Enzyme Function Research Articles

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase

Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

Nitazoxanide mitigates methotrexate hepatotoxicity in rats: role in inhibiting apoptosis and regulating endoplasmic reticulum stress

ObjectivesHepatotoxicity is a severe outcome of methotrexate (MTX) therapy, limiting its clinical use and contributing to its related morbidity and mortality. This study investigated the hepatoprotective effects of nitazoxanide (NTZ), an antiprotozoal drug, against MTX-induced hepatotoxicity and whether endoplasmic reticulum (ER) stress-modulation underlies the expected beneficial effects of NTZ.MethodsThirty-six rats were allocated to six groups, one control group and five MTX groups, where induction of hepatotoxicity was achieved via injecting MTX (20 mg/kg). Groups were assigned as MTX-vehicle, NTZ-100, and NTZ-200 groups (at 100 and 200 mg/kg/day, gavage, respectively), N-acetyl cysteine (NAC) group (500 mg/kg), and 4-phenyl butyric acid (4-PBA) group (150 mg/kg, i.p). Liver function enzymes in serum, hepatic oxidative stress, proinflammatory cytokines, apoptosis, and ER-stress biomarkers were assessed. A histopathological examination was performed.ResultsTreatment with NTZ lessened the serum liver enzymes, reduced malondialdehyde (lipid peroxidation product), enhanced antioxidant capacity, attenuated proinflammatory cytokines, and suppressed apoptosis. The protective effect of NTZ was dose-dependent, and the findings observed with the high-dose NTZ were similar to those obtained with the ER-stress inhibitor (4-PBA).ConclusionNTZ exerted a hepatoprotective effect in MTX-challenged rats that is mediated via modulation of ER stress and inhibiting apoptosis.

Simultaneous nitrification and denitrification framework for decentralized systems: Long-term study utilizing rope-type biofilm media under field conditions

This research introduces a novel approach to achieve simultaneous nitrification-denitrification (SND) under dynamic load conditions using a cost-effective rope-type biofilm technology. The approach represents a significant advancement in wastewater treatment, particularly beneficial for remote and decentralized communities. The biofilm-based SND process was developed using a pilot-scale flow-through reactor by implementing upstream carbon management with constant-timer-based aeration control versus dynamic-sensor-based aeration control strategies. The findings indicate that adding an upstream anaerobic pretreatment process to handle excess carbon plays a substantial role in achieving a sustainable SND process under a dynamic load environment using simple aeration on-off control. The most optimal nitrification performance of 0.32 g NH3-N/m2/d (89 % removal) was achieved under a 1-hour ON/30-minute OFF aeration. The process sustained an average bulk liquid DO of 5.16 mg/L and 3.80 mg/L during the aeration ON and OFF periods, respectively, facilitating a 0.13 g N/m2/d (41 %) total inorganic nitrogen (TIN) removal, notably, implementing advanced aeration strategies driven by DO, NH3, and NO3 sensors enhanced TIN removal efficiency to 72 %. The nitrification performance remained comparable (89 % removal), resulting in 3 and 10 mg N/L effluent ammonia and TIN concentration, respectively. Additionally, utilizing two multivariate approaches accounting for 82 % and 64 % of the variance, this study discerned patterns in monitored variables and performance. Additionally, the analysis underscored the difference of bulk liquid DO levels in the biofilm versus suspended systems inhibiting the SND process. Distinct bacterial communities were established in biofilms under aerobic, anaerobic, and SND conditions, with the SND reactor showing a hierarchy of functional group and enzymes, enriched sequentially from heterotrophs to denitrifiers, nitrifiers, and anammox bacteria. These innovations underline the potential of tailored control strategies to enhance a passive biofilm-based SND process efficiency under dynamic conditions, providing scalable solutions for diverse target water quality demands in remote communities and decentralized systems.

