Natural phytocompounds physalin D, withaferin a and withanone target L-asparaginase of Mycobacterium tuberculosis: a molecular dynamics study.

Tuberculosis is a major infectious disease that is responsible for high mortality in humans. The reason for the global burden is the emergence of new antibiotic resistant strains of Mycobacteria that showed resistance against the currently given therapy. It is identified that the pathogen utilizes the L-asparaginase enzyme as a virulence factor for survival benefits inside the host. Therefore, L-asparaginase of Mycobacterium tuberculosis is a promising therapeutic drug target. In view of the light, the present study explores thirty phytocompounds from medicinal plants to determine the binding affinity in the catalytic site of L-asparaginase. The studies initiated with the construction of the 3 D structure of L-asparaginase using homology modeling. Using the robustness of molecular docking with binding energy cut-off value < -9.0 kcal/mol and 100 ns molecular dynamics simulations, three phytocompounds viz., Physalin D (-9.11 kcal/mol), Withanone (-9.45 kcal/mol) and Withaferin A (-9. 67 kcal/mol) showed strong binding potential compared to the product, L-aspartate (-5.87 kcal/mol). The active site residues identified are Thr 12, Asp 51, Ser 53, Thr 84, Asp 85, and Lys 157. Upon MD simulations, the phytocompounds and the product L-aspartate remain present in the same catalytic pocket of the enzyme. The RMSD, RMSF, radius of gyration and H-bond analysis of enzyme ligand complexes efficiently showed the stability of ligands at the docked site. Further, ADME studies distinctly demonstrate the potential of selected phytoconstituents as therapeutics. Thus, serve as safe and low-cost alternatives to chemical compounds to be used in combination therapy for treatment of tuberculosis.Communicated by Ramaswamy H. Sarma.

Molecular cloning, structural modeling and characterization of a novel glutaminase-free L-asparaginase from Cobetia amphilecti AMI6.

The exploration of new sources of L-asparaginase with low glutaminase activity is of great interest in both medical and food applications. In the current study, a novel L-asparaginase gene (CobAsnase) from halotolerant Cobetia amphilecti AMI6 was cloned and over-expressed in Escherichia coli. The enzyme had a molecular mass of 37 kDa on SDS-PAGE and dynamic light scattering (DLS) analysis revealed that CobAsnase is a homotetramer in solution. The purified enzyme showed optimum activity at pH and temperature of 7 and 60 °C, respectively, with obvious thermal stability. It exhibited strict substrate specificity towards L-asparagine with no detectable activity on L-glutamine. Pre-treatment of potato slices by CobAsnase prior to frying reduced the acrylamide contents in the processed chips up to 81% compared with untreated control. These results suggest that CobAsnase is a potential candidate for applications in the food industry for mitigation of acrylamide formation in fried potato and baked foods.

Development and catalytic characterization of L-asparaginase nano-bioconjugates.

The present paper describes efficient immobilization of L-glutaminase free L-asparaginase for developing a new therapeutic system for anticancer therapy. L-asparaginase (L-ASNase) was covalently immobilized on the functionalized aluminum oxide nanoparticles (AONP) and titanium oxide nanoparticles (TONP). The nano-bioconjugates (AONP-ASNase and TONP-ASNase) were characterized by scanning electron microscope (SEM), Fourier-transform infrared spectroscopy (FTIR) and UV-Vis spectral analysis that revealed the successful immobilization. The nano-bioconjugates were optimally active at pH 7.0 and 40 °C. TONP-ASNase activity was enhanced in the presence of NH4+ (160%) and Mn2+ (165%) while AONP-ASNase bioconjugates showed increased relative activity with ethyl acetate (142%) and toluene (160%). The nano-bioconjugates displayed excellent reusability and maintained >90% average activity after nine successive cycles. Maximum cytotoxicity (61%) was noticed with AONP-ASNase (10 µg/ml) against human leukemia MOLT-4 cells. Regarding kinetic values, AONP-ASNase showed better affinity (Km 1.9 µmol) to L-asparagine as compared to free L-ASNase. After 23 days storage at 37 °C, bioconjugates retained 40% residual activity while free L-ASNase was completely deactivated. Thermodynamic characterization revealed higher conversion rate of the E-S complex in case of nano-bioconjugates.

