Characterization of unexplored amidohydrolase enzyme-pterin deaminase

Construing recombinant ZFP160 from Aspergillus terreus as pterin deaminase enzyme

Pterin deaminase stands as a metalloenzyme and exhibits both antitumor and anticancer activities. Therefore, this study aimed to explore the molecular function of zinc finger protein-160 (zfp160) from Aspergillus terreus with its enzyme mechanism in detail. Subsequently, preliminary molecular docking studies on zfp160 from A. terreus were done. Next, the cloning and expression of zfp160 protein were carried out. Following, protein expression was induced and purified through nickel NTA column with imidazole gradient elution. Through the Mascot search engine tool, the expressed protein of MALDI-TOF was confirmed by 32 kDa bands of SDS-PAGE. Furthermore, its enzymatic characterization and biochemical categorization were also explored. The optimum conditions for enzyme were determined to be pH 8, temperature 35°C, km 50 μm with folic acid as substrate, and Vmax of 24.16 (IU/mL). Further, in silico analysis tried to explore the interactions and binding affinity of various substrates to the modeled pterin deaminase from A. terreus. Our results revealed the binding mode of different substrate molecules with pterin deaminase using the approximate scoring functions that possibly correlate with actual experimental binding affinities. Following this, molecular dynamic simulations provided the in-depth knowledge on deciphering functional mechanisms of pterin deaminase over other drugs.

Identification and structural prediction of the unrevealed amidohydrolase enzyme: Pterin deaminase from Agrobacterium tumefaciens LBA4404

Microbes make a remarkable contribution to the health and well-being of living beings all over the world. Interestingly, pterin deaminase is an amidohydrolase enzyme that exhibits antitumor, anticancer activities and antioxidant properties. With the existing evidence of the presence of pterin deaminase from microbial sources, an attempt was made to reveal the existence of this enzyme in the unexplored bacterium Agrobacterium tumefaciens LBA4404. After, the cells were harvested and characterized as intracellular enzymes and then partially purified through acetone precipitation. Subsequently, further purification step was carried out with an ion-exchange chromatogram (HiTrap Q FF) using the Fast-Protein Liquid Chromatography technique (FPLC). Henceforward, the approximate molecular weight of the purified pterin deaminase was determined through SDS-PAGE. Furthermore, the purified protein was identified accurately by MALDI-TOF, and the sequence was explored through a Mascot search engine. Additionally, the three-dimensional structure was predicted and then validated, as well as ligand-binding sites, and the stability of this enzyme was confirmed for the first time. Thus, the present study revealed the selected parameters showing a considerable impact on the identification and purification of pterin deaminase from A. tumefaciens LBA4404 for the first time. The enzyme specificity makes it a favorable choice as a potent anticancer agent.

An Overview of Emerging Cyanide Bioremediation Methods

Cyanide compounds are hazardous compounds which are extremely toxic to living organisms, especially free cyanide in the form of hydrogen cyanide gas (HCN) and cyanide ion (CN−). These cyanide compounds are metabolic inhibitors since they can tightly bind to the metals of metalloenzymes. Anthropogenic sources contribute significantly to CN− contamination in the environment, more specifically to surface and underground waters. The treatment processes, such as chemical and physical treatment processes, have been implemented. However, these processes have drawbacks since they generate additional contaminants which further exacerbates the environmental pollution. The biological treatment techniques are mostly overlooked as an alternative to the conventional physical and chemical methods. However, the recent research has focused substantially on this method, with different reactor configurations that were proposed. However, minimal attention was given to the emerging technologies that sought to accelerate the treatment with a subsequent resource recovery from the process. Hence, this review focuses on the recent emerging tools that can be used to accelerate cyanide biodegradation. These tools include, amongst others, electro-bioremediation, anaerobic biodegradation and the use of microbial fuel cell technology. These processes were demonstrated to have the possibility of producing value-added products, such as biogas, co-factors of neurotransmitters and electricity from the treatment process.

Establishing pteridine metabolism in a progressive isogenic breast cancer cell model - part II

INTRODUCTION

Determining the biological significance of pteridines in cancer development and progression remains an important step in understanding the altered levels of urinary pteridines seen in certain cancers. Our companion study revealed that several folate-derived pteridines and lumazines correlated with tumorigenicity in an isogenic, progressive breast cancer cell model, providing direct evidence for the tumorigenic origin of pteridines.

OBJECTIVES

This study sought to elucidate the pteridine biosynthetic pathway in a progressive breast cancer model via direct pteridine dosing to determine how pteridine metabolism changes with tumorigenicity.