Functional Profiling of Abundant Glycosyltransferases in the Rhizospheric Bacteriome of Abutilon fruticosum

In this study, we undertook an extensive exploration of the rhizospheric bacteriome of Abutilon fruticosum, focusing on the activities of Carbohydrate-Active Enzymes (CAZymes) of class glycosyltransferases (GTs), and their potential impact on plant growth and fortification against environmental adversities and soil-borne pathogens. Investigation revealed a predominance of families GT1, GT31, GT35, GT39, and GT51, mainly ascribed to bacterial genera Microvirga, Arthrobacter, Blastococcus, Bacillus, Nocardioides, and Kocuria. Our findings unveiled the pivotal role of phenylalanine, mostly exuded by plant roots, serving as the primary substrate for the catalytic activities of the identified CAZymes. With glucosylation emerging as the predominant enzymatic function, we propose UDP-D-glucose as the central core intermediate metabolite, orchestrating a multifaceted network of interrelated metabolic pathways. Subsequent profiling delineated a diverse array of metabolites synthesized by 10 CAZymes actively participating in 10 crosstalking pathways. Functional analyses of these metabolites underscore their significance in the biosynthesis of flavonoids, anthocyanins, and related derivatives, crucial for the reproductive success of plants by serving as visual cues for insect pollinators and conferring protection against deleterious effects of radiation. Certain other metabolites play vital roles in reinforcing the structural integrity of plant cell walls, thus enhancing resistance against enzymatic degradation while augmenting cytokinin activity. In conclusion, our study elucidates a novel paradigm of plant-bacteria mutualistic interaction, offering insights into the intricate mechanisms underlying plant-microbe symbiosis. We posit that the integration of high-throughput technologies with metabolic engineering strategies presents a promising approach for applying cost-effective and environmentally benign alternatives to conventional agricultural practices. (249 words)

Diagnosing Late-Onset Tay-Sachs Through Next Generation Sequencing and Functional Enzyme Testing

Diagnosing Late-Onset Tay-Sachs Through Next Generation Sequencing and Functional Enzyme Testing

Fine-Tuning the Function of Farnesene Synthases for Selective Synthesis of Farnesene Stereoisomers.

Farnesene synthase from Artemisia annua (AaFS) catalyzes the reaction from farnesyl pyrophosphate (FPP) to give the sesquiterpene β-farnesene, a key building block for the biosynthesis of vitamin E. However, an insufficient yield of β-farnesene precludes its industrialization. Understanding the mechanism would be essential for attaining β-farnesene in high yield. Guided by structure-based enzyme engineering, we designed several potent variants, among which L326I increased the β-farnesene yield from 450.65 to 3877.42 mg/L. Furthermore, we found that the function of β-farnesene synthase AaFS can be modulated at two positions; W299 is responsible for tuning the enzyme's function to give its isomeric product α-farnesene and Y402 is the key residue for diverting from the linear farnesene products to the monocyclic α-bisabolol product. These findings provide valuable insights into the catalytic mechanism and functional modulation of farnesene synthases and set the basis for rational engineering of farnesene synthases for selective biosynthesis of diverse sesquiterpene natural products.

Possible lessons of a model experiment: To what extent can UV activate the production of leaf phenolics in indoor plant cultivation?

Tobacco (Nicotiana tabacum L.) plants were grown outdoors (N°46.07, E°18.18) under either natural or UV-deprived sunlight for 25 days in the summer. High PAR resulted in high polyphenol content, which was selectively affected by solar UV-A and UV-B irradiation. Solar UV-A irradiation increased anthocyanins, but not flavonoids, in the epidermis, and this additional protection resulted in higher photochemical yields and lower NPQ. The simultaneous presence of UV-B overrode the effects of UV-A, increased epidermal flavonoids, and decreased anthocyanins. Leaves grown in full sunlight had the same photochemical yields of NPQ as those grown under a UV-excluding filter. A combination of these effects can falsely dismiss the effects of UV-B on outdoor photosynthesis. Phenolic acid content, corresponding to approximately 80% of phenolic compounds, did not depend on solar UV, and total flavonoids increased under full solar UV irradiation, but not under UV-A only. The polyphenol content in outdoor leaves also served as a reference point for an indoor experiment, which showed that even a short, 4-day exposure of low PAR grown plants to UV from an artificial source increased the amount of some, although not all, components close to or even above outdoor levels. In indoor leaves, a selective increase in quercetin glycosides (to 62–85% of outdoor levels) supports both enzymatic and non-enzymatic antioxidant functions, and the increase in crypto- and neochlorogenic acids (to 76% and 117% of outdoor levels, respectively) suggests a redistribution among biosynthesis pathways. These results demonstrate the potential and efficiency of cultivation systems without sunlight.

