Catalytic properties of catechol 1,2-dioxygenase from Acinetobacter radioresistens S13 immobilized on nanosponges

Characterization of Gentisate 1,2-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and Its Stabilization by Immobilization on Nickel-Functionalized Magnetic Nanoparticles

The aim of this study was the biochemical and kinetic characterization of the gentisate 1,2-dioxygenase (GDO) from Pseudarthrobacter phenanthrenivorans Sphe3 and the development of a nanobiocatalyst by its immobilization on Ni2+-functionalized Fe3O4-polydopamine magnetic nanoparticles (Ni2+-PDA-MNPs). This is the first GDO to be immobilized. The gene encoding the GDO was cloned with an N-terminal His-tag and overexpressed in E. coli. The nanoparticles showed a high purification efficiency of GDO from crude cell lysates with a maximum activity recovery of 97%. The immobilized enzyme was characterized by Fourier transform infrared spectroscopy (FTIR). The reaction product was identified by 1H NMR. Both free and immobilized GDO exhibited Michaelis–Menten kinetics with Km values of 25.9 ± 4.4 and 82.5 ± 14.2 μM and Vmax values of 1.2 ± 0.1 and 0.03 ± 0.002 mM*s−1, respectively. The thermal stability of the immobilized GDO was enhanced at 30 °C, 40 °C, and 50 °C, compared to the free GDO. Stored at −20 °C, immobilized GDO retained more than 60% of its initial activity after 30 d, while the free enzyme completely lost its activity after 10 d. Furthermore, the immobilized nanoparticle–enzyme conjugate retained more than 50% enzyme activity up to the fifth cycle.

Sustainable production and co-immobilization of cold-active enzymes from Pseudomonas sp. for BTEX biodegradation

Toluene/o-Xylene Monooxygenase (ToMO) is equipped with a broad spectrum of aromatic substrate specificity (such as BTEX; benzene, toluene, ethylbenzene, and isomers of xylenes). TOMO has can hydroxylate more than a single position of aromatic rings in two consecutive monooxygenation reactions. Catechol 1,2-dioxygenase (C1,2D) is an iron-containing enzyme able to cleave the ring of catechol (the converted product from ToMO) for complete detoxification of BTEX. In this study, cold-active ToMO and C1,2D were produced using newly isolated psychrophilic Pseudomonas S2TR-14 in the minimal salt medium supplemented with crustacean waste and different concentrations of used motor oil (0.2-2% (v/v)). Crude ToMO and C1,2D were immobilized into micro/nano biochar-chitosan matrices and used for BTEX biodegradation. The results showed that the highest enzyme production (12 U/mg for ToMO and 22 U/mg for C1,2D) was achieved at the presence of 0.5% v/v used motor oil compared to the control group without motor oil (0.07 and 0.06 U/mg). High immobilization yield was achieved due to covalent bonding of ToMO (92.26% for micro matrix and 77.20% for nano matrix) and C1,2D (87.57% for micro matrix and 74.79% for nano matrix) with matrices. FTIR spectra confirmed the immobilization of enzymes on the surface of microbiochar and nanobiochar-chitosan matrices as proper support. The immobilization increased the storage stability of the enzymes with more than 50% residual activity after 30 days at 4 ± 1 °C, while the free form of enzymes had less than 10% of its activity. Immobilized enzymes degraded more than 80% of BTEX (~200 mg/L in groundwater and ~10,000 mg/kg in soil) at 10 ± 1 °C in groundwater and soil. Therefore, integrated use of microbiochar and nanobiochar with chitosan for co-immobilization of ToMO and C1,2D can be a potential way to remove petroleum hydrocarbons with higher efficiency from contaminated groundwater and soil.