METHODS

First, MCF10AT breast cancer cells were dosed individually with 15 pteridines to determine which pteridines were being metabolized and what metabolic products were being produced. Second, pteridines that were significantly metabolized were dosed individually across the progressive breast cancer cell model (MCF10A, MCF10AT, and MCF10ACA1a) to determine the relationship between each metabolic reaction and breast cancer tumorigenicity.

RESULTS

Several pteridines were found to have altered metabolism in breast cancer cell lines, including pterin, isoxanthopterin, xanthopterin, sepiapterin, 6-biopterin, lumazine, and 7-hydroxylumazine (p < 0.05). In particular, isoxanthopterin and 6-biopterin concentrations were differentially expressed (p < 0.05) with respect to tumorigenicity following dosing with pterin and sepiapterin, respectively. Finally, the pteridine biosynthetic pathway in breast cancer cells was proposed based on these findings.

CONCLUSIONS

This study, along with its companion study, demonstrates that pteridine metabolism becomes disrupted in breast cancer tumor cells. This work highlights several key metabolic reactions within the pteridine biosynthetic pathway that may be targeted for further investigation and clinical applications.

Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites

For using targeted covalent inhibitors (TCIs) as anticancer and antiviral drugs, we establish that the model compounds PCMPS (p-chloromercuriphenyl sulfate) and PCMB (p-chloromercuribenzoate) are inhibitors of the DEDDh family of exonucleases. The underlying mechanism is analyzed by X-ray crystallography, activity/nucleic acid-binding assays, and all-atom molecular dynamics (MD) simulations. The first TCI-complexed structures of a DEDDh enzyme, the Lassa fever virus NP exonuclease (NPexo), are resolved to elucidate that the Cys409 binding site is away from the active site and the RNA-binding lid. The NPexo C409A structures indicate Cys461 as the alternative distal site for obstructing the equally active mutant. All-atom MD simulations of the wild type and mutant NPexos in explicit solvent uncover an allosteric inhibition mechanism that the local perturbation induced by PCMPS sulfonate propagates to impact the RNA-binding lid conformation. Binding assay studies confirm that PCMPS does affect the RNA binding of NPexo. The predicted relative potency between PCMPS and PCMB is also in line with experiments. The structural data and inhibition mechanism established in this work provide an important molecular basis for the drug development of TCIs.

Simultaneous degradation of triazophos, methamidophos and carbofuran pesticides in wastewater using an Enterobacter bacterial bioreactor and analysis of toxicity and biosafety

Triazophos (TAP), methamidophos (MAP) and carbofuran (CF) pesticides are highly toxic, soluble and absorbable. Efficient co-degradation of multi-pesticides is rare reported. The objectives of this study were to investigate TAP, MAP and CF co-degradative ability of Enterobacter sp. Z1 and study the degradation mechanisms. Strain Z1 was shown to efficiently co-degrade TAP, MAP and CF when they were used as primary carbon sources. The degradation occurred over a wide range of temperatures, pH values and pesticide concentrations and followed first-order kinetics. Under the optimum conditions (37 °C, pH 7 and 100 mg/L of each pesticide), the degradation efficiencies were 100%, 100%, and 95.3% for TAP, MAP and CF, respectively. In addition, strain Z1 could simultaneously degrade TAP, MAP, CF and total nitrogen in wastewater in a batch bioreactor, with high removal efficiencies of 98.3%, 100%, 98.7% and 100%, respectively. Genomics, proteomics, qRT-PCR and gene overexpression analyses revealed that the degradation mechanisms involved the activities of multiple proteins, among which, organophosphorus hydrolase (Oph) and 3-hydroxyacyl-CoA dehydrogenase (PaaC) are primarily responsible for TAP and MAP degradation, while carbofuran hydrolase (Mcd) and amidohydrolase (RamA) primarily degrade CF. Among these enzymes, PaaC and RamA are newly identified pesticide-degrading enzymes. Toxicity assays of strain Z1 using reporter recombinase gene (recA) and zebrafish showed that there was no accumulation of toxic metabolites during the degradation process. Biosafety test using zebrafish showed that the strain was nontoxic toward zebrafish. Strain Z1 provides a good purification effect for pesticides-containing wastewater and novel microbial pesticide-degrading mechanisms were discovered.

Naturally Occurring Lumazines

Natural products containing a lumazine motif were first isolated from natural sources in 1940. These natural products are relatively rare, with fewer than 100 lumazines known to occur in Nature. This review discusses the isolation of lumazines, their biological activity, and their biosynthesis, where known.