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate.

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID, toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.IMPORTANCEArchaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5'-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.

Establishment and mechanism of thioacetamide-induced hepatopancreas injury model in red swamp crayfish Procambarus clarkii

The red swamp crayfish (Procambarus clarkii), widely farmed in China, frequently suffers from hepatopancreatic diseases due to the expansion and environmental degradation of aquaculture. Hepatopancreatic injury models are essential for studying disease mechanisms and treatments, yet few exist for crustaceans. This study aims to establish a hepatopancreatic injury model in P. clarkii using the hepatotoxic compound thioacetamide (TAA) and investigate the underlying damage mechanisms. P. clarkii were intramuscularly injected with TAA at concentrations of 0.2, 0.4, and 0.8 mg/g and observed at 6, 12, 24, and 48 h. The results showed that TAA at 0.2–0.8 mg/g significantly affected hepatopancreatic function and oxidative stress-related enzymes in P. clarkii. However, only 0.8 mg/g TAA produced a time-dependent damage effect suitable for a hepatopancreatic injury model. Histopathological analysis revealed that P. clarkii injected with 0.8 mg/g TAA exhibited key model features, including R cell adhesion and swelling, hepatic tubule rupture, and numerous small vacuoles. Therefore, 0.8 mg/g TAA intramuscular injection can effectively establish a hepatopancreatic injury model in P. clarkii. Transcriptomic and metabolomic analyses revealed that metabolic disruptions in energy, amino acid, lipid, and nucleotide pathways are central to TAA-induced hepatopancreatic injury in P. clarkii. CYP2L1X1, CYP2U1lX1, and CYP2D14l are likely key contributors to the hepatopancreatic injury induced by TAA in P. clarkii. The results of this study will provide support for further research on the mechanisms of hepatopancreatic diseases in freshwater crayfish and the development of preventive and therapeutic drugs.

The Protective Effects of Carvacrol Against Doxorubicin-Induced Cardiotoxicity In Vitro and In Vivo.

Doxorubicin (DOX) is a remarkable chemotherapeutic agent, however, its adverse effect on DOX-induced cardiotoxicity (DIC) is a rising concern. Recent research has identified carvacrol (CAR), an antioxidant and anti-inflammatory agent, as a promising natural compound for protecting against DIC. This study aims to investigate the potential cardioprotective effects properties of CAR in vitro and in vivo. The cardioprotective effect of CAR was assessed by pretreating H9c2 cells with non-toxic CAR for 24h, followed by co-treatment with DOX (10μM) for an additional 24h. The cell viability was determined using an MTT assay. For the in vivo study, male Sprague-Dawley rats (200-250g) were randomly divided into three groups: control, cardiotoxicity (DOX), and treatment (CAR + DOX) groups. CAR (50mg/kg, BW) was administered orally to the CAR + DOX groups for 14days. Then, a single dose of DOX (15mg/kg/i.p, BW) was administered on day 15 for DOX and CAR + DOX groups. The rats were allowed to recover for 3days before being sacrificed. Our results demonstrated that DOX (10µM) significantly reduced H9c2 cell viability by 50% (p < 0.0001), and CAR (0.067µM) protected H9c2 cells from DIC (p = 0.0045). In the rat model, CAR pretreatment effectively mitigated DOX-induced reductions in systolic pressure (p = 0.0007), pulse pressure (p = 0.0213), hypertrophy (p = 0.0049), and cardiac fibrosis (p = 0.0006). However, the pretreatment did not alter the heart function, oxidative stress, and antioxidant enzymes. In conclusion, our results indicate that CAR could potentially serve as an adjuvant to reduce cardiotoxicity by ameliorating myocardial fibrosis and hypertrophy.

Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza.

