Generation of streptocarbazoles with cytotoxicities by pathway engineering and insights into their biosynthesis

Streptocarbazoles are a class of indolocarbazole (ICZ) compounds produced by Streptomyces strains that feature unique cyclic N-glycosidic linkages between the 1,3-carbon atoms of the glycosyl moiety and the two indole nitrogen atoms. Although several streptocarbazole compounds display effective cytotoxic activity, their biosynthesis remains unclear. Herein, through the inactivation of the aminotransferase gene spcI in the staurosporine biosynthetic gene cluster spc followed by heterologous expression, two new streptocarbazole derivatives (1 and 3) and three known ICZs (2, 4, and 5) were generated. Their structures were determined by a combination of spectroscopic methods, circular dichroism measurements, and single-crystal X-ray diffraction. Compounds 1-4 displayed moderate cytotoxicity against HCT-116 cell line, and compounds 3 and 4 were effective against Huh 7 cell line. Double-gene knockout experiments allowed us to propose a biosynthetic pathway for streptocarbazole productions. Furthermore, by overexpression of the involving key enzymes, the production of streptocarbazoles 1 and 3 were improved by approximately 1.5-2.5 fold.

IMPORTANCE

Indolocarbazoles (ICZs) are a group of antitumor agents, with several analogs used in clinical trials. Therefore, the identification of novel ICZ compounds is important for drug discovery. Streptocarbazoles harbor unique N-glycosidic linkages (N13-C1' and N12-C3'), distinguishing them from the representative ICZ compound staurosporine; however, their biosynthesis remains unclear. In this study, two new streptocarbazoles (1 and 3) with cytotoxic activities were obtained by manipulating the staurosporine biosynthetic gene cluster spc followed by heterologous expression. The biosynthetic pathway of streptocarbazoles was proposed, and their productions were improved through the overexpression of the key enzymes involved. This study enriches the structural diversity of ICZ compounds and would facilitate the discovery of new streptocarbazoles via synthetic biological strategies.

Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation

To elucidate why plasmid-borne catabolic ability differs among host bacteria, we assessed the expression dynamics of the Pant promoter on the carbazole-degradative conjugative plasmid pCAR1 in Pseudomonas putida KT2440(pCAR1) (hereafter, KTPC) and Pseudomonas resinovorans CA10. The Pant promoter regulates the transcription of both the car and ant operons, which are responsible for converting carbazole into anthranilate and anthranilate into catechol, respectively. In the presence of anthranilate, transcription of the Pant promoter is induced by the AraC/XylS family regulator AntR, encoded on pCAR1. A reporter cassette containing the Pant promoter followed by gfp was inserted into the chromosomes of KTPC and CA10. After adding anthranilate, GFP expression in the population of CA10 showed an unimodal distribution, whereas a small population with low GFP fluorescence intensity appeared for KTPC. CA10 has a gene, antRCA, that encodes an iso-functional homolog of AntR on its chromosome. When antRCA was disrupted, a small population with low GFP fluorescence intensity appeared. In contrast, overexpression of pCAR1-encoded AntR in KTPC resulted in unimodal expression under the Pant promoter. These results suggest that the expression of pCAR1-encoded AntR is insufficient to ameliorate the stochastic expression of the Pant promoter. Raman spectra of single cells collected using deuterium-labeled carbazole showed that the C-D Raman signal exhibited greater variability for KTPC than CA10. These results indicate that heterogeneity at the transcriptional level of the Pant promoter due to insufficient AntR availability causes fluctuations in the pCAR1-borne carbazole-degrading capacity of host bacterial cells.IMPORTANCEHorizontally acquired genes increase the competitiveness of host bacteria under selective conditions, although unregulated expression of foreign genes may impose fitness costs. The "appropriate" host for a plasmid is empirically known to maximize the expression of plasmid-borne traits. In the case of pCAR1-harboring Pseudomonas strains, P. resinovorans CA10 exhibits strong carbazole-degrading capacity, whereas P. putida KT2440 harboring pCAR1 exhibits low degradation capacity. Our results suggest that a chromosomally encoded transcription factor affects transcriptional and metabolic fluctuations in host cells, resulting in different carbazole-degrading capacities as a population. This study may provide a clue for determining appropriate hosts for a plasmid and for regulating the expression of plasmid-borne traits, such as the degradation of xenobiotics and antibiotic resistance.

Carbazole-based mitochondria-targeted fluorescent probes for in vivo viscosity and cyanide detection in cells and zebrafish

Cells of most eukaryotic species contain mitochondria, which play a role in physiological processes such as cellular senescence, metabolism, and autophagy. Viscosity is considered a key marker for many illnesses and is involved in several crucial physiological processes. Cyanide (CN-) can target cytochrome-c oxidase, disrupting the mitochondrial electron transport chain and causing cell death through asphyxiation. In this study, a fluorescent probe named HL-1, which targets mitochondria and measures viscosity and CN- levels, was designed and synthesized. HL-1 is viscosity-sensitive, with a linear correlation coefficient of up to 0.992. In addition, HL-1 was found to change color substantially during a nucleophilic addition reaction with CN-, which has a low detection limit of 47 nM. HL-1 not only detects viscosity and exogenous CN- in SKOV-3 cells and zebrafish but also monitors viscosity changes during mitochondrial autophagy in real time. Furthermore, HL-1 has been used successfully to monitor changes in mitochondrial membrane potential during apoptosis. Endogenous CN- in plant samples was quantified. HL-1 provides new ideas for studying viscosity and CN-.

Effects of the polyhalogenated carbazoles 3-bromocarbazole and 1,3,6,8-tetrabromocarbazole on soil microbial communities

Soil ecosystems are being more contaminated with polyhalogenated carbazoles (PHCZs), which raising much attention about their impact on soil microorganisms. 3-Bromocarbazole (3-BCZ) and 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) are two typical PHCZs with high detection rates in the soil environment. However, ecological risk research on these two PHCZs in soil is still lacking. In the present study, after 80 days of exposure, the ecological influence of 3-BCZ and 1,3,6,8-TBCZ was investigated based on 16S rDNA sequencing, ITS sequencing, gene (16S rDNA, ITS, amoA, nifH, narG and cbbL) abundance and soil enzyme activity. The results showed that the bacterial 16S rDNA gene abundance significantly decreased under 3-BCZ and 1,3,6,8-TBCZ exposure after 80 days of incubation. The fungal ITS gene abundance significantly decreased under 1,3,6,8-TBCZ (10 mg/kg) exposure. PHCZs contributed to the alteration of bacteria and fungi community abundance. Bacteria Sphingomonas, RB41 and fungus Mortierella, Cercophora were identified as the most dominant genera. The two PHCZs consistently decreased the relative abundance of Sphingomonas, Lysobacter, Dokdonella, Mortierella and Cercophora etc at 80th day. These keystone taxa are related to the degradation of organic compounds, carbon metabolism, and nitrogen metabolism and may thus have influence on soil ecological functions. Bacterial and fungal functions were estimated using functional annotation of prokaryotic taxa (FAPROTAX) and fungi functional guild (FUNGuild), respectively. The nitrogen and carbon metabolism pathway were affected by 3-BCZ and 1,3,6,8-TBCZ. The soil nitrogen-related functions of aerobic ammonia oxidation were decreased but the soil carbon-related functions of methanol oxidation, fermentation, and hydrocarbon degradation were increased at 80th day. The effects of 3-BCZ and 1,3,6,8-TBCZ on the abundances of the amoA, nifH, narG, and cbbL genes showed a negative trend. These results elucidate the ecological effects of PHCZs and extend our knowledge on the structure and function of soil microorganisms in PHCZ-contaminated ecosystems.