Identification and validation of l-asparaginase as a potential metabolic target against Mycobacterium tuberculosis.

Multidrug-resistant Mycobacterium tuberculosis (Mtb) has emerged as a major health challenge, necessitating the search for new molecular targets. A secretory amidohydrolase, l-asparaginase of Mtb (MtA), originally implicated in nitrogen assimilation and neutralization of acidic microenvironment inside human alveolar macrophages, has been proposed as a crucial metabolic enzyme. To investigate whether this enzyme could serve as a potential drug target, it was studied for structural details and active site-specific inhibitors were tested on cultured Mycobacterial strain. The structural details of MtA obtained through comparative modeling and molecular dynamics simulations provided insights about the orchestration of an alternate reaction mechanism at the active site. This was contrary to the critical Tyr flipping mechanism reported in other asparaginases. We report the novel finding of Tyr to Val replacement in catalytic triad I along with the structural reorganization of a ß-hairpin loop upon substrate binding in MtA active site. Further, 5 MtA-specific, active-site-based inhibitors were obtained by following a rigorous differential screening protocol. When tested on Mycobacterium culture, 3 of these, M3 (ZINC 4740895), M26 (ZINC 33535), and doxorubicin showed promising results with inhibitory concentrations (IC 50 ) of 431, 100, and 56 µM, respectively. Based on our findings and considering stark differences with human asparaginase, we project MtA as a promising molecular target against which the selected inhibitors may be used to counteract Mtb infection effectively.

Synthesis, characterization and synergistic activity of cerium-selenium nanobiocomposite of fungal l-asparaginase against lung cancer.

Cerium selenium nanobiocomposites are novel lung cancer drug as they possess combined anti-cancer property of nanocomposite with l-asparaginase working in synergetic manner. Cerium selenium nanobiocomposites were synthesized using simple co-precipitation method. The size of the nanocomposite was found to be in the range 60-90 nm. Maximum absorption was observed using UV spectrum in the range of 350-490 nm. The nanobiocomposites was characterized using H-NMR and FTIR analysis it was found that secondary alkyl, allylic carbon, monosubstituted alkenes and sp2 hybridized CH bonds of alkenes were involved in binding of cerium and selenium nanoparticles with l-asparaginase for the formation of cerium selenium nanobiocomposite. The spherical shape of the cerium selenium nanobiocomposites were confirmed using SEM. Anticancer activity was checked by performing MTT assay resulting in 70.84% and 48.78% toxicity for maximum concentration of 1000 (µg/ml) and IC50 concentration of 125 (µg/ml) respectively on A549 lung cancer cell line using fluorescent microscopic analysis.

Catalytic characteristics and application of l-asparaginase immobilized on aluminum oxide pellets.

l-asparaginase from Escherichia coli (l-ASNase) was covalently immobilized on aluminum oxide pellets (AlOPs) using a cross-linking agent, glutaraldehyde. Maximum immobilization yield (85.0%) was obtained after optimizing immobilization parameters using response surface methodology (RSM). Both free and immobilized l-ASNase (AlOP-ASNase) were optimally active at 37°C and pH7.5. However, the bioconjugate exhibited enhanced activity and stability at different pH and temperatures. It had higher affinity (low Km) and was comparatively more stable in presence of some solvents (ethyl acetate, acetone, acetonitrile), metal ions (Ag+, Zn2+) and ß-mercaptoethanol. AlOP-ASNase was reused in a glass column reactor for l-asparagine hydrolysis upto nine successive cycles without any loss in activity. The AlOP-ASNase was effective in lowering l-asparagine level in blanched potato chips indicating its potential use in mitigating acrylamide formation in starchy foods. This cost-effective enzyme preparation had shelf-life of more than 30days and can be effectively used in starch based food industries.

