Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria.

Infection by the human bacterial pathogen Listeria monocytogenes is mainly controlled by the positive regulatory factor A (PrfA), a member of the Crp/Fnr family of transcriptional activators. Published data suggest that PrfA requires the binding of a cofactor for full activity, and it was recently proposed that glutathione (GSH) could fulfill this function. Here we report the crystal structures of PrfA in complex with GSH and in complex with GSH and its cognate DNA, the hly operator PrfA box motif. These structures reveal the structural basis for a GSH-mediated allosteric mode of activation of PrfA in the cytosol of the host cell. The crystal structure of PrfAWT in complex only with DNA confirms that PrfAWT can adopt a DNA binding-compatible structure without binding the GSH activator molecule. By binding to PrfA in the cytosol of the host cell, GSH induces the correct fold of the HTH motifs, thus priming the PrfA protein for DNA interaction.

Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.

Thyroid disruption by xenobiotics is associated with a broad spectrum of severe adverse outcomes. One possible molecular target of thyroid hormone disrupting chemicals (THDCs) is transthyretin (TTR), a thyroid hormone transporter in vertebrates. To better understand the interactions between TTR and THDCs, we determined the crystallographic structures of human TTR in complex with perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), and 2,2',4,4'-tetrahydroxybenzophenone (BP2). The molecular interactions between the ligands and TTR were further characterized using molecular dynamics simulations. A structure-based virtual screening (VS) protocol was developed with the intention of providing an efficient tool for the discovery of novel TTR-binders from the Tox21 inventory. Among the 192 predicted binders, 12 representatives were selected, and their TTR binding affinities were studied with isothermal titration calorimetry, of which seven compounds had binding affinities between 0.26 and 100 µM. To elucidate structural details in their binding to TTR, crystal structures were determined of TTR in complex with four of the identified compounds including 2,6-dinitro-p-cresol, bisphenol S, clonixin, and triclopyr. The compounds were found to bind in the TTR hormone binding sites as predicted. Our results show that the developed VS protocol is able to successfully identify potential THDCs, and we suggest that it can be used to propose THDCs for future toxicological evaluations.

Staphylococcus aureus thiaminase II: oligomerization warrants proteolytic protection against serine proteases.

Staphylococcus aureus TenA (SaTenA) is a thiaminase type II enzyme that catalyzes the deamination of aminopyrimidine, as well as the cleavage of thiamine into 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 5-(2-hydroxyethyl)-4-methylthiazole (THZ), within thiamine (vitamin B1) metabolism. Further, by analogy with studies of Bacillus subtilis TenA, SaTenA may act as a regulator controlling the secretion of extracellular proteases such as the subtilisin type of enzymes in bacteria. Thiamine biosynthesis has been identified as a potential drug target of the multi-resistant pathogen S. aureus and therefore all enzymes involved in the S. aureus thiamine pathway are presently being investigated in detail. Here, the structure of SaTenA, determined by molecular replacement and refined at 2.7 Šresolution to an R factor of 21.6% with one homotetramer in the asymmetric unit in the orthorhombic space group P212121, is presented. The tetrameric state of wild-type (WT) SaTenA was postulated to be the functional biological unit and was confirmed by small-angle X-ray scattering (SAXS) experiments in solution. To obtain insights into structural and functional features of the oligomeric SaTenA, comparative kinetic investigations as well as experiments analyzing the structural stability of the WT SaTenA tetramer versus a monomeric SaTenA mutant were performed.

Transthyretin Binding Mode Dichotomy of Fluorescent trans-Stilbene Ligands.

The orientations of ligands bound to the transthyretin (TTR) thyroxine (T4) binding site are difficult to predict. Conflicting binding modes of resveratrol have been reported. We previously reported two resveratrol based trans-stilbene fluorescent ligands, (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol (SB-11) and (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol (SB-14), that bind native and misfolded protofibrillar TTR. The binding orientations of these two analogous ligands to native tetrameric TTR were predicted to be opposite. Herein we report the crystal structures of these TTR:ligand complexes. Opposite binding modes were verified but were different than predicted. The reverse binding mode (SB-14) placing the naphthalene moiety toward the opening of the binding pocket renders the fluorescent ligand pH sensitive due to changes in Lys15 amine protonation. Conversely, the forward binding mode (SB-11) placing the naphthalene inward mediates a stabilizing conformational change, allowing intersubunit H-bonding between Ser117 of different monomers across the dimer interface. Our structures of TTR complexes answer important questions in ligand design and interpretation of trans-stilbene binding modes to the TTR T4 binding site.

Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study.

Misfolding and aggregation of transthyretin (TTR) cause several amyloid diseases. Besides being an amyloidogenic protein, TTR has an affinity for bicyclic small-molecule ligands in its thyroxine (T4) binding site. One class of TTR ligands are trans-stilbenes. The trans-stilbene scaffold is also widely applied for amyloid fibril-specific ligands used as fluorescence probes and as positron emission tomography tracers for amyloid detection and diagnosis of amyloidosis. We have shown that native tetrameric TTR binds to amyloid ligands based on the trans-stilbene scaffold providing a platform for the determination of high-resolution structures of these important molecules bound to protein. In this study, we provide spectroscopic evidence of binding and X-ray crystallographic structure data on tetrameric TTR complex with the fluorescent salicylic acid-based pyrene amyloid ligand (Py1SA), an analogue of the Congo red analogue X-34. The ambiguous electron density from the X-ray diffraction, however, did not permit Py1SA placement with enough confidence likely due to partial ligand occupancy. Instead, the preferred orientation of the Py1SA ligand in the binding pocket was determined by molecular dynamics and umbrella sampling approaches. We find a distinct preference for the binding modes with the salicylic acid group pointing into the pocket and the pyrene moiety outward to the opening of the T4 binding site. Our work provides insight into TTR binding mode preference for trans-stilbene salicylic acid derivatives as well as a framework for determining structures of TTR-ligand complexes.

Purification, crystallization and preliminary X-ray diffraction analysis of the thiaminase type II from Staphylococcus aureus.

Thiaminase type II (TenA) catalyzes the deamination of aminopyrimidines, including the cleavage of thiamine to 4-amino-5-hydroxymethyl-2-methylpyrimidine and 5-(2-hydroxyethyl)-4-methylthiazole in the metabolism of thiamine (vitamin B1), in Staphylococcus aureus (Sa). SaTenA was crystallized by the vapour-diffusion method and the resulting crystal diffracted to 2.6 Šresolution usng synchrotron radiation. The crystal is orthorhombic, belonging to space group P2(1)2(1)2(1) with unit-cell parameters a=103.5, b=104.1, c=109.6 Å. With four molecules in the asymmetric unit, the Matthews coefficient is 2.85 Å3 Da(-1). Initial attempts to solve the structure by molecular-replacement techniques were successful.

Characterization and antiglycation activity of phenolic constituents from Viscum album (European Mistletoe).

4'-O-[beta-D-Apiosyl(1-->2)]-beta-D-glucosyl]-5-hydroxyl-7-O-sinapylflavanone (1), 3-(4-acetoxy-3,5-dimethoxy)-phenyl-2E-propenyl-beta-D-glucopyranoside (2), 3-(4-hydroxy-3,5-dimethoxy)-phenyl-2E-propenyl-beta-D-glucopyranoside (3), 5,7-dimethoxy-4'-O-beta-D-glucopyranoside flavanone (4), 4',5-dimethoxy-7-hydroxy flavanone (5), and 5,7-dimethoxy-4'-hydroxy flavanone (6), were isolated from the organic extracts of Viscum album L. (European Mistletoe). These compounds were studied for their anti-glycation and antioxidant properties. The structures of new compounds 1 and 2 were deduced on the basis of spectroscopic evidence.

Rosenones A and B, new anthraquinone derivatives from Aitchisonia rosea.

Rosenones A (1) and B (2), new anthraquinone derivatives, have been isolated from the ethyl acetate soluble fraction of Aitchisonia rosea along with 1,3,6-trihydroxy-2-methylanthraquinone (3) reported for the first time from this species.

Aitchisonides A and B, new iridoid glucosides from Aitchisonia rosea.

Aitchisonides A (1) and B (2), new iridoid glucosides, were isolated from the n-butanolic fraction of Aitchisonia rosea along with deacetylasperulosidic acid (3) and nepetanudoside B (4), which were reported for the first time from the genus Aitchisonia. Their structures have been assigned on the basis of spectral analysis including (1)H and (13)C NMR spectra and by DEPT, 2D COSY, NOESY, and HMBC experiments.

Impact of N-glycosylation site variants during human PrP aggregation and fibril nucleation.