Biotransformation Of l-Tryptophan To Produce Arcyriaflavin A With Pseudomonas putida KT2440

Natural products such as indolocarbazoles are a valuable source of highly bioactive compounds with numerous potential applications in the pharmaceutical industry. Arcyriaflavin A, isolated from marine invertebrates and slime molds, is one representative of this group and acts as a cyclin D1-cyclin-dependent kinase 4 inhibitor. To date, access to this compound has mostly relied on multi-step total synthesis. In this study, biosynthetic access to arcyriaflavin A was explored using recombinant Pseudomonas putida KT2440 based on a previously generated producer strain. We used a Design of Experiment approach to analyze four key parameters, which led to the optimization of the bioprocess. By engineering the formation of outer membrane vesicles and using an adsorbent in the culture broth, we succeeded to increase the yield of arcyriaflavin A in the cell-free supernatant, resulting in a nearly eight-fold increase in the overall production titers. Finally, we managed to scale up the bioprocess leading to a final yield of 4.7 mg arcyriaflavin A product isolated from 1 L of bacterial culture. Thus, this study showcases an integrative approach to improve biotransformation and moreover also provides starting points for further optimization of indolocarbazole production in P. putida.

Effect of storage duration on carprofen concentration measurements in dog plasma

BACKGROUND

Storage of samples may be necessary prior to testing drug levels in certain study designs; however, the effect of storage duration on measured drug levels is not known for all drugs.

OBJECTIVES

The objective of this study was to evaluate the stability of carprofen in canine plasma when stored at -80°C for 6 months.

METHODS

Six healthy dogs were enrolled (1-10 years old, 17-35 kg) and received compounded carprofen at 2.2 mg/kg orally every 12 h for 2 days. On the third day, blood was collected immediately before the morning dose (trough), then 1 and 6 h after the dose (sampling timepoint). Whole blood was immediately centrifuged, and plasma was stored at -80°C. Plasma carprofen concentration was measured at day 2, week 2 and then monthly for 6 months using reversed-phase high-performance liquid chromatography. The measured carprofen concentrations were analysed statistically using a linear mixed effects model.

RESULTS

There was no effect of storage time over 6 months (p = 0.891) on measured carprofen levels. Although there was an effect of sampling timepoint (0, 1 and 6 h) (p < 0.001), the interaction between storage timepoint and sampling timepoint was not statistically significant (p = 1).

CONCLUSIONS

Carprofen-laden canine plasma samples can be stored for up to 6 months before analysis with no degradation in carprofen concentrations expected.

Efficient bioelectricity generation and carbazole biodegradation using an electrochemically active bacterium Sphingobium yanoikuyae XLDN2-5

Carbazole and its derivatives are polycyclic aromatic heterocycles with unusual toxicity and mutagenicity. However, disposal of these polycyclic aromatic heterocycles remains a significant challenge. This study focused on efficient resource recovery from carbazole using an obligate aerobe, Sphingobium yanoikuyae XLDN2-5, in microbial fuel cells (MFCs). S. yanoikuyae XLDN2-5 successfully achieved carbazole degradation and simultaneously electricity generation in MFCs with a maximum power density of 496.8 mW m^-2 and carbazole degradation rate of 100%. It is the first time that S. yanoikuyae XLDN2-5 was discovered as an electrochemically active bacterium with high extracellular electron transfer (EET) capability. Redox mediator analysis indicated that no self-produced redox mediators were found for S. yanoikuyae XLDN2-5 under analysis conditions, and the exogenous redox mediators used in this study did not promote its EET. The nanowires produced by S. yanoikuyae XLDN2-5 cells were found in the biofilm by morphology characterization and the growth process of the nanowires was consistent with the discharge process of the MFC. Conductivity determination further verified that the nanowires produced by S. yanoikuyae XLDN2-5 cells were electrically conductive. Based on these results, it is speculated that S. yanoikuyae XLDN2-5 may mainly utilize conductive nanowires produced by itself rather than redox mediators to meet the requirements of normal energy metabolism when it grows in the low dissolved oxygen zone of the anodic biofilm. These novel findings on the EET mechanism of S. yanoikuyae XLDN2-5 lay a foundation for further exploration of polycyclic aromatic heterocyclic pollutants treatment in electrochemical devices, which may create new biotechnology processes for these pollutants control.

Isolation and identification of 1,3,6,8-tetrabromocarbazole - degrading bacteria

Halogenated carbazoles are a new class of persistent organic pollutants with dioxin-like toxicity, and this study focused on the microbial degradation of 1,3,6,8-tetrabromocarbazole. In this study, a novel 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) degrading strain TB-1 was isolated from contaminated soil and identified as Achromobacter sp. based on its 16S rRNA gene sequence analysis, morphological, physiological, and biochemical characteristics. The soil sample was collected from a pharmaceutical factory in Suzhou, China. The strain was able to effectively degrade 1 mg L^-1 1,3,6,8-TBCZ in 7 d at pH 7.0 and 30 °C with 80% degradation rate. During the process, the intermediate metabolites were identified as Tribromocarbazole, dibromocarbazole and bromocarbazole via gas chromatography mass spectrometry (GC-MS). The results indicated that strain TB-1 may contribute to the bioremediation of polyhalogenated carbazoles (PHCs) in contaminated environment.

AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors

ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.

An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals

Cryptochrome 1 (CRY1) and CRY2 are core regulators of the circadian clock, and the development of isoform-selective modulators is important for the elucidation of their redundant and distinct functions. Here, we report the identification and functional characterization of a small-molecule modulator of the mammalian circadian clock that selectively controls CRY1. Cell-based circadian chemical screening identified a thienopyrimidine derivative KL201 that lengthened the period of circadian rhythms in cells and tissues. Functional assays revealed stabilization of CRY1 but not CRY2 by KL201. A structure-activity relationship study of KL201 derivatives in combination with X-ray crystallography of the CRY1-KL201 complex uncovered critical sites and interactions required for CRY1 regulation. KL201 bound to CRY1 in overlap with FBXL3, a subunit of ubiquitin ligase complex, and the effect of KL201 was blunted by knockdown of FBXL3. KL201 will facilitate isoform-selective regulation of CRY1 to accelerate chronobiology research and therapeutics against clock-related diseases.

How the AHR Became Important in Intestinal Homeostasis-A Diurnal FICZ/AHR/CYP1A1 Feedback Controls Both Immunity and Immunopathology

Ever since the 1970s, when profound immunosuppression caused by exogenous dioxin-like compounds was first observed, the involvement of the aryl hydrocarbon receptor (AHR) in immunomodulation has been the focus of considerable research interest. Today it is established that activation of this receptor by its high-affinity endogenous ligand, 6-formylindolo[3,2-b]carbazole (FICZ), plays important physiological roles in maintaining epithelial barriers. In the gut lumen, the small amounts of FICZ that are produced from L-tryptophan by microbes are normally degraded rapidly by the inducible cytochrome P4501A1 (CYP1A1) enzyme. This review describes how when the metabolic clearance of FICZ is attenuated by inhibition of CYP1A1, this compound passes through the intestinal epithelium to immune cells in the lamina propria. FICZ, the level of which is thus modulated by this autoregulatory loop involving FICZ itself, the AHR and CYP1A1, plays a central role in maintaining gut homeostasis by potently up-regulating the expression of interleukin 22 (IL-22) by group 3 innate lymphoid cells (ILC3s). IL-22 stimulates various epithelial cells to produce antimicrobial peptides and mucus, thereby both strengthening the epithelial barrier against pathogenic microbes and promoting colonization by beneficial bacteria. Dietary phytochemicals stimulate this process by inhibiting CYP1A1 and causing changes in the composition of the intestinal microbiota. The activity of CYP1A1 can be increased by other microbial products, including the short-chain fatty acids, thereby accelerating clearance of FICZ. In particular, butyrate enhances both the level of the AHR and CYP1A1 activity by stimulating histone acetylation, a process involved in the daily cycle of the FICZ/AHR/CYP1A1 feedback loop. It is now of key interest to examine the potential involvement of FICZ, a major physiological activator of the AHR, in inflammatory disorders and autoimmunity.