Biochemical characterization of a novel L-asparaginase from Paenibacillus barengoltzii being suitable for acrylamide reduction in potato chips and mooncakes.

A novel L-asparaginase gene (PbAsnase) from Paenibaeillus barengoltzii CAU904 was cloned and expressed in Escherichia coli. The L-asparaginase gene was 1011bp encoding 336 amino acids. Multiple sequence alignment of PbAsnase with other known L-asparaginases revealed that the enzyme showed high similarities with some Rhizobial-type L-asparaginases, sharing the highest identity of 32% with a characterized L-asparaginase from Rhizobium etli CFN 42, suggesting that it should be a novel L-asparaginase. The recombinant L-asparaginase (PbAsnase) was purified to homogeneity and biochemically characterized. The purified enzyme was optimally active at pH 8.5 and 45°C, respectively. It was stable within pH 5.5-10.0 and at temperatures below 55°C. PbAsnase exhibited strict substrate specificity towards L-asparagine (35.2U/mg), with Km and Vmax values of 3.6mM and 162.2µmol/min/mg, respectively, but displayed trace activity towards L-glutamine. Moreover, the application potential of PbAsnase on acrylamide migration in potato chips and mooncakes was evaluated. The pretreatment by PbAsnase significantly decreased the acrylamide contents in potato chips and mooncakes by 86% and 52%, respectively. The unique properties of PbAsnase may make it a good candidate in industries, especially in food safety.

Biochemical characterization and immobilization of Erwinia carotovoral-asparaginase in a microplate for high-throughput biosensing of l-asparagine.

l-Asparaginases (l-ASNase, E.C. 3.5.1.1) catalyze the conversion of l-asparagine to l-aspartic acid and ammonia. In the present work, a new form of l-ASNase from a strain of Erwinia carotovora (EcaL-ASNase) was cloned, expressed in Escherichia coli as a soluble protein and characterized. The enzyme was purified to homogeneity by a single-step procedure comprising ion-exchange chromatography. The properties of the recombinant enzyme were investigated employing kinetic analysis and molecular modelling and the kinetic parameters (Km, kcat) were determined for a number of substrates. The enzyme was used to assemble a microplate-based biosensor that was used for the development of a simple assay for the determination of l-asparagine in biological samples. In this sensor, the enzyme was immobilized by crosslinking with glutaraldehyde and deposited into the well of a microplate in 96-well format. The sensing scheme was based on the colorimetric measurement of ammonia formation using the Nessler's reagent. This format is ideal for micro-volume applications and allows the use of the proposed biosensor in high-throughput applications for monitoring l-asparagine levels in serum and foods samples. Calibration curve was obtained for l-asparagine, with useful concentration range 10-200µΜ. The biosensor had a detection limit of 10µM for l-asparagine. The method's reproducibility was in the order of ±3-6% and l-asparagine mean recoveries were 101.5%.

A novel bacterial type II l-asparaginase and evaluation of its enzymatic acrylamide reduction in French fries.

This study reports the identification of a novel bacterial type II l-asparaginase, abASNase2, from Aquabacterium sp. A7-Y. The enzyme contains 319 amino acids and shared 35% identity with Escherichia coli type II l-asparaginase (EcAII), a commercial enzyme trademarked Elspar® that is widely used for medical applications. abASNase2 had high specific activity (458.9U/mg) toward l-asparagine, very low activity toward l-glutamine and d-glutamine and no activity toward d-asparagine. The optimal enzymatic activity conditions for abASNase2 were found to be 50mM Tris-HCl buffer (pH 9.0) at 60°C. It was very stable in the pH range of 7.0-11.0 and exhibited up to 80% relative activity after 2h below 40°C. The Km and kcat of abASNase2 were 1.8×10-3M and 241.9s-1, respectively. In addition, abASNase2's ability to remove acrylamide from fried potato strips was evaluated. Compared to untreated potato strips (acrylamide content: 0.823±0.0457mg/kg), 88.2% acrylamide was removed in the abASNase2-treated group (acrylamide content: 0.097±0.0157mg/kg). These results indicate that the novel l-asparaginase abASNase2 is a potential candidate for applications in the food processing industry.