Misfolding and aggregation of the human prion protein (PrP) cause neurodegenerative transmissible spongiform encephalopathies such as Creutzfeldt-Jakob disease. Mature native PrP is composed of 209 residues and is folded into a C-terminal globular domain (residues 125-209) comprising a small two-stranded ß-sheet and three α-helices. The N-terminal domain (residues 23-124) is intrinsically disordered. Expression of truncated PrP (residues 90-231) is sufficient to cause prion disease and residues 90/100-231 is comprising the amyloid-like fibril core of misfolded infectious PrP. During PrP fibril formation under native conditions in vitro, the disordered N-terminal domain slows down fibril formation likely due to a mechanism of initial aggregation forming morphologically disordered aggregates. The morphological disordered aggregate is a transient phase. Nucleation of fibrils occurs from this initial aggregate. The aggregate phase is largely circumvented by seeding with preformed PrP fibrils. In vivo PrP is N-glycosylated at positions Asn181 and Asn197. Little is known about the importance of these positions and their glycans for PrP stability, aggregation and fibril formation. We have in this study taken a step towards that goal by mutating residues 181 and 197 for cysteines to study the positional impact on these processes. We have further by organic synthetic chemistry and chemical modification generated synthetic glycosylations in these positions. Our data shows that residue 181 when mutated to a cysteine is a key residue for self-chaperoning, rendering a trap in the initial aggregate preventing conformational changes towards amyloid fibril formation. Position 197 is less involved in the aggregate trapping and is more geared towards ß-sheet structure conversion within amyloid fibrils. As expected, synthetic glycosylated 197 is less affected towards fibril formation compared to glycosylated 181. Our data are rather compatible with the parallel in-register intermolecular ß-sheet model structure of the PrP90-231 fibril and sheds light on the misfolding transitions of PrP in vitro. We hypothesize that glycosylation of position 181 is a key site for prion strain differentiation in vivo.

Inhibitory effect of macabarterin, a polyoxygenated ellagitannin from Macaranga barteri, on human neutrophil respiratory burst activity.

An ellagitannin with a 2,4-acyl group, named macabarterin (1), and a new ellagic acid glycoside, 3-O-methylellagic acid 4-O-ß-d-xylopyranoside (2), were isolated from the stem bark extract of Macaranga barteri along with five known phenolic compounds, ellagic acid (3), 3-O-methylellagic acid (4), gallic acid (5), methyl gallate (6), and scopoletin (7). The structures of 1 and 2, as well as those of the known compounds, were elucidated on the basis of spectroscopic data and by comparison with reported data. Compounds 1-5 and 7 were tested for their anti-inflammatory potential in a cell-based respiratory burst assay, compound 1 being found an inhibitor of the superoxides produced in the cellular system.

Two new antioxidant phenylpropanoids from Lindelofia stylosa.

Two new phenylpropanoids were isolated from Lindelofia stylosa (Kar. and Kir.) and characterized as 4-hydroxy-N-{4-[(E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enamido]butyl}benzamide (1) and 2-[3-hydroxy-4-(4-hydroxyphenoxy)phenyl]-1-(methoxycarbonyl)ethyl (E)-3-(3,4-dihydroxyphenyl)prop-2-enoate (2). Four known compounds, i.e. two phenylpropanoids, p-coumaric acid (=(E)-3-(4-hydroxyphenyl)prop-2-enoic acid; 3) and ferulic acid (=(E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoic acid; 4), and two naphthalene glycosides, 8-O-beta-D-glucopyranosyltorachrysone (5) and 8-O-beta-D-glucopyranosyl-6-demethoxytorachrysone (6), were also isolated for the first time from the plant. Compounds 1-6 were subjected to various antioxidant assays, including DPPH radical- and superoxide anion-scavenging, and Fe(2+)-chelation assays. Compound 2 was found to be most active in all assays with potency nearly similar to that of propyl gallate. Besides 2, compounds 1 and 5 were also found to be active in DPPH radical-scavenging standard assay.

Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes.

Listeria monocytogenes is a bacterial pathogen that controls much of its virulence through the transcriptional regulator PrfA. In this study, we describe structure-guided design and synthesis of a set of PrfA inhibitors based on ring-fused 2-pyridone heterocycles. Our most effective compound decreased virulence factor expression, reduced bacterial uptake into eukaryotic cells, and improved survival of chicken embryos infected with L. monocytogenes compared to previously identified compounds. Crystal structures identified an intraprotein "tunnel" as the main inhibitor binding site (AI), where the compounds participate in an extensive hydrophobic network that restricts the protein's ability to form functional DNA-binding helix-turn-helix (HTH) motifs. Our studies also revealed a hitherto unsuspected structural plasticity of the HTH motif. In conclusion, we have designed 2-pyridone analogues that function as site-AI selective PrfA inhibitors with potent antivirulence properties.