Recent Advances in the Biosynthesis of Carbazoles Produced by Actinomycetes

Structurally diverse carbazole alkaloids are valuable due to their pharmaceutical properties and have been isolated from nature. Experimental knowledge on carbazole biosynthesis is limited. The latest development of in silico analysis of the biosynthetic gene clusters for bacterial carbazoles has allowed studies on the biosynthesis of a carbazole skeleton, which was established by sequential enzyme-coupling reactions associated with an unprecedented carbazole synthase, a thiamine-dependent enzyme, and a ketosynthase-like enzyme. This review describes the carbazole biosynthetic mechanism, which includes a key step in enzymatic formation of a tricyclic carbazole skeleton, followed by modifications such as prenylation and hydroxylation in the skeleton.

Halogenation-Guided Chemical Screening Provides Insight into Tjipanazole Biosynthesis by the Cyanobacterium Fischerella ambigua

Halogenated natural products (HNPs) show a wide range of interesting biological activities. Chemistry-guided screening with a software tool dedicated to identifying halogenated compounds in HPLC-MS data indicated the presence of several uncharacterised HNPs in an extract of the cyanobacterium Fischerella ambigua (Näg.) Gomont 108b. Three new natural products, tjipanazoles K, L, and M, were isolated from this strain together with the known tjipanazoles D and I. Taking into account the structures of all tjipanazole derivatives detected in this strain, reanalysis of the tjipanazole biosynthetic gene cluster allowed us to propose a biosynthetic pathway for the tjipanazoles. As the isolated tjipanazoles show structural similarity to arcyriaflavin A, an inhibitor of the clinically relevant multidrug-transporter ABCG2 overexpressed by different cancer cell lines, the isolated compounds were tested for ABCG2 inhibitory activity. Only tjipanazole K showed appreciable transporter inhibition, whereas the compounds lacking the pyrrolo[3,4-c] ring or featuring additional chloro substituents were found to be much less active.

Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism

Genome-wide analysis of the mode of action of GSK983, a potent antiviral agent, led to the identification of dihydroorotate dehydrogenase as its target along with the discovery that genetic knockdown of pyrimidine salvage sensitized cells to GSK983. Because GSK983 is an ineffective antiviral in the presence of physiological uridine concentrations, we explored combining GSK983 with pyrimidine salvage inhibitors. We synthesized and evaluated analogs of cyclopentenyl uracil (CPU), an inhibitor of uridine salvage. We found that CPU was converted into its triphosphate in cells. When combined with GSK983, CPU resulted in large drops in cellular UTP and CTP pools. Consequently, CPU-GSK983 suppressed dengue virus replication in the presence of physiological concentrations of uridine. In addition, the CPU-GSK983 combination markedly enhanced the effect of RNA-dependent RNA polymerase (RdRp) inhibition on viral infection. Our findings highlight a new host-targeting strategy for potentiating the antiviral activity of RdRp inhibitors.

Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition

Since the outbreak of the COVID-19 pandemic in December 2019 and its rapid spread worldwide, the scientific community has been under pressure to react and make progress in the development of an effective treatment against the virus responsible for the disease. Here, we implement an original virtual screening (VS) protocol for repositioning approved drugs in order to predict which of them could inhibit the main protease of the virus (M-pro), a key target for antiviral drugs given its essential role in the virus' replication. Two different libraries of approved drugs were docked against the structure of M-pro using Glide, FRED and AutoDock Vina, and only the equivalent high affinity binding modes predicted simultaneously by the three docking programs were considered to correspond to bioactive poses. In this way, we took advantage of the three sampling algorithms to generate hypothetic binding modes without relying on a single scoring function to rank the results. Seven possible SARS-CoV-2 M-pro inhibitors were predicted using this approach: Perampanel, Carprofen, Celecoxib, Alprazolam, Trovafloxacin, Sarafloxacin and ethyl biscoumacetate. Carprofen and Celecoxib have been selected by the COVID Moonshot initiative for in vitro testing; they show 3.97 and 11.90% M-pro inhibition at 50 µM, respectively.

Oxyanion transport across lipid bilayers: direct measurements in large and giant unilamellar vesicles

A simple di(thioamido)carbazole 1 serves as a potent multispecific transporter for various biologically relevant oxyanions, such as drugs, metabolites and model organic phosphate. The transport kinetics of a wide range of oxyanions can be easily quantified by a modified lucigenin assay in both large and giant unilamellar vesicles.

7H-Dibenzo[c,g]carbazole: Metabolic pathways and toxicity

7H-Dibenzo[c,g]carbazole (DBC), a local and systemic carcinogen in animal studies, is a common environmental pollutant. It generally co-occurs in a variety of organic complex mixtures derived from incomplete combustion of organic matter. Despite high lipophilicity, DBC is more water-soluble and faster metabolized than the homocyclic aromatics. Moreover, greater polarity, high bioaccumulation potential, and persistence in the environment may imply DBC's higher biological significance and impact on human health, even at lower concentrations. The biotransformation pathways of DBC are incompletely known and the ultimate carcinogenic metabolite(s) are not clearly identified as yet. Structure-biological studies suggest two ways of activation: at the ring carbon atoms and at the pyrrole nitrogen. It is supposed that the particular pathway of biotransformation might be connected with the tissue/organ specificity of DBC. Cytochrome P450 (CYP) family of enzymes plays a pivotal role in the metabolism of DBC; though, the one-electron activation and the aldo-keto reductase-catalyzed oxidation are also involved in metabolic activation. Additionally, DBC can be photoactivated even at physiologically relevant doses of UVA light due to the extended aromatic ring system resulting in strong genotoxicity and oxidative stress. The goal of this review is to summarize current knowledge on mechanisms of DBC activation and possible implications for toxicity, genotoxicity, and carcinogenicity.

Expression of Translocator Protein and [18F]-GE180 Ligand Uptake in Multiple Sclerosis Animal Models

Positron emission tomography (PET) ligands targeting the translocator protein (TSPO) represent promising tools to visualize neuroinflammation in multiple sclerosis (MS). Although it is known that TSPO is expressed in the outer mitochondria membrane, its cellular localization in the central nervous system under physiological and pathological conditions is not entirely clear. The purpose of this study was to assess the feasibility of utilizing PET imaging with the TSPO tracer, [18F]-GE180, to detect histopathological changes during experimental demyelination, and to determine which cell types express TSPO. C57BL/6 mice were fed with cuprizone for up to 5 weeks to induce demyelination. Groups of mice were investigated by [18F]-GE180 PET imaging at week 5. Recruitment of peripheral immune cells was triggered by combining cuprizone intoxication with MOG_35–55 immunization (i.e., Cup/EAE). Immunofluorescence double-labelling and transgene mice were used to determine which cell types express TSPO. [18F]-GE180-PET reliably detected the cuprizone-induced pathology in various white and grey matter regions, including the corpus callosum, cortex, hippocampus, thalamus and caudoputamen. Cuprizone-induced demyelination was paralleled by an increase in TSPO expression, glia activation and axonal injury. Most of the microglia and around one-third of the astrocytes expressed TSPO. TSPO expression induction was more severe in the white matter corpus callosum compared to the grey matter cortex. Although mitochondria accumulate at sites of focal axonal injury, these mitochondria do not express TSPO. In Cup/EAE mice, both microglia and recruited monocytes contribute to the TSPO expressing cell populations. These findings support the notion that TSPO is a valuable marker for the in vivo visualization and quantification of neuropathological changes in the MS brain. The pathological substrate of an increase in TSPO-ligand binding might be diverse including microglia activation, peripheral monocyte recruitment, or astrocytosis, but not axonal injury.

Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study

BACKGROUND

Aryl hydrocarbon receptor (AhR) ligands may act as potential carcinogens or anti-tumor agents. Understanding how some of the residues in AhR ligand binding domain (AhRLBD) modulate their interactions with ligands would be useful in assessing their divergent roles including toxic and beneficial effects. To this end, we have analysed the nature of AhRLBD interactions with 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), 6-formylindolo[3,2-b]carbazole (FICZ), indole-3-carbinol (I3C) and its degradation product, 3,3'-diindolylmethane (DIM), Resveratrol (RES) and its analogue, Piceatannol (PTL) using molecular modeling approach followed by molecular dynamic simulations.

RESULTS

Results showed that each of the AhR ligands, TCDD, FICZ, I3C, DIM, RES and PTL affect the local and global conformations of AhRLBD.

CONCLUSION

The data presented in this study provide a structural understanding of AhR with its ligands and set the basis for its functions in several pathways and their related diseases.

Cyclodextrin-based poly(pseudo)rotaxanes for transdermal delivery of carvedilol

This work aimed to design supramolecular gels combining Soluplus or Solutol and alfa- and hydroxypropyl-β-cyclodextrin (α-CD, HPβ-CD) for carvedilol (CAR) transdermal delivery. Poly(pseudo)rotaxane formation (appearance, SEM, ¹H NMR), drug solubilization, rheological properties and in vitro release were investigated. CAR-CD complexes were prepared in situ or by spray drying. For Solutol, poly(pseudo)rotaxanes were formed immediately after mixing with α-CD and did not influence CAR solubility. Differently, Soluplus poly(pseudo)rotaxanes took 24-48 h to be formed and CAR solubility decreased compared to Soluplus micelles. Soluplus 20% + α-CD (5-10%) showed higher G' and G'' but also faster CAR release than Solutol poly(pseudo)rotaxanes, which is explained by the different location of PEG chains in the two amphiphilic polymers. Faster drug release was achieved incorporating HPβ-CD or CAR-HPβ-CD spray-dried complexes. The results evidenced the versatility of the formulations in terms of rheological behavior and drug release patterns, which can be adjusted for CAR transdermal delivery.

Proteome and acylome analyses of the functional interaction network between the carbazole-degradative plasmid pCAR1 and host Pseudomonas putida KT2440

Understanding the interplay between a plasmid and its host system is a bottleneck towards prediction of the fate of plasmid-harbouring strains in the natural environments. Here, we studied the impact of the conjugative plasmid pCAR1, involved in carbazole degradation, on the proteome of Pseudomonas putida KT2440 using SILAC method. Furthermore, we investigated two acyl lysine modifications (acetylation and succinylation) that respond to the metabolic status of the cell and are implicated in regulation of various cellular processes. The total proteome analysis revealed that the abundance of key proteins involved in metabolism, signal transduction and motility was affected by pCAR1 carriage. In total, we identified 1359 unique acetylation sites on 637 proteins and 567 unique succinylation sites on 259 proteins. Changes in the acylation status of proteins involved in metabolism and translation by pCAR1 carriage were detected. Remarkably, acylation was identified on proteins involved in important plasmid functions, including partitioning and carbazole degradation, and on nucleoid-associated proteins that play a key role in the functional interaction with the chromosome. This study provides a novel insight on the functional consequences of plasmid carriage and improves our understanding of the plasmid-host cross-talk.

Carbazole Derivatives' Binding to c-KIT G-Quadruplex DNA

The binding affinities of three carbazole derivatives to the intramolecular G-quadruplex (GQ) DNA formed by the sequence 5′-AGGGAGGGCGCTGGGAGGAGGG-3′, derived from the c-KIT 1 oncogene region, were investigated. All carbazole cationic ligands that differed in the substituents on the nitrogen atom were able to stabilize G-quadruplex, as demonstrated using UV-Vis, fluorescence and CD spectroscopic techniques as well as molecular modeling. The spectrophotometric titration results showed spectral features characteristic of these ligands-bathochromic shifts and initial hypochromicity followed by hyperchromicity at higher GQ concentrations. All free carbazole ligands exhibited modest fluorescent properties, but after binding to the DNA the fluorescence intensity increased significantly. The binding affinities of carbazole ligands to the c-KIT 1 DNA were comparable showing values in the order of 10⁵ M−1. Molecular modeling highlights the differences in interactions between each particular ligand and studied G-quadruplex, which potentially influenced binding strength. Obtained results relevant that all three investigated ligands have stabilization properties on studied G-quadruplex.

Cytochrome P4501-inhibiting chemicals amplify aryl hydrocarbon receptor activation and IL-22 production in T helper 17 cells

The aryl hydrocarbon receptor (AHR) controls interleukin 22 production by T helper 17 cells (Th17). IL-22 contributes to intestinal homeostasis but has also been implicated in chronic inflammatory disorders and colorectal cancer, highlighting the need for appropriate regulation of IL-22 production. Upon activation, the AHR induces expression of cytochrome P4501 (CYP1) enzymes which in turn play an important feedback role that curtails the duration of AHR signaling by metabolizing AHR ligands. Recently we described how agents that inhibit CYP1 function potentiate AHR signaling by disrupting metabolic clearance of the endogenous ligand 6-formylindolo[3,2-b]carbazole (FICZ). In the present study, we investigated the immune-modulating effects of environmental pollutants such as polycyclic aromatic hydrocarbons on Th17 differentiation and IL-22 production. Using Th17 cells deficient in CYP1 enzymes (Cyp1a1/1a2/1b1-/-) we show that these chemicals potentiate AHR activation through inhibition of CYP1 enzymes which leads to increases in intracellular AHR agonists. Our findings demonstrate that IL-22 production by Th17 cells is profoundly enhanced by impaired CYP1-function and strongly suggest that chemicals able to modify CYP1 function or expression may disrupt AHR-mediated immune regulation by altering the levels of endogenous AHR agonist(s).

Design, synthesis and biological evaluation of new carbazole derivatives as anti-cancer and anti-migratory agents

Based on the efficacy of EHop-016 as an inhibitor of migration and Rac1 activation, a new series of carbazole derivatives has been synthesized. Cytotoxic and anti-migratory effects of these compounds were evaluated in MCF-7 and MDA-MB-231 breast cancer cell lines. Preliminary investigations of their anticancer activity demonstrated that several compounds have moderate antiproliferative effects on cancer cell lines with GI50 values in the range of 13-50 µM. Furthermore, compounds 3b and 11b inhibit migration activity of metastatic cell line MDA-MB-231 by 32% and 34%, respectively. Compound 11b was shown to inhibit activation of the Rho GTPase Rac1 by 55% at 250 nM in both MDA-MB-231 and MDA-MB-435 cell lines. Compared with the IC50 of Rac1 inhibition by lead compound EHop-016 of 1.1 µM, compound 11b demonstrates 4X improved in vitro efficacy.

Isolation and identification of 3-bromocarbazole-degrading bacteria

In this study, a bacterial strain, CH-1, capable of degrading 3-bromocarbazole (3-BCZ) was isolated from a polluted soil. Based on its physio-biochemical characteristics and 16S rRNA genes, strain CH-1 was identified as a Stenotrophomonas sp. Strain CH-1 was able to degrade 70% of 50 mg/L 3-BCZ within 8 d at pH 7.0 and 30°C in mineral salt medium (MSM). During the process, the main intermediate metabolite was identified as (2E, 4Z)-6-(2-amino-5-bromophenyl)-2-hydroxy-6-oxhexa-2, 4-dienoic by gas (2E, 4Z)-6-(2-amino-5-bromophenyl)-2-hydroxy-6-oxhexa-2,4-dienoic via gas chromatograph-mass spectrometry (GC-MS) analysis. The metabolite disappeared after 14 d, suggesting that the metabolite can also be degraded by strain CH-1. 3-BCZ is a new persistent organic pollutant. This is the first report of the biodegradation of 3-BCZ. The results indicated that strain CH-1 may be a promising bacterial candidate for the bioremediation of environments polluted with polyhalogenated carbazoles (PHCs).