QDPR homologues in Danio rerio regulate melanin synthesis, early gliogenesis, and glutamine homeostasis

Dihydropteridine reductase (QDPR) catalyzes the recycling of tetrahydrobiopterin (BH₄), a cofactor in dopamine, serotonin, and phenylalanine metabolism. QDPR-deficient patients develop neurological symptoms including hypokinesia, truncal hypotonia, intellectual disability and seizures. The underlying pathomechanisms are poorly understood. We established a zebrafish model for QDPR deficiency and analyzed the expression as well as function of all zebrafish QDPR homologues during embryonic development. The homologues qdpra is essential for pigmentation and phenylalanine metabolism. Qdprb1 is expressed in the proliferative zones of the optic tectum and eye. Knockdown of qdprb1 leads to up-regulation of pro-proliferative genes and increased number of phospho-histone3 positive mitotic cells. Expression of neuronal and astroglial marker genes is concomitantly decreased. Qdprb1 hypomorphic embryos develop microcephaly and reduced eye size indicating a role for qdprb1 in the transition from cell proliferation to differentiation. Glutamine accumulation biochemically accompanies the developmental changes. Our findings provide novel insights into the neuropathogenesis of QDPR deficiency.

Biotransformation of Sulfonamide Antibiotics in Activated Sludge: The Formation of Pterin-Conjugates Leads to Sustained Risk

The presence of antibiotics in treated wastewater and consequently in surface and groundwater resources raises concerns about the formation and spread of antibiotic resistance. Improving the removal of antibiotics during wastewater treatment therefore is a prime objective of environmental engineering. Here we obtained a detailed picture of the fate of sulfonamide antibiotics during activated sludge treatment using a combination of analytical methods. We show that pterin-sulfonamide conjugates, which are formed when sulfonamides interact with their target enzyme to inhibit folic acid synthesis, represent a major biotransformation route for sulfonamides in laboratory batch experiments with activated sludge. The same major conjugates were also present in the effluents of nine Swiss wastewater treatment plants. The demonstration of this biotransformation route, which is related to bacterial growth, helps explain seemingly contradictory views on optimal conditions for sulfonamide removal. More importantly, since pterin-sulfonamide conjugates show retained antibiotic activity, our findings suggest that risk from exposure to sulfonamide antibiotics may be less reduced during wastewater treatment than previously assumed. Our results thus further emphasize the inadequacy of focusing on parent compound removal and the importance of investigating biotransformation pathways and removal of bioactivity to properly assess contaminant removal in both engineered and natural systems.

Molecular architecture of pterin deaminase from Saccharomyces cerevisiae NCIM 3458

As early as 1974, reports have confirmed the anticancer activity of pterin deaminase isolated from fungi. The enzyme has also been reported in bacteria, fungi and slime mold genera, but the enzyme characterization was effetely done. The present study attempted to purify and characterize pterin deaminase enzyme from Saccharomyces cerevisiae NCIM 3458. The protein was extracted from the extracellular extract by using the ethanol precipitation method. Partial purification of pterin deaminase enzyme was achieved by ion exchange chromatography (Hi-Trap QFF) by fast protein liquid chromatography (AKTA purifier). The molecular weight of the protein was apparently determined by SDS-PAGE, and the presence of pterin deaminase was confirmed by activity staining. The purified enzyme was further biochemically characterized. Molecular docking studies showed higher binding affinity towards folic acid interaction. The structural characterization of this protein may open the windows for new drug targets for cancer therapy.

The role of urinary pteridines as disease biomarkers

Pteridines and their derivatives function as intermediates in the metabolism of several vitamins and cofactors, and their relevance to disease has inspired new efforts to study their roles as disease biomarkers. Recent analytical advances, such as the emergence of sensitive mass spectrometry techniques, new workflows for measuring pteridine derivatives in their native oxidation states and increased multiplexing capacities for the simultaneous determination of many pteridine derivatives, have enabled researchers to explore the roles of urinary pteridines as disease biomarkers at much lower levels with greater accuracy than with previous technologies or methods. As a result, urinary pteridines are being increasingly studied as putative cancer biomarkers with promising results being reported from exploratory studies. In addition, the role of urinary neopterin as a universal biomarker for immune system activation is being investigated in new diseases where it is anticipated to become a useful supplementary marker in clinical diagnostic settings. In summary, this review provides an overview of recent developments in the clinical study of urinary pteridines as disease biomarkers, covers the most promising aspects of advanced analytical techniques being developed for the determination of urinary pteridines and discusses the major challenges associated with implementing pteridine biomarkers in clinical laboratory settings.