Cinnamate derivatives of fructo-oligosaccharides from Lindelofia stylosa.

Phytochemical investigation on the whole plants of Lindelofia stylosa (Kar. and Kir.) has led to the isolation of eight fructo-oligosaccharide cinnamate esters 1-8. Six new compounds 1, 2, and 5-8 were isolated from the butanol extract of the plant. Compounds 1-4 belong to sucrose derivatives, while compounds 5-6 and 7-8 belong to 1-kestose- and nystose-type oligosaccharides, respectively. The fructo-oligosaccharides have been obtained from L. stylosa for the first time.

Phytochemical, antibacterial and antioxidant screening of Artemisia santolinifolia various parts

The current study was carried out to explore the phytochemical, antioxidant potential and antibacterial activities of the crude methanolic extract of A. santolinifolia Turcz. Ex Besser. The antioxidant activity was carried out by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) assay, while methanolic extract displayed the highest scavenging activity (DPPH) was 61.31µg/ml on Artemisia santolinifolia root and the lowest (51.05µg/ml) was record for their leaves. Similarly, in (ABTS) the highest activity (89.16µg/ml) was recorded for roots of A. santolinifolia followed by leaves (68.14µg/ml). In low inhibitory concentration assay, the crude methanolic extracts showed significant inhibition against all tested microbes on different concentrations like 25 µg/ml, 50 µg/ml, and 100 µg/ml. The leaves extract of A. santolinifolia AsL showed MIC of 12.5µg/ml for B. subtilis, a gram-positive bacterium, 50µg/ml for gram positive bacteria S. aureus and 37.5 µg/ml for gram negative bacteria P. aeruginosa that is almost equal to the response of standard ciprofloxacin. Our current study revealed that Artemisia santolinifolia root (AsR) exhibited a significant antioxidant potential while AsL showed good antibacterial effect which is suggested to be used for treatment and management of different infectious diseases.

Modifications of the 7-Hydroxyl Group of the Transthyretin Ligand Luteolin Provide Mechanistic Insights into Its Binding Properties and High Plasma Specificity.

Amyloid formation of the plasma protein transthyretin (TTR) has been linked to familial amyloid polyneuropathy and senile systemic amyloidosis. Binding of ligands within its natural hormone binding site can stabilize the tetrameric structure and impair amyloid formation. We have recently shown that the flavonoid luteolin stabilizes TTR in human plasma with a very high selectivity. Luteolin, however, is inactivated in vivo via glucuronidation for which the preferred site is the hydroxy group at position 7 on its aromatic A-ring. We have evaluated the properties of two luteolin variants in which the 7-hydroxy group has been exchanged for a chlorine (7-Cl-Lut) or a methoxy group (7-MeO-Lut). Using an in vitro model, based on human liver microsomes, we verified that these modifications increase the persistence of the drug. Crystal structure determinations show that 7-Cl-Lut binds similarly to luteolin. The larger MeO substituent cannot be accommodated within the same space as the chlorine or hydroxy group and as a result 7-MeO-Lut binds in the opposite direction with the methoxy group in position 7 facing the solvent. Both 7-Cl-Lut and 7-MeO-Lut qualify as high-affinity binders, but in contrast to luteolin, they display a highly non-specific binding to other plasma components. The binding of the two conformations and the key-interactions to TTR are discussed in detail. Taken together, these results show a proof-of-concept that the persistence of luteolin towards enzymatic modification can be increased. We reveal two alternative high-affinity binding modes of luteolin to TTR and that modification in position 7 is restricted only to small substituents if the original orientation of luteolin should be preserved. In addition, the present work provides a general and convenient method to evaluate the efficacy of TTR-stabilizing drugs under conditions similar to an in vivo environment.

Tetrabromobisphenol A Is an Efficient Stabilizer of the Transthyretin Tetramer.