The genus Oryza is of utmost importance to human civilization as two of its species became agronomically productive and widely cultivated, and also because wild rice is a treasure trove of beneficial alleles that can be used for crop improvement. Most of the wild rice genotypes are known for their stress tolerance several times more than the domesticated rice varieties. In this study, we aimed to carry out an exhaustive genomic survey to identify glyoxalase I (GLYI) and glyoxalase II (GLYII) genes across the 11 rice genomes sequenced so far. Notably, we found the putatively functional metal-dependent GLYI and GLYII enzymes to be conserved throughout domestication and a few homologous pairs to have undergone beneficial mutations to drive positive selection, and thus, acquire newer functions. Interestingly, we also report four newly identified GLYII members in O. sativa subsp. japonica in addition to the three previously reported GLYII genes. The presence of different types of cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under various developmental processes besides stress adaptation. Publicly available data suggests the role of glyoxalase genes particularly in salinity stress in both wild and cultivated rice as is also confirmed through qRT-PCR. Interestingly, we found less accumulation of MG and concurrently higher enzymatic activity of GLYI and GLYII proteins in stressed seedlings of selected wild rice genotypes indicating that glyoxalases indeed contribute to the intrinsic stress tolerance of wild rice.

Effects of Vitamin E and/or selenium nanoparticles on organ histology, hemato-biochemical parameters, immunity, gene expression, and growth performance in Nile tilapia challenged with Enterococcus faecalis

A two-month feeding experiment was conducted to assess the impact of dietary selenium nanoparticles (SeNPs), sodium selenite (Se), and vitamin E (Vit E) on the growth performance, hematology profile, innate immune response, histomorphology of the liver, intestine, and gills, as well as gene expression in Nile tilapia (Oreochromis niloticus) challenged with the pathogenic bacteria Enterococcus faecalis. A total of 360 fish were allocated into six experimental groups and fed diets containing 1 mg/kg of SeNPs (SeNPs), 1 mg /kg of sodium selenite (Se), 100 mg/kg of Vit E (VE), SeNPs+ Vit E, Se+ Vit E and a control group (CON) without any additives. The results showed that SeNPs and SeNPs+ Vit E diets significantly improved the growth performance (final body weight, feed intake, fish biomass, specific growth rate, and feed conversion ratio) and blood parameters compared to the other groups (P<0.05). Liver enzymes (AST, ALT, and ALP) were significantly decreased, while immune responses were enhanced in the serum of fish in the SeNPs and SeNPs+ Vit E groups before and after the E. faecalis challenge. The expression of pro-inflammatory genes (TNF-α and IL-8) was significantly lower in the SeNPs and SeNPs+ Vit E groups, both before and after the E. faecalis challenge, compared to the other groups (P<0.05). Nile tilapia fed the control diet and challenged with E. faecalis exhibited a high mortality rate (85 %), whereas mortality was significantly lower in fish fed supplemental SeNPs (45 %) and SeNPs+ Vit E (40 %). Histological examination also revealed improvements in liver, intestine, and gill functions in Nile tilapia fed SeNPs+ Vit E. These results suggest that dietary SeNPs, either alone or in combination with Vit E, can significantly enhance fish performance, innate immune response, liver function enzymes, and reduce the expression of pro-inflammatory genes in Nile tilapia. They can also mitigate the pathological effects caused by the E. faecalis challenge.

Evolutionary analysis of Quinone Reductases 1 and 2 suggests that NQO2 evolved to function as a pseudoenzyme.

Quinone reductases 1 and 2 (NQO1 and NQO2) are paralogous FAD-linked enzymes found in all amniotes. NQO1 and NQO2 have similar structures, and both catalyze the reduction of quinones and other electrophiles; however, the two enzymes differ in their cosubstrate preference. While NQO1 can use both redox couples NADH and NADPH, NQO2 is almost inactive with these cosubstrates and instead must use dihydronicotinamide riboside (NRH) and small synthetic cosubstrates such as N-benzyl-dihydronicotinamide (BNAH) for efficient catalysis. We used ancestral sequence reconstruction to investigate the catalytic properties of a predicted common ancestor and two additional ancestors from each of the evolutionary pathways to extant NQO1 and NQO2. In all cases, the small nicotinamide cosubstrates NRH and BNAH were good cosubstrates for the common ancestor and the enzymes along both the NQO1 and NQO2 lineages. In contrast, with NADH as cosubstrate, extant NQO1 evolved to a catalytic efficiency 100 times higher than the common ancestor, while NQO2 has evolved to a catalytic efficiency 3000 times lower than the common ancestor. The evolutionary analysis combined with site-directed mutagenesis revealed a potential site of interaction for the ADP portion of NAD(P)H in NQO1 that is altered in charge and structure in NQO2. The results indicate that while NQO1 evolved to have greater efficiency with NAD(P)H, befitting an enzymatic function in cells, NQO2 was under selective pressure to acquire extremely low catalytic efficiency with NAD(P)H. These divergent trajectories have implications for the functions of both enzymes.