Drug-Encapsulated Cyclodextrin Nanosponges

To date, a number of nanocarriers, either inorganic or organic, have been developed to improve the delivery and therapeutic efficacy of various drugs. Drug delivery systems have attempted to overcome the undesirable pharmacokinetic problems encountered. Among the various nanomaterials that have been designed as potential nanocarriers, cyclodextrin-based polymers are of particular interest in this review.Cyclodextrins (CD) are a class of cyclic glucopyranose oligomers, obtained from starch by enzymatic action, with a characteristic toroidal shape that forms a truncated cone-shaped lipophilic cavity. The main common native cyclodextrins are named α, β, and γ which comprise six, seven, and eight glucopyranose units, respectively. Cyclodextrins have the capability to include compounds whose size and polarity are compatible with those of their cavity.Cyclodextrin-based cross-linked polymers, often referred to as "cyclodextrin nanosponges" (CDNSs), attract great attention from researchers for solving major bioavailability problems such as inadequate solubility, poor dissolution rate, and limited stability of some agents, as well as increasing their effectiveness and decreasing unwanted side effects.Registered patents about this novel system in various fields, different pharmaceutical applications, and classes of drugs encapsulated by CDNSs are detailed. The features outlined make CDNSs a promising platform for the development of innovative and advanced delivery systems.

History of Cyclodextrin Nanosponges

Nowadays, research in the field of nanotechnology and nanomedicine has become increasingly predominant, focusing on the manipulation and development of materials on a nanometer scale. Polysaccharides have often been used as they are safe, non-toxic, hydrophilic, biodegradable and are low cost. Among them, starch derivatives and, in particular, cyclodextrin-based nanosponges (CD NSs) have recently emerged due to the outstanding properties attributable to their peculiar structure. In fact, alongside the common polysaccharide features, such as the presence of tunable functional groups and their ability to interact with biological tissues, thus giving rise to bioadhesion, which is particularly useful in drug delivery, what makes CD NSs unique is their three-dimensional network made up of crosslinked cyclodextrin units. The name “nanosponge” appeared for the first time in the 1990s due to their nanoporous, sponge-like structure and responded to the need to overcome the limitations of native cyclodextrins (CDs), particularly their water solubility and inability to encapsulate charged and large molecules efficiently. Since CD NSs were introduced, efforts have been made over the years to understand their mechanism of action and their capability to host molecules with low or high molecular weight, charged, hydrophobic or hydrophilic by changing the type of cyclodextrin, crosslinker and degree of crosslinking used. They enabled great advances to be made in various fields such as agroscience, pharmaceutical, biomedical and biotechnological sectors, and NS research is far from reaching its conclusion. This review gives an overview of CD NS research, focusing on the origin and key points of the historical development in the last 50 years, progressing from relatively simple crosslinked networks in the 1960s to today’s multifunctional polymers. The approach adopted in writing the present study consisted in exploring the historical evolution of NSs in order to understand their role today, and imagine their future.

Evaluation of solubility enhancement, antioxidant activity, and cytotoxicity studies of kynurenic acid loaded cyclodextrin nanosponge

Kynurenic acid demonstrates antioxidant, neuroprotective and free radical scavenging properties. However, low aqueous solubility of kynurenic acid limits its therapeutic activity. In the present study, cyclodextrin nanosponges were used to improve the solubility and therapeutic activity of kynurenic acid. The formation of kynurenic acid loaded nanosponge was confirmed by different characterization techniques. The solubility of kynurenic acid was significantly increased with nanosponge (111.1 μg/ml) compared to free kynurenic acid (16.4 μg/ml) and β-cyclodextrin (28.6 μg/ml). High drug loading (19.06%) and encapsulation efficiency (95.31%) were achieved with NS. The particle size and zeta potential of kynurenic acid loaded nanosponge was around 255.8 nm and -23 mV respectively. Moreover, higher solubilization of kynurenic acid loaded nanosponge produced better antioxidant activity compared to free kynurenic acid. The kynurenic acid loaded nanosponge and blank nanosponge were found nontoxic in the cytotoxicity assay. Thus, these studies demonstrated that nanosponges can be used as a carrier for the delivery of kynurenic acid.

Organic micropollutants paracetamol and ibuprofen-toxicity, biodegradation, and genetic background of their utilization by bacteria

Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition.