Microbial detoxification of carvedilol, a β-adrenergic antagonist, by the filamentous fungus Cunninghamella echinulata

Beta adrenergic antagonists like carvedilol are typical environmental pollutants detected in wastewater and surface water. Human metabolism of carvedilol is well investigated, while its environmental fates are still unknown. In recent years, there have been appearing reports on high toxicity of β-blockers toward aquatic organisms. In this paper the ability of the filamentous fungus C. echinulata to eliminate the β-blocker has been described for the first time. An 83% loss of carvedilol was observed after 120 h incubation of the tested fungus with the compound, where hydroxylated carvedilol metabolites were identified as the major biotransformation products. Carvedilol degradation by C. echinulata was proceeded by hydroxylation and conjugation reactions similar to its mammalian metabolism. Glucose conjugate was found in the fungi cultures, whereas glucuronide conjugates were detected in mammals. The impact of carvedilol on the functionality of fungal cells was also evaluated. A 2-fold decrease in the PC/PE ratio was noticed in the C. echinulata cell membrane after the exposition to carvedilol compared to control mycelium incubated without the β-blocker. The change can denote perturbation of fungal cell membrane integration by carvedilol. Moreover, 2.8-fold lower toxicity of postcultures supernatants toward D. magna were shown in contrast to abiotic control.

From Sediment to Top Predators: Broad Exposure of Polyhalogenated Carbazoles in San Francisco Bay (U.S.A.)

The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZs) contamination in an aquatic ecosystem. PHCZs have been found in soil and aquatic sediment from several different regions, but knowledge of their bioaccumulation and trophodynamics is extremely scarce. This work investigated a suite of 11 PHCZ congeners in San Francisco Bay (United States) sediment and organisms, including bivalves (n = 6 composites), sport fish (n = 12 composites), harbor seal blubber (n = 18), and bird eggs (n = 8 composites). The most detectable congeners included 3,6-dichlorocarbazole (36-CCZ), 3,6-dibromocarbazole (36-BCZ), 1,3,6-tribromocarbazole (136-BCZ), 1,3,6,8-tetrabromocarbazole (1368-BCZ), and 1,8-dibromo-3,6-dichlorocarbazole (18-B-36-CCZ). The median concentrations of ΣPHCZs were 9.3 ng/g dry weight in sediment and ranged from 33.7 to 164 ng/g lipid weight in various species. Biomagnification was observed from fish to harbor seal and was mainly driven by chlorinated carbazoles, particularly 36-CCZ. Congener compositions of PHCZs differed among species, suggesting that individual congeners may be subject to different bioaccumulation or metabolism in species occupying various trophic levels in the studied aquatic system. Toxic equivalent (TEQ) values of PHCZs were determined on the basis of their relative effect potencies (REP) compared to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The median TEQ was 1.2 pg TEQ/g dry weight in sediment and 4.8-19.5 pg TEQ/g lipid weight in biological tissues. Our study demonstrated the broad exposure of PHCZs in San Francisco Bay and their characteristics of bioaccumulation and biomagnification along with dioxin-like effects. These findings raise the need for additional research to better elucidate their sources, environmental behavior, and fate in global environments.

In vitro and in silico evaluation of transactivation potencies of avian AHR1 and AHR2 by endogenous ligands: Implications for the physiological role of avian AHR2

Aryl hydrocarbon receptor (AHR) is well conserved from invertebrates to vertebrates, and it mediates the toxic effects of exogenous ligands, including dioxins. Recent studies reported that AHRs activated by endogenous ligands play critical roles in mammalian physiological homeostasis. Avian species possess at least two AHR isoforms (AHR1 and AHR2), which exhibit species- and isoform-specific transactivation potencies to exogenous ligands, whereas mammals possess a single AHR. To delineate the profiles and roles of endogenous ligands for avian AHR isoforms, we investigated in vitro transactivation potencies of avian AHRs (AHR1 and AHR2 from the jungle crow, Corvus macrorhynchos; common cormorant, Phalacrocorax carbo; and black-footed albatross, Phoebastria nigripes) treated with the endogenous tryptophan metabolites 6-formylindolo [3,2-b] carbazole (FICZ), l-kynurenine (l-Kyn), kynurenic acid (KYNA), and indoxyl sulfate (IS). Furthermore, we analyzed the binding mode of these ligands to each avian AHR isoform by in silico docking simulations. The EC50 of FICZ (0.009-0.032nM) was similar regardless of the species or isoform of AHR. The estimated in silico binding mode of FICZ to AHRs was well conserved in both isoforms. The transactivation potencies of avian AHRs to other tryptophan metabolites were 10(5)-10(7) fold lower than those for FICZ, and EC50 values varied in a species- and isoform-specific manner. This was consistent with poor conservation of the binding mode of l-Kyn, KYNA, and IS predicted in in silico docking simulations. Our results suggest that in avian species, FICZ is the most potent endogenous AHR ligand, and that AHR1 and AHR2 are physiologically functional.

A novel integration system of magnetically immobilized cells and a pair of graphite plate-stainless iron mesh electrodes for the bioremediation of coking wastewater

Magnetically immobilized cells of Comamonas sp. JB coupling with electrode reaction was developed to enhance the treatment efficiency of coking wastewater containing phenol, carbazole (CA), dibenzofuran (DBF), and dibenzothiophene (DBT). The pair of graphite plate-stainless iron mesh electrodes was chosen as the most suitable electrodes. Magnetically immobilized cells coupling with graphite plate-stainless iron mesh electrodes (coupling system) exhibited high degradation activity for all the compounds, which were significantly higher than the sum by single magnetically immobilized cells and electrode reaction at the optimal voltage. Recycling experiments demonstrated that the degradation activity of coupling system increased gradually during eight recycles, indicating that there was a coupling effect between the biodegradation and electrode reaction. Phenol hydroxylase and qPCR assays confirmed that appropriate electrical stimulation could improve phenol hydroxylase activity and promote cells growth. Toxicity assessment suggested the treatment of the coking wastewater by coupling system led to less toxicity than untreated wastewater.

Protective Antioxidant Effects of Carvedilol in a Rat Model of Ischaemia-reperfusion Injury

This study investigated the protective effects of carvedilol, a potent antioxidant, in a rat model of tourniquet-induced ischaemia-reperfusion injury of the hind limb. Thirty rats were divided equally into three groups: the control group (group 1) was only anaesthetized, without creating an ischaemia-reperfusion injury; group 2 was submitted to ischaemia (4 h), followed by a 2-h reperfusion period; and group 3 was pre-treated with carvedilol (2 mg/kg per day) for 10 days prior to ischaemia-reperfusion. Ischaemia-reperfusion produced a significant decrease in superoxide dismutase and glutathione peroxidase activities in the liver, lungs, muscle and serum compared with control treatment, and pre-treatment with carvedilol prevented these changes. Ischaemia-reperfusion caused a significant increase in malondialdehyde and nitric oxide (NO) levels in liver, lungs, muscle (except NO) and serum compared with control treatment, and carvedilol prevented these changes. In conclusion, it might be inferred that carvedilol could be used safely to prevent oxidative injury during reperfusion following ischaemia in humans.

Synthesis of Linearly Fused Benzodipyrrole Based Organic Materials

The objective of this review is to give an overview of the synthetic methods to prepare different indolo[3,2-b]carbazoles and similar systems with a potential use in electro-optical devices such as OLEDs (organic light emitting diode), OPVs (organic photovoltaic) and OFETs (organic field effect transistor). Some further modifications to the core units and their implications for specific applications are also discussed.

Smad7 Knockdown Restores Aryl Hydrocarbon Receptor-mediated Protective Signals in the Gut

BACKGROUND AND AIM

In Crohn's disease [CD], the pathological process is driven by an excessive immune response that is poorly counterbalanced by regulatory mechanisms. One such a mechanism involves aryl hydrocarbon receptor [AhR], a transcription factor that delivers protective signals in the gut. Expression of AhR is reduced in CD lamina propria mononuclear cells [LPMC] even though factors accounting for such a defect remain unknown. Since CD LPMC express elevated levels of Smad7, an inhibitor of transforming growth factor beta 1 [TGF-β1] activity, and TGF-β1 regulates AhR in other systems, we examined the link between AhR and Smad7 in the gut.

METHODS

AhR and interleukin [IL]-22 were evaluated in normal LPMC stimulated with TGF-β1 and 6-formylindolo[3,2-b]carbazole [Ficz], an activator of AhR, and in CD LPMC incubated with a Smad7 antisense oligonucleotide and then stimulated with Ficz and TGF-β1. AhR and IL-22 expression was evaluated in LPMC of Smad7-transgenic mice. Finally, we evaluated the protective effect of Ficz on colitis in RAG1 mice injected with naïve or Smad7-overexpressing T cells.

RESULTS

In normal LPMC, TGF-β1 induced AhR and this event was associated with increased production of IL-22 following stimulation with Ficz. Treatment of CD LPMC with Smad7 antisense oligonucleotide enabled TGF-β1 to enhance AhR expression. Consistently, AhR expression and Ficz-induced IL-22 production were markedly reduced in T cells of Smad7-transgenic mice. In RAG1 mice, Ficz ameliorated colitis induced by wild type T cells but did not affect colitis induced by transfer of Smad7-overexpressing T cells.

CONCLUSIONS

The inverse correlation between Smad7 and AhR expression helps to propagate inflammatory signals in the gut.

Effects of carbazole-degradative plasmid pCAR1 on biofilm morphology in Pseudomonas putida KT2440

Bacteria typically form biofilms under natural conditions. To elucidate the effect of the carriage of carbazole-degradative plasmid pCAR1 on biofilm formation by host bacteria, we compared the biofilm morphology, using confocal laser scanning microscopy, of three pCAR1-free and pCAR1-carrying Pseudomonas hosts: P. putida KT2440, P. aeruginosa PAO1 and P. fluorescens Pf0-1. Although pCAR1 did not significantly affect biofilm formation by PAO1 or Pf0-1, pCAR1-carrying KT2440 became filamentous and formed flat biofilms, whereas pCAR1-free KT2440 formed mushroom-like biofilms. pCAR1 contains three genes encoding nucleoid-associated proteins (NAPs), namely, Pmr, Pnd and Phu. The enhanced filamentous morphology was observed in two double mutants [KT2440(pCAR1ΔpmrΔpnd) and KT2440(pCAR1ΔpmrΔphu)], suggesting that these NAPs are involved in modulating the filamentous phenotype. Transcriptome analyses of the double mutants identified 32 candidate genes that may be involved in filamentation of KT2440. Overexpression of PP_2193 in KT2440 induced filamentation and overexpression of PP_0308 or PP_0309 in KT2440(pCAR1) enhanced filamentation of cells over time. This suggests that pCAR1 induces development of an abnormal filamentous morphology by KT2440 via a process involving overexpression of several genes, such as PP_2193. In addition, pCAR1-encoded NAPs partly suppress too much filamentation of KT2440(pCAR1) by repressing transcription of some genes, such as PP_0308 and PP_0309.

Carbazole hydroxylation by the filamentous fungi of the Cunninghamella species

Nitrogen heterocyclic compounds, especially carbazole, quinolone, and pyridine are common types of environmental pollutants. Carbazole has a toxic influence on living organisms, and the knowledge of its persistence and bioconversion in ecosystems is still not complete. There is an increasing interest in detoxification of hazardous xenobiotics by microorganisms. In this study, the ability of three filamentous fungi of the Cunninghamella species to eliminate carbazole was evaluated. The Cunninghamella elegans IM 1785/21Gp and Cunninghamella echinulata IM 2611 strains efficiently removed carbazole. The IM 1785/21Gp and IM 2611 strains converted 93 and 82 % of the initial concentration of the xenobiotic (200 mg L(-1)) after 120 h incubation. 2-Hydroxycarbazole was for the first time identified as a carbazole metabolite formed by the filamentous fungi of the Cunninghamella species. There was no increase in the toxicity of the postculture extracts toward Artemia franciscana. Moreover, we showed an influence of carbazole on the phospholipid composition of the cells of the tested filamentous fungi, which indicated its harmful effect on the fungal cell membrane. The most significant modification of phospholipid levels after the cultivation of filamentous fungi with the addition of carbazole was showed for IM 1785/21Gp strain.

Characterization of Early Enzymes Involved in TDP-Aminodideoxypentose Biosynthesis en Route to Indolocarbazole AT2433

The characterization of TDP-α-D-glucose dehydrogenase (AtmS8), TDP-α-D-glucuronic acid decarboxylase (AtmS9), and TDP-4-keto-α-D-xylose 2,3-dehydratase (AtmS14), involved in Actinomadura melliaura AT2433 aminodideoxypentose biosynthesis, is reported. This study provides the first biochemical evidence that both deoxypentose and deoxyhexose biosynthetic pathways share common strategies for sugar 2,3-dehydration/reduction and implicates the sugar nucleotide base specificity of AtmS14 as a potential mechanism for sugar nucleotide commitment to secondary metabolism. In addition, a re-evaluation of the AtmS9 homologue involved in calicheamicin aminodeoxypentose biosynthesis (CalS9) reveals that CalS9 catalyzes UDP-4-keto-α-D-xylose as the predominant product, rather than UDP-α-D-xylose as previously reported. Cumulatively, this work provides additional fundamental insights regarding the biosynthesis of novel pentoses attached to complex bacterial secondary metabolites.

Characterization of a novel cometabolic degradation carbazole pathway by a phenol-cultivated Arthrobacter sp. W1

Arthrobacter sp. W1 was used to characterize the pathways involved in cometabolic degradation of carbazole (CA) with phenol as the primary substrate. To clarify the upper pathway of cometabolic degradation CA, Escherichia coli strain BL21 expressing phenol hydroxylase from strain W1 (PHIND) was investigated to degrade CA. Firstly, CA was initially monohydroxylated at C-2 and C-4 positions to produce 2- and 4-hydroxycarbazole, followed by successively hydroxylated to the corresponding 1,2- and 3,4-dihydroxycarbazole, of which 3,4-dihydroxycarbazole was unequivocally identified for the first time. To characterize the downstream cometabolic degradation CA pathway, purified 3,4-dihydroxycarbazole was used as the substrate for phenol-grown W1, and a series of novel indole derivatives were identified. These results suggested that a novel pathway of CA catabolism was employed by strain W1 via a successive hydroxylation and meta-cleavage pathway. These findings provide new insights into the cometabolic degradation CA process and have potential applications in biotechnology and bioremediation.

Ultraviolet A radiation potentiates the cytotoxic and genotoxic effects of 7 H-dibenzo[c,g]carbazole and its methyl derivatives

7H-Dibenzo[c,g]carbazole (DBC) is a heterocyclic aromatic hydrocarbon that is carcinogenic in many species and tissues. DBC is a common environmental pollutant, and is therefore constantly exposed to sunlight. However, there are limited data exploring the toxicity of DBC photoexcitation products. Here, we investigated the impact of ultraviolet (UV) A radiation on the biological activity of DBC and its methyl derivatives, 5,9-dibenzo[c,g]carbazole and N-methyl dibenzo[c,g]carbazole, on human skin HaCaT keratinocytes. Co-exposure of HaCaT cells to UVA and DBC derivatives resulted in a sharp dose-dependent decrease in cell survival and apparent changes in cell morphology. Under the same treatment conditions, significant increases in DNA strand breaks, intracellular reactive oxygen species, and oxidative damage to DNA were observed in HaCaT cells. Consistent with these results, an apparent inhibition in superoxide dismutase, but not glutathione peroxidase activity, was detected in cells treated with DBC and its derivatives under UVA irradiation. The photoactivation-induced toxicity of individual DBC derivatives correlated with the electron excitation energies approximately expressed as the energy difference between the highest occupied and the lowest vacant molecular orbital. Our data provide the first evidence that UVA can enhance the toxicity of DBC and its derivatives. Photoactivation-induced conversion of harmless chemical compounds to toxic photoproducts associated with reactive oxygen species generation may substantially amplify the adverse health effects of UVA radiation and contribute to increased incidence of skin cancer.

In silico analysis of the interaction of avian aryl hydrocarbon receptors and dioxins to decipher isoform-, ligand-, and species-specific activations

The aryl hydrocarbon receptor (AHR) mediates toxic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other dioxin-like compounds (DLCs). Avian species possess multiple AHR isoforms (AHR1, AHR1β, and AHR2) that exhibit species- and isoform-specific responses to ligands. To account for the ligand preference in terms of the structural features of avian AHRs, we generated in silico homology models of the ligand-binding domain of avian AHRs based on holo human HIF-2α (PDB entry 3H7W ). Molecular docking simulations of TCDD and other DLCs with avian AHR1s and AHR2s using ASEDock indicated that the interaction energy increased with the number of substituted chlorine atoms in congeners, supporting AHR transactivation potencies and World Health Organization TCDD toxic equivalency factors of congeners. The potential interaction energies of an endogenous AHR ligand, 6-formylindolo [3,2-b] carbazole (FICZ) to avian AHRs were lower than those of TCDD, which was supported by a greater potency of FICZ for in vitro AHR-mediated transactivation than TCDD. The molecular dynamics simulation revealed that mean square displacements in Ile324 and Ser380 of TCDD-bound AHR1 of the chicken, the most sensitive species to TCDD, were smaller than those in other avian AHR1s, suggesting that the dynamic stability of these amino acid residues contribute to TCDD preference. For avian AHR2, the corresponding residues (Val/Ser or Val/Ala type) were not responsible for differential TCDD sensitivity. Application of the three-dimensional reference interaction site model showed that the stabilization of TCDD binding to avian AHRs may be due to the solvation effect depending on the characteristics of two amino acids corresponding to Ile324 and Ser380 in chicken AHR1. This study demonstrates that in silico simulations of AHRs and ligands could be used to predict isoform-, ligand-, and species-specific interactions.

Molecular Modeling and Evaluation of Novel Dibenzopyrrole Derivatives as Telomerase Inhibitors and Potential Drug for Cancer Therapy

During previous years, many studies on synthesis, as well as on anti-tumor, anti-inflammatory and anti-bacterial activities of the pyrazole derivatives have been described. Certain pyrazole derivatives exhibit important pharmacological activities and have proved to be useful template in drug research. Considering importance of pyrazole template, in current work the series of novel inhibitors were designed by replacing central ring of acridine with pyrazole ring. These heterocyclic compounds were proposed as a new potential base for telomerase inhibitors. Obtained dibenzopyrrole structure was used as a novel scaffold structure and extension of inhibitors was done by different functional groups. Docking of newly designed compounds in the telomerase active site (telomerase catalytic subunit TERT) was carried out. All dibenzopyrrole derivatives were evaluated by three docking programs: CDOCKER, Ligandfit docking (Scoring Functions) and AutoDock. Compound C_9g, C_9k and C_9l performed best in comparison to all designed inhibitors during the docking in all methods and in interaction analysis. Introduction of pyrazole and extension of dibenzopyrrole in compounds confirm that such compound may act as potential telomerase inhibitors.

P7C3 and an unbiased approach to drug discovery for neurodegenerative diseases

A novel neuroprotective small molecule was discovered using a target-agnostic in vivo screen in living mice. This aminopropyl carbazole, named P7C3, is orally bioavailable, crosses the blood-brain barrier, and is non-toxic at doses several fold higher than the efficacious dose. The potency and drug-like properties of P7C3 were optimized through a medicinal chemistry campaign, providing analogues for detailed examination. Improved versions, such as (-)-P7C3-S243 and P7C3-A20, displayed neuroprotective properties in rodent models of Parkinson's disease, amyotrophic lateral sclerosis, traumatic brain injury and age-related cognitive decline. Derivatives appended with immobilizing moieties may reveal the protein targets of the P7C3 class of neuroprotective compounds. Our results indicate that unbiased, in vivo screens might provide starting points for the development of treatments for neurodegenerative diseases as well as tools to study the biology underlying these disorders.

Crystal structures of PRK1 in complex with the clinical compounds lestaurtinib and tofacitinib reveal ligand induced conformational changes

Protein kinase C related kinase 1 (PRK1) is a component of Rho-GTPase, androgen receptor, histone demethylase and histone deacetylase signaling pathways implicated in prostate and ovarian cancer. Herein we describe the crystal structure of PRK1 in apo form, and also in complex with a panel of literature inhibitors including the clinical candidates lestaurtinib and tofacitinib, as well as the staurosporine analog Ro-31-8220. PRK1 is a member of the AGC-kinase class, and as such exhibits the characteristic regulatory sequence at the C-terminus of the catalytic domain – the ‘C-tail’. The C-tail fully encircles the catalytic domain placing a phenylalanine in the ATP-binding site. Our inhibitor structures include examples of molecules which both interact with, and displace the C-tail from the active site. This information may assist in the design of inhibitors targeting both PRK and other members of the AGC kinase family.

Bioremediation of coking wastewater containing carbazole, dibenzofuran and dibenzothiophene by immobilized naphthalene-cultivated Arthrobacter sp. W1 in magnetic gellan gum

In this study, the cometabolic degradation of carbazole (CA), dibenzofuran (DBF), and dibenzothiophene (DBT) by immobilized Arthrobacter sp. W1 cells pregrown with naphthalene was investigated. Four kinds of polymers were evaluated as immobilization supports for strain W1. After comparison with agar, alginate, and κ-carrageenan, gellan gum was selected as the optimal immobilization support. Furthermore, magnetic Fe₃O₄ nanoparticle was selected as most suitable nanoparticle for immobilization and the optimal concentration was 80 mg/L. The relationship between specific degradation rate and the initial concentration of CA, DBF and DBT was described well by Michaelis-Menten kinetics. The recycling experiments demonstrated that the magnetically immobilized cells coupling with activation zeolite showed highly bioremediation activity on the coking wastewater containing high concentration of phenol, naphthalene, CA, DBF and DBT during seven recycles. Toxicity assessment indicated the treatment of the coking wastewater by magnetically immobilized cells with activation zeolite led to less toxicity than untreated wastewater.

Bioremediation of coking wastewater containing carbazole, dibenzofuran, dibenzothiophene and naphthalene by a naphthalene-cultivated Arthrobacter sp. W1

A naphthalene-utilizing bacterium, Arthrobacter sp. W1, was used to investigate the cometabolic degradation of carbazole (CA), dibenzofuran (DBF) and dibenzothiophene (DBT) using naphthalene as the primary substrate. Both the growing and washed cells of strain W1 could degrade CA, DBF, DBT, and naphthalene simultaneously and quickly. Inhibition kinetics confirmed that the presence of CA, DBF and DBT in the growing system would inhibit the cells growth and biodegradability of strain W1. The relationship between ln(C/C0) and time, and specific degradation rate and CA, DBF and DBT concentration could be described well by First-order and Michaelis-Menten kinetics. The treatment of real coking wastewater containing high concentration of phenol, naphthalene, CA, DBF, DBT and NH3-N was shown to be highly efficient by naphthalene-grown W1 coupling with activation zeolite. Toxicity assessment indicated the treatment of the coking wastewater by strain W1 coupling with activation led to less toxicity than untreated wastewater.

Carbazole angular dioxygenation and mineralization by bacteria isolated from hydrocarbon-contaminated tropical African soil

Four bacterial strains isolated from hydrocarbon-contaminated soils in Lagos, Nigeria, displayed extensive degradation abilities on carbazole, an N-heterocyclic aromatic hydrocarbon. Physicochemical analyses of the sampling sites (ACPP, MWO, NESU) indicate gross pollution of the soils with a high hydrocarbon content (157,067.9 mg/kg) and presence of heavy metals. Phylogenetic analysis of the four strains indicated that they were identified as Achromobacter sp. strain SL1, Pseudomonas sp. strain SL4, Microbacterium esteraromaticum strain SL6, and Stenotrophomonas maltophilia strain BA. The rates of degradation of carbazole by the four isolates during 30 days of incubation were 0.057, 0.062, 0.036, and 0.050 mg L(-1) h(-1) for strains SL1, SL4, SL6, and BA. Gas chromatographic (GC) analyses of residual carbazole after 30 days of incubation revealed that 81.3, 85, 64.4, and 76 % of 50 mg l(-1) carbazole were degraded by strains SL1, SL4, SL6, and BA, respectively. GC-mass spectrometry and high-performance liquid chromatographic analyses of the extracts from the growing and resting cells of strains SL1, SL4, and SL6 cultured on carbazole showed detection of anthranilic acid and catechol while these metabolites were not detected in strain BA under the same conditions. This study has established for the first time carbazole angular dioxygenation and mineralization by isolates from African environment.

Cellular and genomic toxicity produced by UV light in Chinese hamster ovary cells

UVB and UVC toxicity was detected in Chinese Hamster Ovary (CHO) cell lines AA8, UV5 and XEM2 (a V79-derived cell line expressing rat P450 1A1). Unlike FICZ-HPLC assay that showed induction of CYP1A1 enzyme activity after 20 minutes and 2 hour UVC exposure, the EROD assay showed no difference in cytochrome P450 1A1 (CYP1A1) activity after exposure to different doses of UVB and UVC light. Different cytotoxic and mutagenic effect of photo lesions induced by UVC and UVB light was investigated with the DRAG and HPRT assays, comparing the wild type cell line AA8 and the Nucleotide Excision Repair (NER) deficient cell line UV5. DRAG assay showed a significant difference in UV induced cytotoxicity between UVC and UVB reflecting the larger energy and toxic effect of UVC along with significant difference in UV induced toxicity between AA8 and UV5 cell lines. This was further validated through the HPRT assay, which also showed a significant difference in UVC (5 J/m(2)) induced mutagenic effect between these cell lines. In addition, HPRT assay showed the mutagenic effect of photosensitizer, acetophenone. These results show that UVB and UVC generate serious damage through photo products on DNA, and might induce the metabolic activity of CYP1A1.

Enzymatic synthesis of bromo- and chlorocarbazoles and elucidation of their structures by molecular modeling

3-Chlorocarbazole, 3,6-dichlorocarbazole, dibromocarbazole, and 1,3,6,8-tetrabromocarbazole are emerging environmental contaminants which have been detected recently in water, sediment, and soil samples. However, their sources and occurrence have not been explained. Here, we report an enzymatic synthesis of bromo- and chlorocarbazoles by chloroperoxidase from Caldariomyces fumago in water. Density functional theory (DFT) method was used to predict the most stable products. Carbazole and chloroperoxidase were assayed in vitro in the presence of hydrogen peroxide, bromide, and chloride ions in different substrate ratio treatments against constant and varying enzyme concentrations. Halogenated carbazoles formed were identified by high-resolution gas chromatography coupled to mass spectrometry. In all treatments, bromination and chlorination took place, but the composition and concentration of compounds formed varied from one treatment to another. Mono-, di-, tri-, and tetra-substituted bromo- and chlorocarbazoles which include the reported environmental contaminants were synthesized. 3-Substituted and 3,6-substituted congeners were relatively higher in concentration. Enzyme concentration did not favor preferential formation of any of the compounds synthesized. However, their synthesis was influenced by halide concentration. Congeners with bromine and chlorine at position of C-3, C-3,6, C-1,3,6, and C-1,3,6,8 were calculated as the stable intermediate sigma complexes by DFT method. Regioselectivity in halogenation is discussed and hypothesis of the likely stable products in the environment explained. This study provides evidence that bromo- and chlorocarbazoles reported previously can be formed enzymatically in the environment, demonstrating the need to consider aromatic pollutants transformation and their potential toxicity enhancements in the management of water pollution and contaminated sites.

External validation of structure-biodegradation relationship (SBR) models for predicting the biodegradability of xenobiotics

Biodegradation is an important mechanism for eliminating xenobiotics by biotransforming them into simple organic and inorganic products. Faced with the ever growing number of chemicals available on the market, structure-biodegradation relationship (SBR) and quantitative structure-biodegradation relationship (QSBR) models are increasingly used as surrogates of the biodegradation tests. Such models have great potential for a quick and cheap estimation of the biodegradation potential of chemicals. The Estimation Programs Interface (EPI) Suite™ includes different models for predicting the potential aerobic biodegradability of organic substances. They are based on different endpoints, methodologies and/or statistical approaches. Among them, Biowin 5 and 6 appeared the most robust, being derived from the largest biodegradation database with results obtained only from the Ministry of International Trade and Industry (MITI) test. The aim of this study was to assess the predictive performances of these two models from a set of 356 chemicals extracted from notification dossiers including compatible biodegradation data. Another set of molecules with no more than four carbon atoms and substituted by various heteroatoms and/or functional groups was also embodied in the validation exercise. Comparisons were made with the predictions obtained with START (Structural Alerts for Reactivity in Toxtree). Biowin 5 and Biowin 6 gave satisfactorily prediction results except for the prediction of readily degradable chemicals. A consensus model built with Biowin 1 allowed the diminution of this tendency.

Structure-function relations of strigolactone analogs: activity as plant hormones and plant interactions

Strigolactones (SLs) have several functions as signaling molecules in their interactions with symbiotic arbuscular mycorrhizal (AM) fungi and the parasitic weeds Orobanche and Striga. SLs are also a new class of plant hormone regulating plant development. In all three organisms, a specific and sensitive receptor-mediated perception system is suggested. By comparing the activity of synthetic SL analogs on Arabidopsis root-hair elongation, Orobanche aegyptiaca seed germination, and hyphal branching of the AM fungus Glomus intraradices, we found that each of the tested organisms differs in its response to the various examined synthetic SL analogs. Structure-function relations of the SL analogs suggest substitutions on the A-ring as the cause of this variation. Moreover, the description of competitive antagonistic analogs suggests that the A-ring of SL can affect not only affinity to the receptor, but also the molecule's ability to activate it. The results support the conclusion that Arabidopsis, Orobanche, and AM fungi possess variations in receptor sensitivity to SL analogs, probably due to variation in SL receptors among the different species.

Experimental and mathematical methodology on the optimization of bacterial consortium for the simultaneous degradation of three nitrogen heterocyclic compounds

This study aims to establish a systematic method to optimize the bacterial consortium for the simultaneous biodegradation of multixenobiotics in wastewater. Three nitrogen heterocyclic compounds (NHCs), pyridine, quinoline, and carbazole, were chosen as the target compounds with each about 200 mg/L. Different consortia originated from six bacteria for degrading pyridine (Paracoccus sp. BW001 and Shinella zoogloeoides BC026), quinoline (Pseudomonas sp. BW003 and BW004), and carbazole (Pseudomonas sp. BC039 and BC046) were tested for the capacity of NHCs simultaneous degradation. Mathematical methods including dummy-variable-laden kinetic modeling, cubic spline regression and interpolation, and dimensionality reduction were employed to evaluate the complex impacts of cocontaminants and coexisting bacteria on the simultaneous biodegradation, and the most efficient consortium was determined. The influences of cocontaminants on the bacterial degradation activity were far greater than the interactions among the mixed bacteria. Integrating the experimental results and mathematical analysis, consortium M19 (BC026, BW004, BC039, and BC046 with dose rate of 1:1:0.5:0.5) was the best one, which degraded over 95% of pyridine, quinoline, and carbazole simultaneously in 15.4 h. The research methodology in this study could be applied to the optimization of a bacterial consortium which might be used in the bioaugmentation and bioremediation of multixenobiotics removal.