A Simple and Cost-Efficient Method for the Production of Recombinant Horseradish Peroxidase in E. coli.

Horseradish peroxidase (HRP) is a chromogenic glycoenzyme widely used in research, diagnostics, and therapeutics. Due to its high demand, various eukaryotic and prokaryotic expression systems have been employed for the production of recombinant HRP. Eukaryotic systems yield properly folded, fully functional enzymes with the necessary post-translational modifications. However, these systems can be costly, time-consuming, and prone to hyperglycosylation. In contrast, prokaryotic systems are simple, inexpensive, and readily available, but achieving proper folding and subsequent modifications can be challenging. In this study, we employed a simple and cost-effective method to produce recombinant HRP in soluble form, using the E. coli expression system. The produced enzyme demonstrated substantial activity (89.75 ± 3.25 U/mg) and resistance to heat (T1/2 = 5 min at 50°C), pH variations (up to 8), and H2O2 concentrations (up to 10 mM). Additionally, we systematically compared our method with those of other researchers, highlighting methodological details and outcomes of HRP production in E. coli.

Value-added biotransformation of agricultural byproducts by cellulolytic fungi: a review.

Agricultural byproducts generally contain abundant bioactive compounds (e.g., cellulose/hemicellulose, phenolic compounds (PCs), and dietary fibers (DFs)), but most of them are neglected and underutilized. Owing to the complicated and rigid structures of agricultural byproducts, a considerable amount of bioactive compounds are entrapped in the polymer matrix, impeding their further development and utilization. In recent years, the prominent performance of cellulolytic fungi to grow and degrade agricultural byproducts has been applied to achieve efficient biotransformation of byproducts to high-value compounds, which is a green and sustainable strategy for the reutilization of agricultural byproducts. This review comprehensively summarizes recent progress in the value-added biotransformation of agricultural byproducts by cellulolytic fungi, including (1) direct utilization of agricultural byproducts for biochemicals and bioethanol production via a consolidated bioprocessing, (2) recovery and biotransformation of bounded PCs from agricultural byproducts for higher bioactive properties, as well as (3) modification and conversion of insoluble DF from agricultural byproducts to produce functional soluble DF. The functional enzymes, potential mechanisms, and metabolic pathways involved are emphasized. Moreover, promising advantages and current bottlenecks using cellulolytic fungi have also been elucidated, shedding further perspectives for sustainable and efficient reutilization of agricultural byproducts by cellulolytic fungi.

Enhancing catalytic efficiency of GAO-5F from Fusarium odoratissimum and its application in development of a polyaldehyde crosslinked gelatin-based edible packaging film

Galactose oxidase has long captured the interest of the biocatalysis and biotechnology communities due to its unique catalytic characteristics and versatility with various substrates. In our previous studies, we demonstrated that galactose oxidase GAO-5F from Fusarium odoratissimum can oxidize agarose to produce a polyaldehyde polymer, which can be further crosslinked with gelatin to produce food packaging films. Despite its commendable catalytic performance, GAO-5F falls short of meeting the requirements for industrial applications. In this study, we employed a combination of multiple sequence comparisons and site-directed mutagenesis to pinpoint key amino acid sites crucial for enhancing the enzyme's catalytic activity, resulting in the creation of the double mutant GAO-5F/AR (D403A/Q484R), showing a six-fold increase in catalytic activity. The catalytic mechanism of mutant was further elucidated through homology modeling and molecular docking. Results highlighted the significance of increased hydrogen bonding interactions between the enzyme and substrate in enhancing catalytic activity. Then, agarose was transformed into a polyaldehyde polymer by oxidation catalyzed by GAO-5F mutant. The resulting polyaldehyde polymer was crosslinked with gelatin to prepare an edible packaging film; the properties and structure of the film were characterized. In this study, we successfully obtained mutants with increased catalytic activity through a semi-rational-driven site-directed mutagenesis strategy. This approach, which combines rational design with targeted mutagenesis, holds promise for furthering our understanding of enzyme function and may find widespread use in comparative functional genomics studies of other natural enzymes. This study provides valuable insights for the improvement of galactose oxidase, and new ideas for the preparation of edible packaging films for use in the food industry.

