bis-cis-Dihydrodiols: A New Class of Metabolites Resulting from Biphenyl Dioxygenase-Catalyzed Sequential Asymmetric cis-Dihydroxylation of Polycyclic Arenes and Heteroarenes

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

Monooxygenase- and Dioxygenase-Catalyzed Oxidative Dearomatization of Thiophenes by Sulfoxidation, cis-Dihydroxylation and Epoxidation

Enzymatic oxidations of thiophenes, including thiophene-containing drugs, are important for biodesulfurization of crude oil and drug metabolism of mono- and poly-cyclic thiophenes. Thiophene oxidative dearomatization pathways involve reactive metabolites, whose detection is important in the pharmaceutical industry, and are catalyzed by monooxygenase (sulfoxidation, epoxidation) and dioxygenase (sulfoxidation, dihydroxylation) enzymes. Sulfoxide and epoxide metabolites of thiophene substrates are often unstable, and, while cis-dihydrodiol metabolites are more stable, significant challenges are presented by both types of metabolite. Prediction of the structure, relative and absolute configuration, and enantiopurity of chiral metabolites obtained from thiophene enzymatic oxidation depends on the substrate, type of oxygenase selected, and molecular docking results. The racemization and dimerization of sulfoxides, cis/trans epimerization of dihydrodiol metabolites, and aromatization of epoxides are all factors associated with the mono- and di-oxygenase-catalyzed metabolism of thiophenes and thiophene-containing drugs and their applications in chemoenzymatic synthesis and medicine.

A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs

High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC-MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.

Enantiopurity and absolute configuration determination of arene cis-dihydrodiol metabolites and derivatives using chiral boronic acids

The relative merits of the methods employed to determine enantiomeric excess (ee) values and absolute configurations of chiral arene and alkene cis-1,2-diol metabolites, including boronate formation, using racemic or enantiopure (+) and (-)-2-(1-methoxyethyl)phenylboronic acid (MEPBA), are discussed. Further applications of: 1) MEPBA derived boronates of chiral mono- and poly-cyclic arene cis-dihydrodiol, cyclohex-2-en-1-one cis-diol, heteroarene cis/trans-2,3-diol, and catechol metabolites in estimating their ee values, and 2) new chiral phenylboronic acids, 2-[1-methoxy-2,2-dimethylpropyl]phenyl boronic acid (MDPBA) and 2-[1-methoxy-1-phenylmethyl]phenyl boronic acid (MPPBA) and their advantages over MEPBA, as reagents for stereochemical analysis of arene and alkene cis-diol metabolites, are presented.

An aryl dioxygenase shows remarkable double dioxygenation capacity for diverse bis-aryl compounds, provided they are carbocyclic

The bacterial dioxygenation of mono- or polycyclic aromatic compounds is an intensely studied field. However, only in a few cases has the repeated dioxygenation of a substrate possessing more than a single aromatic ring been described. We previously characterized the aryl-hydroxylating dioxygenase BphA-B4h, an artificial hybrid of the dioxygenases of the biphenyl degraders Burkholderia xenovorans LB400 and Pseudomonas sp. strain B4-Magdeburg, which contains the active site of the latter enzyme, as an exceptionally powerful biocatalyst. We now show that this dioxygenase possesses a remarkable capacity for the double dioxygenation of various bicyclic aromatic compounds, provided that they are carbocyclic. Two groups of biphenyl analogues were examined: series A compounds containing one heterocyclic aromatic ring and series B compounds containing two homocyclic aromatic rings. Whereas all of the seven partially heterocyclic biphenyl analogues were solely dioxygenated in the homocyclic ring, four of the six carbocyclic bis-aryls were converted into ortho,meta-hydroxylated bis-dihydrodiols. Potential reasons for failure of heterocyclic dioxygenations are discussed. The obtained bis-dihydrodiols may, as we also show here, be enzymatically re-aromatized to yield the corresponding tetraphenols. This opens a way to a range of new polyphenolic products, a class of compounds known to exert multiple biological activities. Several of the obtained compounds are novel molecules.

Chemoenzymatic synthesis of enantiopure hydroxy sulfoxides derived from substituted arenes

Enantiopure β-hydroxy sulfoxides, phenol sulfoxides and catechol sulfoxides were obtained by chemoenzymatic synthesis and evaluated as chiral synthons and ligands.

Novel approach to ecotoxicological risk assessment of sediments cores around the shipwreck by the use of self-organizing maps

Marine and coastal pollution plays an increasingly important role due to recent severe accidents which drew attention to the consequences of oil spills causing widespread devastation of marine ecosystems. All these problems cannot be solved without conducting environmental studies in the area of possible oil spill and performing chemometric evaluation of the data obtained looking for similar patterns among pollutants and optimize environmental monitoring during eventual spills and possible remediation actions - what is the aim of the work presented. Following the chemical and ecotoxicological studies self-organising maps technique has been applied as a competitive learning algorithm based on unsupervised learning process. Summarizing it can be stated that biotests enable assessing the impact of complex chemical mixtures on the organisms inhabiting particular ecosystems. Short and simple application of biotests cannot easily explain the observable toxicity without more complex chemometric evaluation of datasets obtained describing dependence between xenobiotics and toxicological results.

