastoma [DAN], Decorin, Endoglin, Follistatin-like 1, Follistatin-like 3, Follistatin-like 4, Noggin, α2 macroglobulin, TGFß receptor 3, Von Willebrand factor C domain-containing 2) had little or no effect. Surface plasmon resonance analysis showed no significant association between FS288 and AMHC , suggesting that FS288 indirectly regulates AMH signaling. Activin A, a direct target of FS288, did not itself induce reporter activity in P19 cells, but did prevent the FS288-induced increase in AMH signaling. Hence, local concentrations of FS288 and Activin A may influence the response of some cell types to AMH.


Subject(s)
Anti-Mullerian Hormone/chemistry , Follistatin/chemistry , Signal Transduction , Surface Plasmon Resonance , Animals , Anti-Mullerian Hormone/genetics , Cell Line , Follistatin/genetics , Follistatin/metabolism , Humans , Mice
14.
Sci Rep ; 7: 40165, 2017 01 09.
Article in English | MEDLINE | ID: mdl-28067272

ABSTRACT

Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.


Subject(s)
Catalysis , Quinone Reductases/chemistry , Quinone Reductases/metabolism , Bacillales , Binding Sites , Dinitrocresols/metabolism , Kinetics , Protein Binding , Reactive Oxygen Species/metabolism
15.
PLoS One ; 11(12): e0168007, 2016.
Article in English | MEDLINE | ID: mdl-27936239

ABSTRACT

Bovine papular stomatitis virus (BPSV) is a Parapoxvirus that induces acute pustular skin lesions in cattle and is transmissible to humans. Previous studies have shown that BPSV encodes a distinctive chemokine-binding protein (CBP). Chemokines are critically involved in the trafficking of immune cells to sites of inflammation and infected tissue, suggesting that the CBP plays a role in immune evasion by preventing immune cells reaching sites of infection. We hypothesised that the BPSV-CBP binds a wide range of inflammatory chemokines particularly those involved in BPSV skin infection, and inhibits the recruitment of immune cells from the blood into inflamed skin. Molecular analysis of the purified protein revealed that the BPSV-CBP is a homodimeric polypeptide with a MW of 82.4 kDa whilst a comprehensive screen of inflammatory chemokines by surface plasmon resonance showed high-affinity binding to a range of chemokines within the CXC, CC and XC subfamilies. Structural analysis of BPSV-CBP, based on the crystal structure of orf virus CBP, provided a probable explanation for these chemokine specificities at a molecular level. Functional analysis of the BPSV-CBP using transwell migration assays demonstrated that it potently inhibited chemotaxis of murine neutrophils and monocytes in response to CXCL1, CXCL2 as well as CCL2, CCL3 and CCL5 chemokines. In order to examine the effects of CBP in vivo, we used murine skin models to determine its impact on inflammatory cell recruitment such as that observed during BPSV infection. Intradermal injection of BPSV-CBP blocked the influx of neutrophils and monocytes in murine skin in which inflammation was induced with lipopolysaccharide. Furthermore, intradermal injection of BPSV-CBP into injured skin, which more closely mimics BPSV lesions, delayed the influx of neutrophils and reduced the recruitment of MHC-II+ immune cells to the wound bed. Our findings suggest that the CBP could be important in pathogenesis of BPSV infections.


Subject(s)
Chemokines/metabolism , Chemotaxis, Leukocyte/physiology , Disease Models, Animal , Inflammation/pathology , Monocytes/pathology , Neutrophils/pathology , Parapoxvirus/metabolism , Viral Proteins/physiology , Wounds and Injuries/pathology , Amino Acid Sequence , Animals , Dimerization , Mice , Protein Conformation , Sequence Homology, Amino Acid , Surface Plasmon Resonance , Viral Proteins/chemistry
16.
Biochem J ; 473(8): 1063-72, 2016 Apr 15.
Article in English | MEDLINE | ID: mdl-26929403

ABSTRACT

CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.


Subject(s)
CRISPR-Associated Proteins/chemistry , CRISPR-Associated Proteins/metabolism , CRISPR-Cas Systems/physiology , Endodeoxyribonucleases/chemistry , Endodeoxyribonucleases/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Crystallization , Crystallography, X-Ray , Pectobacterium/metabolism , Protein Structure, Secondary , Protein Structure, Tertiary
17.
Biochem J ; 473(9): 1267-80, 2016 05 01.
Article in English | MEDLINE | ID: mdl-26964898

ABSTRACT

Glutamate racemase (MurI) is responsible for providing D-glutamate for peptidoglycan biosynthesis in bacteria and has been a favoured target in pharmaceutical drug design efforts. It has recently been proven to be essential in Mycobacterium tuberculosis, the causative organism of tuberculosis, a disease for which new medications are urgently needed. In the present study, we have determined the protein crystal structures of MurI from both M. tuberculosis and Mycobacterium smegmatis in complex with D-glutamate to 2.3 Å and 1.8 Å resolution respectively. These structures are conserved, but reveal differences in their active site architecture compared with that of other MurI structures. Furthermore, compounds designed to target other glutamate racemases have been screened but do not inhibit mycobacterial MurI, suggesting that a new drug design effort will be needed to develop inhibitors. A new type of MurI dimer arrangement has been observed in both structures, and this arrangement becomes the third biological dimer geometry for MurI found to date. The mycobacterial MurI dimer is tightly associated, with a KD in the nanomolar range. The enzyme binds D- and L-glutamate specifically, but is inactive in solution unless the dimer interface is mutated. We created triple mutants of this interface in the M. smegmatis glutamate racemase (D26R/R105A/G194R or E) that have appreciable activity (kcat=0.056-0.160 min(-1) and KM=0.26-0.51 mM) and can be utilized to screen proposed antimicrobial candidates for inhibition.