Combination of carbon nanotube and cyclodextrin nanosponge chemistry to develop a heterogeneous Pd-based catalyst for ligand and copper free C-C coupling reactions

Carbon nanotubes and cyclodextrin nanosponge were hybridized and used as a support for embedding Pd(0) nanoparticles and developing a novel and heterogeneous catalyst, Pd@CDNS-CNT, for promoting ligand and copper-free Sonogashira and Heck coupling reactions in aqueous media and mild reaction condition. Cyclodextrin nanosponge could contribute to catalysis through encapsulating the reagents and transferring them in the vicinity of Pd nanoparticles. The results established that the catalytic activity of Pd@CDNS-CNT was superior to those of Pd@CNT, Pd@CDNS and Pd@CNT + CDNS, indicating the synergism between the components of the hybrid system. Notably, various aryl halides including aryl iodide, bromide and chloride were useful substrates for the coupling reactions and affording the corresponding products in high to excellent yields in short reaction times. Moreover, the catalyst was recyclable up to six reaction runs with negligible Pd leaching.

A polypyrrole–methyl anthranilate functionalized worm-like titanium dioxide nanocomposite as an innovative tool for immobilization of lipase: preparation, activity, stability and molecular docking investigations

Schematic of the novel synthesised nanobioconjugates.

Highly Efficient and Stable Novel NanoBiohybrid Catalyst to Avert 3,4-Dihydroxybenzoic Acid Pollutant in Water

The present study reported for the first time covalent immobilization of protocatechuate 3,4-dioxygenase (3,4-POD) onto functionalized multi-walled carbon nanotubes (F-MWCNT) for degrading the toxic 3,4-dihydroxybenzoic acid (3,4-DHBA) pollutant in water. The F-MWCNTs had a maximum 3,4-POD loading of 1060 μg/mg. Immobilized 3,4 POD had 44% of relative structural changes to its free configurations. Nevertheless, >90% of relative activity and about 50% of catalytic efficiency were retained to the free enzyme. Immobilized 3,4-POD demonstrated higher alkaline stability and thermostability than the free 3,4-POD. The free and immobilized 3,4-POD lost 82% and 66% of relative activities, respectively after 180 min of incubations at 90 °C. Excellent shelf-life was observed for the immobilized 3,4-POD with residual activity of 56% compared with 41% and 39% of the free 3,4-POD at 4 °C and 25 °C over 30 days storage. Immobilized 3,4-POD showed >60% of catalytic activity retention even after ten-cycle uses, defraying the expenses of free 3,4-POD productions for long term uses. Finally, the immobilized 3,4-POD removed 71% of 3,4-DHBA from water in <4 h, paving its future application for water purification with reduced costs and time.

Noncovalent and covalent immobilization of oxygenase on single-walled carbon nanotube for enzymatic decomposition of aromatic hydrocarbon intermediates

The decomposition of various aromatic hydrocarbon intermediates was examined using a recombinant oxidative enzyme immobilized on single-walled carbon nanotubes (SWCNTs). Hydroxyquinol 1,2-dioxygenase (CphA-I), which catalyzes ring cleavage of catechol and its analogues, was obtained from Arthrobacter chlorophenolicus A6 via cloning, overexpression, and subsequent purification. This recombinant enzyme was immobilized on SWCNTs by physical adsorption and covalent coupling in the absence and presence of N-hydroxysuccinimide. The immobilization yield was as high as 52.1%, and a high level of enzyme activity of up to 64.7% was preserved after immobilization. Kinetic analysis showed that the substrate utilization rates (vmax) and catalytic efficiencies (kcat/KM) of the immobilized enzyme for all substrates evaluated were similar to those of the free enzyme, indicating minimal loss of enzyme activity during immobilization. The immobilized enzyme was more stable toward extreme pH, temperature, and ionic strength conditions than the free enzyme. Thus, the oxidative enzyme immobilized on SWCNTs can be used as an effective and stable biocatalyst for the biochemical remediation process if further investigations would be carried out under field conditions.