Amyloid formation of the human plasma protein transthyretin (TTR) is associated with several human disorders, including familial amyloidotic polyneuropathy (FAP) and senile systemic amyloidosis. Dissociation of TTR's native tetrameric assembly is the rate-limiting step in the conversion into amyloid, and this feature presents an avenue for intervention because binding of an appropriate ligand to the thyroxin hormone binding sites of TTR stabilizes the native tetrameric assembly and impairs conversion into amyloid. The desired features for an effective TTR stabilizer include high affinity for TTR, high selectivity in the presence of other proteins, no adverse side effects at the effective concentrations, and a long half-life in the body. In this study we show that the commonly used flame retardant tetrabromobisphenol A (TBBPA) efficiently stabilizes the tetrameric structure of TTR. The X-ray crystal structure shows TBBPA binding in the thyroxine binding pocket with bromines occupying two of the three halogen binding sites. Interestingly, TBBPA binds TTR with an extremely high selectivity in human plasma, and the effect is equal to the recently approved drug tafamidis and better than diflunisal, both of which have shown therapeutic effects against FAP. TBBPA consequently present an interesting scaffold for drug design. Its absorption, metabolism, and potential side-effects are discussed.

Attenuating Listeria monocytogenes Virulence by Targeting the Regulatory Protein PrfA.

The transcriptional activator PrfA, a member of the Crp/Fnr family, controls the expression of some key virulence factors necessary for infection by the human bacterial pathogen Listeria monocytogenes. Phenotypic screening identified ring-fused 2-pyridone molecules that at low micromolar concentrations attenuate L. monocytogenes cellular uptake by reducing the expression of virulence genes. These inhibitors bind the transcriptional regulator PrfA and decrease its affinity for the consensus DNA-binding site. Structural characterization of this interaction revealed that one of the ring-fused 2-pyridones, compound 1, binds at two separate sites on the protein: one within a hydrophobic pocket or tunnel, located between the C- and N-terminal domains of PrfA, and the second in the vicinity of the DNA-binding helix-turn-helix motif. At both sites the compound interacts with residues important for PrfA activation and helix-turn-helix formation. Ring-fused 2-pyridones represent a new class of chemical probes for studying virulence in L. monocytogenes.

The flavonoid luteolin, but not luteolin-7-O-glucoside, prevents a transthyretin mediated toxic response.

Transthyretin (TTR) is a homotetrameric plasma protein with amyloidogenic properties that has been linked to the development of familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy, and senile systemic amyloidosis. The in vivo role of TTR is associated with transport of thyroxine hormone T4 and retinol-binding protein. Loss of the tetrameric integrity of TTR is a rate-limiting step in the process of TTR amyloid formation, and ligands with the ability to bind within the thyroxin binding site (TBS) can stabilize the tetramer, a feature that is currently used as a therapeutic approach for FAP. Several different flavonoids have recently been identified that impair amyloid formation. The flavonoid luteolin shows therapeutic potential with low incidence of unwanted side effects. In this work, we show that luteolin effectively attenuates the cytotoxic response to TTR in cultured neuronal cells and rescues the phenotype of a Drosophila melanogaster model of FAP. The plant-derived luteolin analogue cynaroside has a glucoside group in position 7 of the flavone A-ring and as opposed to luteolin is unable to stabilize TTR tetramers and thus prevents a cytotoxic effect. We generated high-resolution crystal-structures of both TTR wild type and the amyloidogenic mutant V30M in complex with luteolin. The results show that the A-ring of luteolin, in contrast to what was previously suggested, is buried within the TBS, consequently explaining the lack of activity from cynaroside. The flavonoids represent an interesting group of drug candidates for TTR amyloidosis. The present investigation shows the potential of luteolin as a stabilizer of TTR in vivo. We also show an alternative orientation of luteolin within the TBS which could represent a general mode of binding of flavonoids to TTR and is of importance concerning the future design of tetramer stabilizing drugs.

Enthalpic Forces Correlate with the Selectivity of Transthyretin-Stabilizing Ligands in Human Plasma.

The plasma protein transthyretin (TTR) is linked to human amyloidosis. Dissociation of its native tetrameric assembly is a rate-limiting step in the conversion from a native structure into a pathological amyloidogenic fold. Binding of small molecule ligands within the thyroxine binding site of TTR can stabilize the tetrameric integrity and is a potential therapeutic approach. However, through the characterization of nine different tetramer-stabilizing ligands we found that unspecific binding to plasma components might significantly compromise ligand efficacy. Surprisingly the binding strength between a particular ligand and TTR does not correlate well with its selectivity in plasma. However, through analysis of the thermodynamic signature using isothermal titration calorimetry we discovered a better correlation between selectivity and the enthalpic component of the interaction. This is of specific interest in the quest for more efficient TTR stabilizers, but a high selectivity is an almost universally desired feature within drug design and the finding might have wide-ranging implications for drug design.