Subject(s)
Amino Acid Isomerases/chemistry , Bacterial Proteins/chemistry , Glutamic Acid/chemistry , Mycobacterium tuberculosis/enzymology , Amino Acid Isomerases/genetics , Amino Acid Substitution , Bacterial Proteins/genetics , Mutation, Missense , Mycobacterium tuberculosis/genetics , Protein Domains
18.
Structure ; 23(11): 2111-21, 2015 Nov 03.
Article in English | MEDLINE | ID: mdl-26455797

ABSTRACT

CCAAT-enhancer binding proteins (C/EBPs) are transcription factors that play a central role in the differentiation of myeloid cells and adipocytes. Tribbles pseudokinases govern levels of C/EBPs by recruiting them to the COP1 ubiquitin ligase for ubiquitination. Here, we present the first crystal structure of a Tribbles protein, which reveals a catalytically inactive TRIB1 pseudokinase domain with a unique adaptation in the αC helix. A second crystal structure and biophysical studies of TRIB1 with its C-terminal extension, which includes the COP1-binding motif, show that the C-terminal extension is sequestered at a site formed by the modified TRIB1 αC helix. In addition, we have identified and characterized the TRIB1 substrate-recognition sequence within C/EBPα, which is evolutionarily conserved in C/EBP transcription factors. Binding studies indicate that C/EBPα recruitment is weaker in the presence of the C-terminal COP1-binding motif, but the magnitude of this effect suggests that the two bind distinct rather directly overlapping binding sites.


Subject(s)
CCAAT-Enhancer-Binding Protein-alpha/metabolism , Enhancer Elements, Genetic , Intracellular Signaling Peptides and Proteins/chemistry , Protein Serine-Threonine Kinases/antagonists & inhibitors , Amino Acid Motifs , Amino Acid Sequence , Binding Sites , CCAAT-Enhancer-Binding Protein-alpha/chemistry , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Molecular Sequence Data , Protein Binding , Protein Serine-Threonine Kinases/chemistry , Protein Serine-Threonine Kinases/metabolism
19.
Structure ; 23(7): 1199-213, 2015 Jul 07.
Article in English | MEDLINE | ID: mdl-26095031

ABSTRACT

The chemokine binding protein (CKBP) from orf virus (ORFV) binds with high affinity to chemokines from three classes, C, CC, and CXC, making it unique among poxvirus CKBPs described to date. We present its crystal structure alone and in complex with three CC chemokines, CCL2, CCL3, and CCL7. ORFV CKBP possesses a ß-sandwich fold that is electrostatically and sterically complementary to its binding partners. Chemokines bind primarily through interactions involving the N-terminal loop and a hydrophobic recess on the ORFV CKBP ß-sheet II surface, and largely polar interactions between the chemokine 20s loop and a negatively charged surface groove located at one end of the CKBP ß-sheet II surface. ORFV CKBP interacts with leukocyte receptor and glycosaminoglycan binding sites found on the surface of bound chemokines. SEC-MALLS and chromatographic evidence is presented supporting that ORFV CKBP is a dimer in solution over a broad range of protein concentrations.


Subject(s)
Chemokines/chemistry , Orf virus/chemistry , Viral Proteins/chemistry , Amino Acid Sequence , Binding Sites , Conserved Sequence , Crystallography, X-Ray , HEK293 Cells , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Molecular Sequence Data , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Quaternary , Protein Structure, Secondary , Solutions
20.
Eur J Med Chem ; 93: 501-10, 2015 Mar 26.
Article in English | MEDLINE | ID: mdl-25743213

ABSTRACT

Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that has roles in the innate immune response, and also contributes to inflammatory disease. While the biological properties of MIF are closely linked to protein-protein interactions, MIF also has tautomerase activity. Inhibition of this activity interferes with the interaction of MIF with protein partners e.g. the CD74 receptor, and tautomerase inhibitors show promise in disease models including multiple sclerosis and colitis. Isothiocyanates inhibit MIF tautomerase activity via covalent modification of the N-terminal proline. We systematically explored variants of benzyl and phenethyl isothiocyanates, to define determinants of inhibition. In particular, substitution with hydroxyl, chloro, fluoro and trifluoro moieties at the para and meta positions were evaluated. In assays on treated cells and recombinant protein, the IC50 varied from 250 nM to >100 µM. X-ray crystal structures of selected complexes revealed that two binding modes are accessed by some compounds, perhaps owing to strain in short linkers between the isothiocyanate and aromatic ring. The variety of binding modes confirms the existence of two subsites for inhibitors and establishes a platform for the development of potent inhibitors of MIF that only need to target one of these subsites.


Subject(s)
Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Intramolecular Oxidoreductases/antagonists & inhibitors , Intramolecular Oxidoreductases/metabolism , Isothiocyanates/metabolism , Isothiocyanates/pharmacology , Macrophage Migration-Inhibitory Factors/antagonists & inhibitors , Macrophage Migration-Inhibitory Factors/metabolism , Drug Design , Humans , Intramolecular Oxidoreductases/chemistry , Jurkat Cells , Macrophage Migration-Inhibitory Factors/chemistry , Molecular Docking Simulation , Protein Binding , Protein Conformation
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