Ludmila Martínková

Glycosides in Medicine: “The Role of Glycosidic Residue in Biological Activity”

Numbers of biologically active compounds are glycosides. Sometimes, the glycosidic residue is crucial for their activity, in other cases glycosylation only improves pharmacokinetic parameters. Recent developments in molecular glycobiology brought better understanding to the aglycone vs. glycoside activities, and made possible to develop new, more active or more effective glycodrugs based on these findings - very illustrative recent example is the story of vancomycin. This paper deals with an array of glycosidic compounds currently used in medicine but also with biological activity of some glycosidic metabolites of the known drugs. It involves glycosides of vitamins, polyphenolic glycosides (flavonoids), alkaloid glycosides, glycosides in the group of antibiotics, glycopeptides, cardiac glycosides, steroid and terpenoid glycosides etc. The physiological role of the glycosyl and structure-activity relations (SAR) in the glycosidic moiety (-ies) are discussed.

Biodegradation potential of the genus Rhodococcus.

A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.

Nitrile- and Amide-converting Microbial Enzymes: Stereo-, Regio- and Chemoselectivity

Biotransformations using microbial nitrile- and amide-converting enzymes have developed considerably in the recent years. Most processes profited from the stereo-, regio- and chemoselectivity of nitrile hydratases, nitrilases and amidases specific for primary or secondary amides. The aim of this review is to discuss the developments in this branch of biotransformations in the last ca. 5 years by taking highlights from research journals, patents and industrial applications.

Biotransformations with nitrilases

The range of possible nitrilase applications has been recently broadened but in most cases the parameters of the reactions need to be improved to establish viable industrial processes. To achieve this goal, several methods have been used, primarily in screening for enzymes from new sources, enzyme improvement, substrate structure modification, medium engineering, and variation in process parameters. New nitrilases have been obtained by for example genome mining and the metagenomic approach. Protein engineering revealed targets for altering substrate specificity, activity or enantioselectivity, and for changing the acid:amide ratio in the nitrilase product. Variation in substrate structure proved to be another means to modify the enantioselectivity and chemoselectivity of the reactions. The utility of nitrilases will be increased further if they can be applied in combination with other enzymes or chemical catalysts without laborious intermediate isolation. Such processes have been developed, for instance, for the synthesis of (S)-mandelic acid, (S)-mandeloamide or glycolic acid.

Fungal nitrilases as biocatalysts: Recent developments.

Of the numerous putative fungal nitrilases available from protein databases only a few enzymes were purified and characterized. The purified nitrilases from Fusarium solani, Fusarium oxysporum f. sp. melonis and Aspergillus niger share a preference for (hetero)aromatic nitriles, temperature optima between 40 and 50 degrees C and pH optima in the slightly alkaline region. On the other hand, they differ in their chemoselectivity, i.e. their tendency to produce amides as by-products. The production of fungal nitrilases is increased by up to three orders of magnitude on the addition of 2-cyanopyridine to the culture media. The whole-cell and subcellular biocatalysts were immobilized by various methods (LentiKats(R); adsorption on hydrophobic or ion exchange resins; cross-linked enzyme aggregates). Operational stability was examined using continuous stirred membrane bioreactors. Fungal nitrilases appear promising for biocatalytic applications and biodegradation of nitrile environmental contaminants.

Hyperinduction of nitrilases in filamentous fungi.

Abstract2-Cyanopyridine proved to act as a powerful nitrilase inducer in Aspergillusniger K10, Fusarium solani O1, Fusarium oxysporum CCF 1414, Fusarium oxysporum CCF 483 and Penicillium multicolor CCF 2244. Valeronitrile also enhanced the nitrilase activity in most of the strains. The highest nitrilase activities were produced by fungi cultivated in a Czapek-Dox medium with both 2-cyanopyridine and valeronitrile. The specific nitrilase activities of these cultures were two to three orders of magnitude higher than those of cultures grown on other nitriles such as 3-cyanopyridine or 4-cyanopyridine.

Biodegradation of brominated aromatics by cultures and laccase of Trametes versicolor.

2-Bromophenol (1), 4-bromophenol (2), 2,4-dibromophenol (3), 2,6-dibromophenol (4), 2,4,6-tribromophenol (5) and tetrabromobisphenol A (6) (1 mM each) added to growing submerged cultures of Trametes versicolor CCBAS 612 were eliminated by 65-85% from the culture medium within 4d. Extracellular laccase activity in the culture medium was influenced by the type of brominated compound added. Maximum level of laccase (63 U L(-1)) was found in the culture with 2-bromophenol. Tetrabromobisphenol A was degraded by a commercial laccase from Trametes versicolor in absence of any oxidation mediator, hydroxylated dibrominated compounds being detected as soluble reaction products by LC/MS. A significant degradation of brominated phenols by laccase was achieved only in the presence of ABTS structural characterization of major products suggesting reaction between bromophenol and ABTS radicals.

Immobilization of fungal nitrilase and bacterial amidase – two enzymes working in accord

A nitrilase from Aspergillus niger and an amidase from Rhodococcus erythropolis co-immobilized on a 1-mL Butyl Sepharose column were used for the hydrolysis of 4-cyanopyridine into isonicotinic acid. The former enzyme converted the nitrile into the acid:amide mixture (molar ratio ca. 3:1), while the latter enzyme hydrolyzed the amide by-product. Therefore, the ratio of amide in the total product decreased to about 5%. Sodium sulfate was used as a component of the elution buffer, as the commonly used ammonium sulfate (0.8 M) acted as an amidase inhibitor. The hydrolysis of 4-cyanopyridine by a nitrilase from F. solani gave isonicotinic acid and isonicotinamide at a molar ratio of about 98:2. When using this enzyme and the amidase immobilized on two columns operated in tandem, the percentage of isonicotinamide in total product decreased to <0.2%.

Biodegradation of phenolic compounds by Basidiomycota and its phenol oxidases: A review.

The phylum Basidiomycota include organisms with enormous bioremediation potential. A variety of processes were proposed at the lab scale for using these fungi and their phenol oxidases in the degradation of phenolics. Here we present a survey of this topic using literature published mostly over the last 10 years. First, the sources of the enzymes are summarized. The laccase and tyrosinase were mainly from Trametes versicolor and Agaricus bisporus, respectively. Recently, however, new promising wild-type producers of the enzymes have emerged and a number of recombinant strains were also constructed, based mainly on yeasts or Aspergillus strains as hosts. The next part of the study summarizes the enzyme and whole-cell applications for the degradation of phenols, polyphenols, cresols, alkylphenols, naphthols, bisphenols and halogenated (bis)phenols in model mixtures or real wastewaters from the food, paper and coal industries, or municipal and hospital sewage. The enzymes were applied as free (crude or purified) enzymes or as enzymes immobilized in various supports or CLEAs, and optionally recycled or used in continuous mode. Alternatively, growing cultures or harvested mycelia were used instead. The products, which were characterized as quinones and their polymers in some cases, could be eliminated by filtration, flocculation or adsorption onto chitosan. The purity of a treated wastewater was monitored using a sensitive aquatic organism. It is concluded that low-cost sources of these enzymes should be searched for and the benefits of enzymatic, biological and physico-chemical methods could be combined to make the processes fit for industrial use.

Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10

BackgroundNitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult.ResultsA nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzymes native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn356) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp298-Val313 peptide was shortened to Asp298-Arg310 in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution.ConclusionsThe nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.