Exploring allosteric activation of LigAB from Sphingobium sp. strain SYK-6 through kinetics, mutagenesis and computational studies

The protocatechuate 4,5-dioxygenase (LigAB) from Sphingobium sp. strain SYK-6 is the defining member of the Type II extradiol dioxygenase superfamily (a.k.a. PCA Dioxygenase Superfamily or PCADSF) and plays a key aromatic ring-opening role in the metabolism of several lignin derived aromatic compounds. In our search for alternate substrates and inhibitors of LigAB, we discovered allosteric rate enhancement in the presence of non-substrate protocatechuate-like aldehydes such as vanillin. LigAB has the broadest substrate utilization profile of all protocatechuate (PCA) 4,5-dioxygenase described in the literature, however, the rate enhancement is only observed with PCA, with vanillin increasing kcat for LigAB by 36%. Computational docking has identified a potential site of allosteric binding near the entrance to the active site. Examination of a multiple sequence alignment reveals that many of the residues contributing to this newly identified allosteric pocket are highly conserved within the LigB family of the PCADSF. Point mutants of Phe103α and Ala18β, two residues located in the putative allosteric pocket, display altered rate enhancement as compared to LigAB-WT, providing support for the computationally identified allosteric binding site. Further investigation of this binding site may provide insight into the mechanism of this never before observed allosteric activation in extradiol dioxygenases.

Immobilization as a strategy for improving enzyme properties-application to oxidoreductases

The main objective of the immobilization of enzymes is to enhance the economics of biocatalytic processes. Immobilization allows one to re-use the enzyme for an extended period of time and enables easier separation of the catalyst from the product. Additionally, immobilization improves many properties of enzymes such as performance in organic solvents, pH tolerance, heat stability or the functional stability. Increasing the structural rigidity of the protein and stabilization of multimeric enzymes which prevents dissociation-related inactivation. In the last decade, several papers about immobilization methods have been published. In our work, we present a relation between the influence of immobilization on the improvement of the properties of selected oxidoreductases and their commercial value. We also present our view on the role that different immobilization methods play in the reduction of enzyme inhibition during biotechnological processes.

Ormosil gels doped with engineered catechol 1,2 dioxygenases for chlorocatechol bioremediation

Enzymes entrapped in wet, nanoporous silica gel have great potential as bioreactors for bioremediation because of their improved thermal, chemical, and mechanical stability with respect to enzymes in solution. The B isozyme of catechol 1,2 dioxygenase from Acinetobacter radioresistens and its mutants of Leu69 and Ala72, designed for an increased reactivity toward the environmental pollutant chlorocatechols, were encapsulated using alkoxysilanes and alkyl alkoxysilanes as precursors in varying proportions. Encapsulation of the mutants in a hydrophobic tetramethoxysilane/dimethoxydimethylsilane-based matrix yielded a remarkable 10- to 12-fold enhancement in reactivity toward chlorocatechols. These gels also showed a fivefold increase in relative reactivity toward chlorocatechols with respect to the natural substrate catechol, thus compensating for their relatively low activity for these substrates in solution. The encapsulated enzyme, unlike the enzyme in solution, proved resilient in assays carried out in urban wastewater and bacteria-contaminated solutions mimicking environmentally relevant conditions. Overall, the combination of a structure-based rational design of enzyme mutants, and the selection of a suitable encapsulation material, proved to be a powerful approach for the production and optimization of a potential bioremediation device, with increased activity and resistance toward bacterial degradation.

Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis

Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.

Cyclodextrin-based nanosponges as drug carriers

Cyclodextrin-based nanosponges, which are proposed as a new nanosized delivery system, are innovative cross-linked cyclodextrin polymers nanostructured within a three-dimensional network. This type of cyclodextrin polymer can form porous insoluble nanoparticles with a crystalline or amorphous structure and spherical shape or swelling properties. The polarity and dimension of the polymer mesh can be easily tuned by varying the type of cross-linker and degree of cross-linking. Nanosponge functionalisation for site-specific targeting can be achieved by conjugating various ligands on their surface. They are a safe and biodegradable material with negligible toxicity on cell cultures and are well-tolerated after injection in mice. Cyclodextrin-based nanosponges can form complexes with different types of lipophilic or hydrophilic molecules. The release of the entrapped molecules can be varied by modifying the structure to achieve prolonged release kinetics or a faster release. The nanosponges could be used to improve the aqueous solubility of poorly water-soluble molecules, protect degradable substances, obtain sustained delivery systems or design innovative drug carriers for nanomedicine.

