Selection of the Optimal L-asparaginase II Against Acute Lymphoblastic Leukemia: An In Silico Approach

Desirable L-asparaginases for treating cancer and current research trends

Amino acid depletion therapy is a promising approach for cancer treatment. It exploits the differences in the metabolic processes between healthy and cancerous cells. Certain microbial enzymes induce cancer cell apoptosis by removing essential amino acids. L-asparaginase is an enzyme approved by the FDA for the treatment of acute lymphoblastic leukemia. The enzymes currently employed in clinics come from two different sources: Escherichia coli and Erwinia chrysanthemi. Nevertheless, the search for improved enzymes and other sources continues because of several factors, including immunogenicity, in vivo instability, and protease degradation. Before determining whether L-asparaginase is clinically useful, research should consider the Michaelis constant, turnover number, and maximal velocity. The identification of L-asparaginase from microbial sources has been the subject of various studies. The primary goals of this review are to explore the most current approaches used in the search for therapeutically useful L-asparaginases and to establish whether these investigations identified the crucial characteristics of L-asparaginases before declaring their therapeutic potential.

Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce

Introduction

Although the composition and succession of microbial communities in soy sauce fermentation have been well-characterized, the understanding of phage communities in soy sauce remains limited.

Methods

This study determined the diversity, taxonomic composition, and predicted function of phage communities and the phage-host interactions in two types of raw soy sauce (Cantonese-type fermentation, NJ; Japanese-type fermentation, PJ) using shotgun metagenomics.

Results and discussion

These two raw soy sauces showed differences in phage composition (121 viral operational taxonomic units (vOTUs) in NJ and 387 vOTUs in PJ), with a higher abundance of the family Siphoviridae (58.50%) in the NJ phage community and a higher abundance of Myoviridae (33.01%) in PJ. Auxiliary metabolic functional annotation analyses showed that phages in the raw soy sauces mostly encoded genes with unknown functions (accounting for 66.33% of COG profiles), but the NJ sample contained genes mostly annotated to conventional functions related to carbohydrate metabolism (0.74%) and lipid metabolism (0.84%), while the PJ sample presented a higher level of amino acid metabolism functions (0.12%). Thirty auxiliary metabolism genes (AMGs) were identified in phage genomes, which were associated with carbohydrate utilization, cysteine and methionine metabolism, and aspartic acid biosynthesis for the host. To identify phage-host interactions, 30 host genomes (affiliated with 22 genera) were also recruited from the metagenomic dataset. The phage-host interaction analysis revealed a wide range of phage hosts, for which a total of 57 phage contigs were associated with 17 host genomes, with Shewanella fodinae and Weissella cibaria infected by the most phages. This study provides a comprehensive understanding of the phage community composition, auxiliary metabolic functions, and interactions with hosts in two different types of raw soy sauce.

Engineering and Expression Strategies for Optimization of L-Asparaginase Development and Production

Genetic engineering for heterologous expression has advanced in recent years. Model systems such as Escherichia coli, Bacillus subtilis and Pichia pastoris are often used as host microorganisms for the enzymatic production of L-asparaginase, an enzyme widely used in the clinic for the treatment of leukemia and in bakeries for the reduction of acrylamide. Newly developed recombinant L-asparaginase (L-ASNase) may have a low affinity for asparagine, reduced catalytic activity, low stability, and increased glutaminase activity or immunogenicity. Some successful commercial preparations of L-ASNase are now available. Therefore, obtaining novel L-ASNases with improved properties suitable for food or clinical applications remains a challenge. The combination of rational design and/or directed evolution and heterologous expression has been used to create enzymes with desired characteristics. Computer design, combined with other methods, could make it possible to generate mutant libraries of novel L-ASNases without costly and time-consuming efforts. In this review, we summarize the strategies and approaches for obtaining and developing L-ASNase with improved properties.

[Approaches for improving L-asparaginase expression in heterologous systems]

L-asparaginase (EC 3.5.1.1) is one of the most demanded enzymes used in the pharmaceutical industry as a drug and in the food industry to prevent the formation of toxic acrylamide. Researchers aimed to improve specific activity and reduce side effects to create safer and more potent enzyme products. However, protein modifications and heterologous expression remain problematic in the production of asparaginases from different species. Heterologous expression in optimized producer strains is rationally organized; therefore, modified and heterologous protein expression is enhanced, which is the main strategy in the production of asparaginase. This strategy solves several problems: incorrect protein folding, metabolic load on the producer strain and codon misreading, which affects translation and final protein domains, leading to a decrease in catalytic activity. The main approaches developed to improve the heterologous expression of L-asparaginases are considered in this paper.

In Vitro Antioxidant and Antimicrobial Potency of Mimosa pudica of Nepalese Terai Region: Insight into L-Mimosine as an Antibacterial Agent

Aim

The study aimed to evaluate the in vitro antioxidant and antimicrobial potency of Mimosa pudica found wildly in the Terai region of Nepal and assess its physicochemical properties, such as total phenolic content (TPC) and total flavonoid content (TFC).

Materials and Methods

The physicochemical properties of ethyl acetate extract of Mimosa pudica (EAMP), such as extractive value, total ash content, loss on drying, and phytochemical screening, were calculated using standard protocols. The TPC was determined by using the Folin-Ciocalteu method taking gallic acid as standard, and TFC was conducted by using the AlCl₃ colorimetric method, using a 96-well plate reader. The in vitro antibacterial activity of different concentrations of the extract against four bacterial ATCC strains was determined by the agar well diffusion method in the Mueller Hinton agar (MHA) medium. The in silico molecular docking model was used to ascertain the antibacterial potency of L-mimosine against the selected strains of bacteria used for the in vitro study by calculating the binding affinity towards the protein of bacteria.

Results

The preliminary screening of the extract showed the presence of several phytochemicals. The total ash content (7.67%), loss on drying (2.30%), and extractive value (8.966%) were determined by analyzing the crude sample. The total phenolic and flavonoid contents were 418.640 ± 0.018 mg GAE/g (dried extract) and 14.126 ± 0.021 mg QE/g (dried extract), respectively. The extract showed a potent free radical scavenging activity with an IC50 value of 158.95 ± 1.12 µg/mL. The plant extract also demonstrated the antibacterial activity against both Gram-positive bacteria Staphylococcus aureus (15 mm) and Bacillus cereus (22 mm) and Gram-negative bacteria Escherichia coli (17 mm) and Klebsiella pneumoniae (16 mm) at 200 mg/mL concentration of extract. There was a noteworthy binding affinity of antibiotics with almost all selected bacterial proteins with binding energy against Escherichia coli DNA gyrase subunit B (-5.7 kcal/mol), Staphylococcus aureus DNA gyrase subunit B (-6.1 kcal/mol), Bacillus cereus metallothiol transferase (-5.2 kcal/mol), and Klebsiella pneumoniaebeta-lactamase (-6.1 kcal/mole), respectively, with the L-mimosine.

Conclusion

The findings of the current study suggest that Mimosa pudica from the Terai region of Nepal is rich in phenolic and flavonoid compounds, has a significant impact on bacterial growth inhibition, and has a notable potential to scavenge free radicals (DPPH). According to the in silico analysis, L-mimosine is a potent antibacterial compound that might be utilised to discover novel antibacterial drugs to combat antibiotic resistance.

Massive annotation of bacterial L-asparaginases reveals their puzzling distribution and frequent gene transfer events

l-Asparaginases, which convert l-asparagine to l-aspartate and ammonia, come in five types, AI-AV. Some bacterial type AII enzymes are a key element in the treatment of acute lymphoblastic leukemia in children, but new l-asparaginases with better therapeutic properties are urgently needed. Here, we search publicly available bacterial genomes to annotate l-asparaginase proteins belonging to the five known types. We characterize taxonomic, phylogenetic, and genomic patterns of l-asparaginase occurrences pointing to frequent horizontal gene transfer (HGT) events, also occurring multiple times in the same recipient species. We show that the reference AV gene, encoding a protein originally found and structurally studied in Rhizobium etli, was acquired via HGT from Burkholderia. We also describe the sequence variability of the five l-asparaginase types and map the conservation levels on the experimental or predicted structures of the reference enzymes, finding the most conserved residues in the protein core near the active site, and the most variable ones on the protein surface. Additionally, we highlight the most common sequence features of bacterial AII proteins that may aid in selecting therapeutic l-asparaginases. Finally, we point to taxonomic units of bacteria that do not contain recognizable sequences of any of the known l-asparaginase types, implying that those microorganisms most likely contain new, as yet unknown types of l-asparaginases. Such novel enzymes, when properly identified and characterized, could hold promise as antileukemic drugs.