Reduction of acrylamide level through blanching with treatment by an extremely thermostable L-asparaginase during French fries processing.

Bacterial L-asparaginase catalyzes the hydrolysis of L-asparagine to L-aspartic acid. It is normally used as an antineoplastic drug applied in lymphoblastic leukemia chemotherapy and as a food processing aid in baked or fried food industry to inhibit the formation of acrylamide. The present study demonstrates cloning, expression, and characterization of a thermostable L-asparaginase from Thermococcus zilligii AN1 TziAN1_1 and also evaluates the potential for enzymatic acrylamide mitigation in French fries using this enzyme. The recombinant L-asparaginase was purified to homogeneity by nickel-affinity chromatography. The purified enzyme displayed the maximum activity at pH 8.5 and 90 °C, and the optimum temperature was the highest ever reported. The K m, k cat, and k cat/K m values toward L-asparagine were measured to be 6.08 mM, 3267 s(-1), and 537.3 mM(-1) s(-1), respectively. The enzyme retained 70 % of its original activity after 2 h of incubation at 85 °C. When potato samples were treated with 10 U/mL of L-asparaginase at 80 °C for only 4 min, the acrylamide content in final French fries was reduced by 80.5 % compared with the untreated control. Results of this study revealed that the enzyme was highly active at elevated temperatures, reflecting the potential of the T. zilligii L-asparaginase in the food processing industry.

L-Asparaginase as a new molecular target against leishmaniasis: insights into the mechanism of action and structure-based inhibitor design.

l-Asparaginases belong to a family of amidohydrolases that catalyze the conversion of l-asparagine into l-aspartic acid and ammonia. Although bacterial l-asparaginases have been used extensively as anti-leukemic agents, their possible role as potential drug targets for pathogenic organisms has not been explored. The presence of genes coding for putative l-asparaginase enzymes in the Leishmania donovani genome hinted towards the specific role of these enzymes in extending survival benefit to the organism. To investigate whether this enzyme can serve as a potential drug target against the Leishmania pathogen, we obtained structural models of one of the putative Leishmania l-asparaginase I (LdAI). Using an integrated computational approach involving molecular modelling, docking and molecular dynamics simulations, we found crucial differences between catalytic residues of LdAI as compared to bacterial l-asparaginases. The deviation from the canonical acid-base pair at triad I, along with the structural reorganization of a ß-hairpin loop in the presence of a substrate, indicated an altogether new mechanism of action of the LdAI enzyme. Moreover, the finding of compositional and functional differences between LdAI and human asparaginase was used as a criterion to identify specific small molecule inhibitors. Through virtual screening of a library of 11 438 compounds, we report five compounds that showed favorable interactions with the active pocket of LdAI, without adversely affecting human asparaginase. One of these compounds when tested on cultured Leishmania promastigotes displayed a promising leishmanicidal effect. Overall, our work not only provides first hand mechanistic insights of LdAI but also proposes five strongly active compounds which may prove as effective anti-leishmaniasis molecules.

Preserving catalytic activity and enhancing biochemical stability of the therapeutic enzyme asparaginase by biocompatible multilayered polyelectrolyte microcapsules.

The present study focuses on the formation of microcapsules containing catalytically active L-asparaginase (L-ASNase), a protein drug of high value in antileukemic therapy. We make use of the layer-by-layer (LbL) technique to coat protein-loaded calcium carbonate (CaCO3) particles with two or three poly dextran/poly-L-arginine-based bilayers. To achieve high loading efficiency, the CaCO3 template was generated by coprecipitation with the enzyme. After assembly of the polymer shell, the CaCO3 core material was dissolved under mild conditions by dialysis against 20 mM EDTA. Biochemical stability of the encapsulated L-asparaginase was analyzed by treating the capsules with the proteases trypsin and thrombin, which are known to degrade and inactivate the enzyme during leukemia treatment, allowing us to test for resistance against proteolysis by physiologically relevant proteases through measurement of residual l-asparaginase activities. In addition, the thermal stability, the stability at the physiological temperature, and the long-term storage stability of the encapsulated enzyme were investigated. We show that encapsulation of l-asparaginase remarkably improves both proteolytic resistance and thermal inactivation at 37 °C, which could considerably prolong the enzyme's in vivo half-life during application in acute lymphoblastic leukemia (ALL). Importantly, the use of low EDTA concentrations for the dissolution of CaCO3 by dialysis could be a general approach in cases where the activity of sensitive biomacromolecules is inhibited, or even irreversibly damaged, when standard protocols for fabrication of such LbL microcapsules are used. Encapsulated and free enzyme showed similar efficacies in driving leukemic cells to apoptosis.

Cloning, expression, and characterization of L-asparaginase from a newly isolated Bacillus subtilis B11-06.

This study focused on the cloning, overexpression, and characterization of the gene encoding L-asparaginase (ansZ) from a nonpathogenic strain of Bacillus subtilis B11-06. The recombinant enzyme showed high thermostability and low affinity to L-glutamine. The ansZ gene, encoding a putative L-asparaginase II, was amplified by PCR and expressed in B. subtilis 168 using the shuttle vector pMA5. The activity of the recombinant enzyme was 9.98 U/mL, which was significantly higher than that of B. subtilis B11-06. The recombinant enzyme was purified by a two-step procedure including ammonium sulfate fractionation and hydrophobic interaction chromatography. The optimum pH and temperature of the recombinant enzyme were 7.5 and 40 °C, respectively. The enzyme was quite stable at a pH range of 6.0-9.0 and exhibited about 14.7 and 9.0% retention of activity following 2 h incubation at 50 or 60 °C, respectively. The Km for L-asparagine was 0.43 mM, and the Vmax was 77.51 µM/min. Results of this study also revealed the potential industrial application of this enzyme in reducing acrylamide formation during the potato frying process.

Structural analysis of K+ dependence in L-asparaginases from Lotus japonicus.

The molecular features responsible for the existence in plants of K+-dependent asparaginases have been investigated. For this purpose, two different cDNAs were isolated in Lotus japonicus, encoding for K+-dependent (LjNSE1) or K+-independent (LjNSE2) asparaginases. Recombinant proteins encoded by these cDNAs have been purified and characterized. Both types of asparaginases are composed by two different subunits, α (20 kDa) and ß (17 kDa), disposed as (αß)2 quaternary structure. Major differences were found in the catalytic efficiency of both enzymes, due to the fact that K+ is able to increase by tenfold the enzyme activity and lowers the K(m) for asparagine specifically in LjNSE1 but not in LjNSE2 isoform. Optimum LjNSE1 activity was found at 5-50 mM K+, with a K(m) for K+ of 0.25 mM. Na+ and Rb+ can, to some extent, substitute for K+ on the activating effect of LjNSE1 more efficiently than Cs+ and Li+ does. In addition, K+ is able to stabilize LjNSE1 against thermal inactivation. Protein homology modelling and molecular dynamics studies, complemented with site-directed mutagenesis, revealed the key importance of E248, D285 and E286 residues for the catalytic activity and K+ dependence of LjNSE1, as well as the crucial relevance of K+ for the proper orientation of asparagine substrate within the enzyme molecule. On the other hand, LjNSE2 but not LjNSE1 showed ß-aspartyl-hydrolase activity (K(m) = 0.54 mM for ß-Asp-His). These results are discussed in terms of the different physiological significance of these isoenzymes in plants.