Biodegradation of m-cresol by aerobic granules in a sequencing batch reactor

The present study was aimed at the development of aerobic granules in a sequencing batch reactor for the biodegradation of m-cresol. The reactor was started with 100 mg L(-1)of m-cresol. Aerobic granules first appeared within 1 month of the start-up of the reactor. The granules were large and strong and had a compact structure. The diameter of stable granules on day 200 was in the range of 1.5 - 5 mm. The integrity coefficient and density of the granules was found to be 98% and 1046 kg m(-3), respectively. The settling velocity of the granules was found to be in the range of 2-6 x 10(-2) m s(-1). The aerobic granules were able to degrade m-cresol up to 800 mg L(-1) at a removal efficiency of 87%. UV and GC/MS studies confirmed that the biodegradation ofm-cresol occurred via catechol via the ortho-cleavage pathway. The specific m-cresol degradation rate in aerobic granules followed the Haldane model for substrate inhibition. A high specific m-cresol degradation rate of up to 0.718 g m-cresol g(-1)VSS(-1)d(-1) was sustained up to an m-cresol concentration of 400 mgL(-1). The higher removal efficiency and good settling characteristics of aerobic granules make the sequencing batch reactor method suitable for enhancing the microorganism potential for biodegradation of inhibitory compounds.

Cyclodextrin nanosponge-sensitized enantiodifferentiating photoisomerization of cyclooctene and 1,3-cyclooctadiene

Enantiodifferentiating geometrical photoisomerizations of (Z)-cyclooctene and (Z,Z)-1,3-cyclooctadiene were performed by using the pyromellitate-linked cyclodextrin network polymer, termed "cyclodextrin nanosponge (CDNS)", as a supramolecular sensitizing host. The photochirogenic behavior of the nanosponges incorporating β- or γ-cyclodextrin was significantly different from that reported for the conventional sensitizer-appended monomeric cyclodextrins, affording chiral (E)-cyclooctene and (E,Z)-cyclooctadiene in enantiomeric excesses critically dependent on the solution pH and solvent composition employed, revealing the active roles of chiral void spaces of CDNS in the photochirogenic reaction.

Biodegradation of p-cresol by aerobic granules in sequencing batch reactor

The cultivation of aerobic granules in sequencing batch reactor for the biodegradation of p-cresol was studied. The reactor was started with 100 mg/L of p-cresol. Aerobic granules first appeared within one month of start up. The granules were large and strong and had a compact structure. The diameter of stable granules was in the range of 1-5 mm. The integrity coefficient and granules density was found to be 96% and 1046 kg/m3, respectively. The settling velocity of granules was found to be in the range of 2x10(-2)-6x10(-2) m/sec. The aerobic granules were able to degrade p-cresol upto 800 mg/L at a removal efficiency of 88%. Specific p-cresol degradation rate in aerobic granules followed Haldane model for substrate inhibition. High specific p-cresol degradation rate up to 0.96 g p-cresol/(g VSS x day) were sustained upto p-cresol concentration of 400 mg/L. Higher removal efficiency, good settling characteristics of aerobic granules, makes sequencing batch reactor suitable for enhancing the microorganism potential for biodegradation of inhibitory compounds.

Functional consortia for cresol-degrading activated sludges: toxicity-to-extinction approach

The conventional roll tube and plating techniques are typically time consuming and can culture in vitro only a small fraction of microbes in natural microflora. This study utilizes a novel, simple, and rapid method, the toxicity-to-extinction approach, to obtain the minimal functional consortium that can effectively degrade meta- (m-), para- (p-), and ortho- (o-) cresols. The original sludge had 16 major bands by denaturing gradient gel electrophoresis (DGGE). Microbial diversity decreased as the cresol concentration increased. The functional strains acquired under toxic stress by dosed cresols that individually degraded m-, p-, and o-cresols were identified. Catechol 1,2-dioxygenase (C12D) and catechol 2,3-dioxygenase (C23D) activities in cell-free extracts were determined spectrophotometrically and were correlated with noted changes in microbial communities under cresol stress. The proposed toxicity-to-extinction approach is feasible for isolating a functional consortium from sludge for cresol degradation.