Polycyclic aromatic hydrocarbon-degrading bacteria from aviation fuel spill site at Ibeno, Nigeria

Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria were isolated from aviation fuel contaminated soil at Inua Eyet Ikot in Ibeno, Nigeria. PAH-degrading bacteria in the contaminated soil were isolated by enrichment culture technique. Isolates with high PAH degrading potential characterized by their extensive growth on PAH-supplemented minimal salt medium were screened for their naphthalene, phenanthrene and chrysene degradability. The screening medium which contained selected PAHs as the sole source of carbon and energy showed that Micrococcus varians AFS-2, Pseudomonas putida AFS-3 and Alcaligenes faecalis AFS-5 exhibited a concentration-dependent growth in all the PAH-compounds tested. There were visible changes in the color of growth medium suggesting the production of different metabolites. Their acclimation to different PAH substrates was also evident as A. faecalis AFS-5 isolated from chrysene grew well on other less complex aromatic compounds. The isolate exhibited best growth (0.44 OD(600)) when exposed to 10 ppm of chrysene for 5 days and could utilize up to 90 ppm of chrysene. This isolate and others with strong PAH-degrading potentials are recommended for bioremediation of PAHs in aviation fuel-contaminated sites in the tropics.

Dioxygenation of the biphenyl dioxygenation product

Two biphenyl dioxygenases (BphAs) were shown to catalyze dioxygenation of biphenyldienediol in the nonoxidized ring to form the respective symmetrical biphenyl-bis-dienediol. This novel metabolite served as a growth substrate for both BphA source strains. Its catabolism through the upper bph pathway of Burkholderia xenovorans LB400 was analyzed.

Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria

Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.

Dioxygenase-catalysed dihydroxylation of arene cis-dihydrodiols and acetonide derivatives: a new approach to the synthesis of enantiopure tetraoxygenated bioproducts from arenes

cis-Dihydrodiols of anthracene and benz[a]anthracene, and acetonide derivatives of the cis-dihydrodiols of benzene, fluorobenzene, biphenyl and phenanthrene have been identified as substrates for dioxygenase enzymes, yielding the corresponding enantiopure arene bioproducts, bis(cis-dihydrodiol)s and cis-diol acetonides respectively.

Metabolism of cytostatically active 6-aminobenzo[c]phenanthridines by human and porcine hepatic microsomes and recombinant cytochrome P450 enzymes

A new and convenient two-step synthesis of 11-substituted 6-amino-11,12-dihydrobenzo[c]phenanthridines and 6-aminobenzo[c]phenanthridines (BPs and BP-Ds) was developed recently in the authors' laboratory. These compounds revealed a high antitumoral activity in in vitro and in vivo test systems. In particular, 11-phenyl-substituted derivatives with two or three methoxy groups showed good activity. It was not clear if the dihydro-derivatives (BPs) were transformed enzymatically into the phenanthridines (BP-Ds), thus acting as prodrugs. The in vitro metabolism of several of these cytostatically active 6-aminobenzo[c]phenanthridines was investigated using human and porcine liver microsomes and a range of expressed human cytochrome P450 enzymes. High-performance liquid chromatography and liquid chromatography-mass spectrometry analysis were used for the quantification and structural identification of the observed metabolites. Aromatic hydroxylation was observed to be the major metabolic pathway in addition to a number of other metabolites. The formation of N-hydroxy- and 6-oxo-derivatives was detected only in very small amounts. BP derivatives are not prodrugs of BP-Ds and no significant differences between human and porcine microsomes were observed, confirming the pig as a good model for metabolism studies of these compounds.

Arene cis-dihydrodiol formation: from biology to application

The range of available arene dihydroxylating dioxygenase enzymes, their structure and mechanism, and recent examples of the application of arene cis-dihydrodiol bioproducts as chiral precursors in the synthesis of natural and unnatural products and chiral ligands are discussed.

cis-Dihydrodiol, arene oxide and phenol metabolites of dictamnine: key intermediates in the biodegradation and biosynthesis of furoquinoline alkaloids

Biotransformation of the parent furoquinoline alkaloid dictamnine and its 4-chlorofuroquinoline precursor, using the B8/36 bacterial mutant strain of Sphingomonas yanoikuyae, yielded, via biphenyl dioxygenase-catalysed dihydroxylation, the first isolable alkaloid cis-dihydrodiol metabolites; these metabolites were used in the chemoenzymatic synthesis of postulated arene oxide and phenol intermediates, and a range of derived furoquinoline alkaloids.

Toluene Dioxygenase-Mediated Oxidation of Bromo(methylsulfanyl)benzenes. Absolute Configuration of Metabolites and Evaluation of Chemo- and Regioselectivity Trends

A series of 2-, 3-, and 4-bromo-1-(methylsulfanyl)benzenes was subjected to whole-cell fermentation withEscherichia coliJM 109 (pDTG601), a recombinant strain that expresses toluene dioxygenase. New metabolites were isolated and their structure and absolute configuration determined by chemical and spectral methods. Experimental details are provided for all new compounds and directing trends in the enzymatic oxidation of substituted aromatics are discussed along with projected applications of these metabolites in asymmetric synthesis.

Dioxygenase-catalyzed cis-dihydroxylation of pyridine-ring systems

Toluene dioxygenase-catalyzed dihydroxylation, in the carbocyclic rings of quinoline, 2-chloroquinoline, 2-methoxyquinoline, and 3-bromoquinoline, was found to yield the corresponding enantiopure cis-5,6- and -7,8-dihy dro diol metabolites using whole cells of Pseudomonas putida UV4. cis-Dihydroxylation at the 3,4-bond of 2-chloroquino line, 2-methoxyquinoline, and 2-quinolone was also found to yield the heterocyclic cis-dihydrodiol metabolite, (+)-cis-(3S,4S)-3,4-dihydroxy-3,4-dihydro-2-quinolone. Heterocyclic cis-dihydrodiol metabolites, resulting from dihydroxylation at the 5,6- and 3,4-bonds of 1-methyl 2-pyridone, were isolated from bacteria containing toluene, naphthalene, and biphenyl dioxygenases. The enantiomeric excess (ee) values (>98%) and the absolute configurations of the carbocyclic cis-dihydrodiol metabolites of quinoline substrates (benzylic R) and of the heterocyclic cis-diols from quinoline, 2-quinolone, and 2-pyridone substrates (allylic S) were found to be in accord with earlier models for dioxygenase-catalyzed cis-dihydroxylation of carbocyclic arenes. Evidence favouring the dioxygenase-catalyzed cis-dihydroxylation of pyridine-ring systems is presented.Key words: dioxygenases; cis-dihydroxylation, pyridines, 2-pyridones, absolute configurations.

Aromatic dioxygenases: molecular biocatalysis and applications

Aromatic dioxygenases have been found to catalyse single and tandem oxidation reactions of conjugated polyenes. Rational selection and design of dioxygenases, allied to substrate shape, size and substitution pattern, has been used to control regiochemistry and stereochemistry during the oxygenation process. The resulting enantiopure bioproducts have been increasingly utilised as precursors for new and alternative routes in chiral synthesis.

Rapid mineralization of benzo[a]pyrene by a microbial consortium growing on diesel fuel

A microbial consortium which rapidly mineralized the environmentally persistent pollutant benzo[a]pyrene was recovered from soil. The consortium cometabolically converted [7-(14)C]benzo[a]pyrene to (14)CO(2) when it was grown on diesel fuel, and the extent of benzo[a]pyrene mineralization was dependent on both diesel fuel and benzo[a]pyrene concentrations. Addition of diesel fuel at concentrations ranging from 0.007 to 0.2% (wt/vol) stimulated the mineralization of 10 mg of benzo[a]pyrene per liter 33 to 65% during a 2-week incubation period. When the benzo[a]pyrene concentration was 10 to 100 mg liter(-1) and the diesel fuel concentration was 0.1% (wt/vol), an inoculum containing 1 mg of cell protein per liter (small inoculum) resulted in mineralization of up to 17.2 mg of benzo[a]pyrene per liter in 16 days. This corresponded to 35% of the added radiolabel when the concentration of benzo[a]pyrene was 50 mg liter(-1). A radiocarbon mass balance analysis recovered 25% of the added benzo[a]pyrene solubilized in the culture suspension prior to mineralization. Populations growing on diesel fuel most likely promoted emulsification of benzo[a]pyrene through the production of surface-active compounds. The consortium was also analyzed by PCR-denaturing gradient gel electrophoresis of 16S rRNA gene fragments, and 12 dominant bands, representing different sequence types, were detected during a 19-day incubation period. The onset of benzo[a]pyrene mineralization was compared to changes in the consortium community structure and was found to correlate with the emergence of at least four sequence types. DNA from 10 sequence types were successfully purified and sequenced, and that data revealed that eight of the consortium members were related to the class Proteobacteria but that the consortium also included members which were related to the genera Mycobacterium and Sphingobacterium.

Aromatic hydrocarbon dioxygenases in environmental biotechnology

Aromatic hydrocarbon dioxygenases belong to a large family of Rieske non-heme iron oxygenases. The dioxygenases have a broad substrate specificity and catalyze enantiospecific reactions with a wide range of substrates. These characteristics make them attractive synthons for the production of industrially and medically important chiral chemicals and also provide essential information for the development of bioremediation technology.