Progress in PGK1 in Prostate Cancer

Phosphoglycerol kinase 1 (PGK1) is the first key metabolic enzyme that produces ATP during glycolysis and is involved in the glycolytic pathway of prostate cancer. PGK 1 can not only act as a metabolic enzyme to affect tumor growth, but also affect the gene expression, energy metabolism, molecular regulation and other processes of tumor cells through its non-metabolic enzyme function, and then mediate the growth, migration and invasion of tumors, and aggravate the biological characteristics of malignant cancer cells. In this review, we reviewed the structure and function of PGK1 and its relationship with prostate cancer to clarify the important role of PGK1 in the progression of advanced adenoma and provide a theoretical basis for targeting PGK1 for drug development.

Possibilities of Predicting Methotrexate-associated Toxicity in Oncohematology Based on Molecular Genetic Testing Methods

The development of highly effective protocols for the treatment of acute lymphoblastic leukemia (ALL) and non-Hodgkin lymphomas (NHL) followed the path of escalation of doses of cytostatic agents and improvement of supportive care. Methotrexate (MTX), used in high doses (1000–5000 mg/m2), radically changed the results of treatment of ALL and NHL in children, increasing patient survival rates. The downside of the anti-tumor effect of MTX is its organ toxicity, and therefore the development of methods for predicting the development of toxic effects of MTX is an important scientific and practical task. In recent years, the genetic factors of the patient’s organism have been considered as one of the reasons for the individual variability of pharmacokinetic and pharmacodynamic parameters of MTX. Abnormal function of folate cycle enzymes, methotrexate transporter proteins, due to gene polymorphism, may affect the effectiveness and toxicity of the drug. This review summarizes and analyzes the known genetic polymorphisms involved in MTX metabolism. The possibilities of predicting toxicity, as well as the prospects for individualizing therapy, taking into account the results of pharmacogenetic testing, are presented.

Analysis of damaging non-synonymous SNPs in GPx1 gene associated with the progression of diverse cancers through a comprehensive in silico approach

Glutathione Peroxidase 1 (GPx1) gene has been reported for its role in cellular redox homeostasis, and the dysregulation of its expression is linked with the progression of diverse cancers. Non-synonymous single nucleotide polymorphism (nsSNPs) have been emerged as the crucial factors, playing their role in GPx1 overexpression. To understand the deleterious mutational effects on the structure and function of GPx1 enzyme, we delved deeper into the exploration of possibly damaging nsSNPs using in-silico based approaches. Eight widely utilized computational tools were employed to roughly shortlist the deleterious nsSNPs. Their damaging effects on structure and function of the genes were evaluated by using different bioinformatics tools. Subsequently, the three final proposed deleterious mutants including mutations rs373838463, rs2107818892, and rs763687242, were docked with their reported binder, TNF receptor-associated factor 2 (TRAF2). The lowest binding affinity and stability of the docked mutant complexes as compared to the wild type GPx1 were validated by molecular dynamic simulation. Finally, the comparison of RMSD, RMSF, RoG and hydrogen bond analyses between wild-type and mutant’s complexes validated the deleterious effects of proposed nsSNPs. This study successfully identified and verified the possibly damaging nsSNPs in GPx1 enzyme, which may be linked the progression of various types of cancer. Our findings underscore the value of in-silico approaches in mutational analysis and encourage further preclinical and clinical trials.

Correction to “Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories”

Correction to “Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories”