Characterization of a recombinant arginine deiminase from Enterococcus faecalis SK32.001 for L-citrulline production

Production of Immobilized Arginine Deiminase Using the Self-Assembling Peptide ELK16 for Efficient l-Citrulline Synthesis

Self-assembling peptide (SAP) tags induce protein self-assembly, forming insoluble protein aggregates. Traditional l-citrulline production using arginine deiminase (ADI) is limited by enzyme instability and low reusability. SAP tags were fused with ADI to overcome these challenges, and ADI-ELK16 demonstrated optimal activity at 55 °C and pH 6.0 with enhanced thermal stability. ADI-ELK16 retained 57.34% of its enzyme activity after 10 cycles, with notable reusability. The protein was characterized by scanning electron microscopy (SEM), dynamic light scattering (DLS), and the zeta potential. Additionally, the conversion of 100 g/L l-arginine to 92.3 g/L l-citrulline over batch reactions validated the industrial potential of ADI-ELK16. Compared with traditional immobilization methods, this approach eliminates the need for carrier materials, simplifying the immobilization process and significantly enhancing the catalytic performance and stability, making ADI-ELK16 a highly efficient and reusable system for industrial applications.

Enhanced thermostability and catalytic activity for arginine deiminase from Enterobacter faecalis SK32.001 via combinatorial mutagenesis

Arginine deiminase (ADI) exhibits potential for clinical and industrial applications, yet its low thermostability and catalytic efficiency under physiological conditions limit its utility. In this work, the ADI of Enterococcus faecalis SK32.001 was rationally designed. A total of 120 combinatorial mutants, ranging from two-point to six-point mutations, were constructed by sequentially stacking single-point positive mutants (F44W, N163P, E220L, N318E, A336G, T340I). Among them, the mutants S604, S700, S601, and S606 exhibited higher Tm values, while the mutants S605, S547, S602, S607, S517, and S557 demonstrated enhanced enzymatic activity. Notably, the five-point mutant S547 (F44W/N163P/E220I/A336G/T340I) exhibited remarkable pH tolerance (pH 4.5-9.5, with over 80 % residual enzyme activity). Its specific enzyme activity reached 131.60 U/mg, which was 2-fold higher than that of wild enzyme. The Tm value of this enzyme increases to 64.04 °C, 11.62 °C higher than that of the wild-type enzyme. The structure predicted by AlphaFold 2 revealed that the increased rigidity, formation of new hydrogen bonds, and an increase in hydrophobic residues may account for the enhanced enzyme activity and thermostability. This research demonstrates that rational design strategies can effectively optimize enzyme properties, providing insights for the development of microbial enzymes with industrial relevance.

Stability of immobilized L-arginine deiminase from Penicillium chrysogenum and evaluation of its anticancer activity

The aim of the present work was to immobilize L-arginine deiminase on suitable supports such as chitosan, alginate, and silica gel to study its stability. Additionally, the study aims to investigate the anticancer effects of the free purified enzyme on hepatocellular carcinoma (Hep-G2) and breast cancer (MCF-7) cell lines. L-arginine deiminase (ADI: EC 3.5.3.6) was immobilized on chitosan, Ca-alginate, and silica gel, with immobilization efficiencies of 89.0%, 72.8%, and 66.5%, respectively. The optimal immobilization time for the highest efficiency was 4 h. Increasing the concentration of glutaraldehyde improved the immobilization efficiency of ADI on chitosan. The chitosan-immobilized ADI retained about 45% of its activity after 8 cycles. The optimal pH values were 6 for the free purified ADI and 7 for the chitosan-immobilized ADI. The optimal temperature increased from 40 °C for the free enzyme to 45 °C after immobilization. The activation energies for the free and chitosan-immobilized enzymes were 71.335 kJ/mol and 64.011 kJ/mol, respectively. The Km values for the free and chitosan-immobilized ADI were 0.76 mM and 0.77 mM, respectively, while the Vmax values were 80.0 U/mg protein for the free ADI and 71.4 U/mg protein for the chitosan-immobilized ADI. After 30 days of storage at 4 °C, the residual activities were 40% for the free purified ADI and 84% for the chitosan-immobilized ADI. At 25 °C, the residual activities were 10% for the free ADI and 75% for the chitosan-immobilized ADI. The chitosan-immobilized ADI exhibited significantly higher stability against proteases such as pepsin and trypsin compared to the free enzyme. The purified ADI also demonstrated enhanced potential anticancer effects and significant cytotoxicity against the Hep-G2 and MCF-7 tumor cell lines compared to doxorubicin. These findings suggest that purified ADI has potential as an anticancer agent, though further in-depth studies are required.

In silico and in vitro analysis of arginine deiminase from Pseudomonas furukawaii as a potential anticancer enzyme

Arginine deiminase (ADI), a promising anticancer enzyme from Mycoplasma hominis, is currently in phase III of clinical trials for the treatment of arginine auxotrophic tumors. However, it has been associated with several drawbacks in terms of low stability at human physiological conditions, high immunogenicity, hypersensitivity and systemic toxicity. In our previous work, Pseudomonas furukawaii 24 was identified as a potent producer of ADI with optimum activity under physiological conditions. In the present study, phylogenetic analysis of microbial ADIs indicated P. furukawaii ADI (PfADI) to be closely related to experimentally characterized ADIs of Pseudomonas sp. with proven anticancer activity. Immunoinformatics analysis was performed indicating lower immunogenicity of PfADI than MhADI (M. hominis ADI) both in terms of number of linear and conformational B-cell epitopes and T-cell epitope density. Overall antigenicity and allergenicity of PfADI was also lower as compared to MhADI, suggesting the applicability of PfADI as an alternative anticancer biotherapeutic. Hence, in vitro experiments were performed in which the ADI coding arcA gene of P. furukawaii was cloned and expressed in E. coli BL21. Recombinant ADI of P. furukawaii was purified, characterized and its anticancer activity was assessed. The enzyme was stable at human physiological conditions (pH 7 and 37 °C) with Km of 1.90 mM. PfADI was found to effectively inhibit the HepG2 cells with an IC50 value of 0.1950 IU/ml. Therefore, the current in silico and in vitro studies establish PfADI as a potential anticancer drug candidate with improved efficacy and low immunogenicity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03292-2.

Characterization of a recombinant arginine deiminase from Halothermothrix orenii and its application in citrulline production

In recent years, arginine deiminase (ADI, EC 3.5.3.6) has attracted much attention as a biocatalyst that produces the functional amino acid l-citrulline from l-arginine and also as an anticancer enzyme. Here, we identified and characterized a putative ADI from the thermophilic bacterium Halothermothrix orenii. The H. orenii ADI (H-ADI) protein was expressed in Escherichia coli BL21(DE3) with a specific activity of 91.8 U/mg protein at 55°C and pH 6.5. The enzyme remained at 74% relative activity after incubation at 45°C for 180 min, only 25% at 50°C. The melting temperature was 56°C. H-ADI is not a metal-requiring enzyme; Ni²⁺ slightly improved the catalytic activity. The K_m and V_max for l-arginine were 55.5 mM and 156.8 μmol/min/mg protein, respectively. Moreover, three residues (Arg183, Arg237, and His273) were key to the formation of l-citrulline, as analyzed by alanine-scanning mutagenesis. Finally, the enzymatic synthesis of l-citrulline was carried out at 50°C with a conversion ratio reaching 99.03%. Together, these findings show that H-ADI is a promising biocatalyst for the production of l-citrulline.

Microbial arginine deiminase: A multifaceted green catalyst in biomedical sciences

Arginine deiminase is a well-recognized guanidino-modifying hydrolase that catalyzes the conversion of L-arginine to citrulline and ammonia. Their biopotential to regress tumors via amino acid deprivation therapy (AADT) has been well established. PEGylated formulation of recombinant Mycoplasma ADI is in the last-phase clinical trials against various arginine-auxotrophic cancers like hepatocellular carcinoma, melanoma, and mesothelioma. Recently, ADIs have attained immense importance in several other biomedical applications, namely treatment of Alzheimer's, as an antiviral drug, bioproduction of nutraceutical L-citrulline and bio-analytics involving L-arginine detection. Considering the wide applications of this biodrug, the demand for ADI is expected to escalate several-fold in the coming years. However, the sustainable production aspects of the enzyme with improved pharmacokinetics is still limited, creating bottlenecks for effective biopharmaceutical development. To circumvent the lacunae in enzyme production with appropriate paradigms of 'quality-by-design' an explicit overview of its properties with 'biobetter' formulations strategies are required. Present review provides an insight into all the potential biomedical applications of ADI along with the improvements required for its reach to clinics. Recent research advances with special emphasis on the development of ADI as a 'biobetter' enzyme have also been comprehensively elaborated.

Arginine deaminase from Pseudomonas aeruginosa PS2: purification, biochemical characterization and in-vitro evaluation of anticancer activity

In the present study, arginine deaminase (ADI) was purified from Pseudomonas aeruginosa PS2 which showed relative molecular mass of 70 ± 3 kDa on native-PAGE and 36 ± 0.5 kDa on SDS-PAGE. Purified ADI exhibited optimum activity at pH 6.5 and temperature 40 ºC. Metal ions, K⁺ and Mg²⁺ had positive, while Mn²⁺, Cr²⁺, Co²⁺, Fe³⁺, Ni²⁺, Cu²⁺, Cd²⁺ and Hg²⁺ had negative effects on catalytic activity of ADI. Purified enzyme showed high substrate specificity towards natural substrate L-arginine and did not hydrolyse its structural analogues. In-vitro serum half-life of purified ADI was 40 h, whereas proteolytic half-life was 28, 27, and 32 min against trypsin, elastase-I and proteinase-K, respectively. Anticancer activity of ADI has been evaluated against panel of human cancer cell lines (LS-180, HCT-116, MCF-7, BT-549, T47D, HL-60, MOLT-4, K-562, and PC-3) but lowest IC₅₀ 1.2 IU ml^-1 was recorded with MCF-7 cells. Colony forming assay, wound-healing migration assay, phase contrast microscopy, DAPI staining, cell cycle analysis and DNA laddering assay revealed that ADI treatment induced apoptotic cell death in dose dependent manner. Increased level of MMP loss, ROS generation and decreased level of SOD, CAT, GPx and GSH displayed ADI treatment induced mitochondrial dysfunctioning. Furthermore, purified ADI had no substantial toxicity against human normal cell lines and blood erythrocytes. These findings suggesting that purified ADI could be developed as an anticancer agent but more in depth studies are warranted.

Microbial enzymes for deprivation of amino acid metabolism in malignant cells: biological strategy for cancer treatment

Amino acid deprivation therapy (AADT) is emerging as a promising strategy for the development of novel therapeutics against cancer. This biological therapy relies upon the differences in the metabolism of cancer and normal cells. The rapid growth of tumors results in decreased expression of certain enzymes leading to auxotrophy for some specific amino acids. These auxotrophic tumors are targeted by amino acid-depleting enzymes. The depletion of amino acid selectively inhibits tumor growth as the normal cells can synthesize amino acids by their usual machinery. The enzymes used in AADT are mostly obtained from microbes for their easy availability. Microbial L-asparaginase is already approved by FDA for the treatment of acute lymphoblastic leukemia. Arginine deiminase and methionase are under clinical trials and the therapeutic potential of lysine oxidase, glutaminase and phenylalanine ammonia lyase is also being explored. The present review provides an overview of microbial amino acid depriving enzymes. Various attributes of these enzymes like structure, mode of action, production, formulations, and targeted cancers are discussed. The challenges faced and the combat strategies to establish AADT in standard cancer armamentarium are also reviewed.Key Points • Amino acid deprivation therapy is a potential therapy for auxotrophic tumors. • Microbial enzymes are used due to their ease of manipulation and high productivity. • Enzyme properties are improved by PEGylation, encapsulation, and genetic engineering. • AADT can be employed as combinational therapy for better containment of cancer.

Multilevel algorithms and evolutionary hybrid tools for enhanced production of arginine deiminase from Pseudomonas furukawaii RS3

In the present study a high arginine deiminase (ADI) yielding bacterium was isolated from soil samples of Haryana, India and identified as Pseudomonas furukawaii. The specific enzyme activity was optimized to 1.420 IU/ml by OFAT and further enhanced to 2.708 IU/ml (an increase of 90.7%) with the help of statistical parametric optimization approaches using GA-ANN and GA-ANFIS. The obtained value of the coefficient of correlation (R = 0.88) for ANN and epoch error (0.12) for ANFIS, indicates the prediction accuracy and strength of these data training models. ADI production was improved significantly in simple super broth media supplemented with 1.5% fructose and 1.75% arginine at pH 7 at 37 °C using multilevel algorithms and evolutionary hybrid tools. The native enzyme was partially purified (ten-fold) up to a specific enzyme activity of 29.559 IU/mg.

Arginine Deiminase: Current Understanding and Applications

BACKGROUND

Arginine deiminase (ADI), an arginine catabolizing enzyme, is considered as an anti-tumor agent for the treatment of arginine auxotrophic cancers. However, some obstacles limit its clinical applications.

OBJECTIVE

This review will summarize the clinical applications of ADI, from a brief history to its limitations, and will discuss the different ways to deal with the clinical limitations.

METHOD

The structure analysis, cloning, expression, protein engineering and applications of arginine deiminase enzyme have been explained in this review.

CONCLUSION

Recent patents on ADI are related to ADI engineering to increase its efficacy for clinical application. The intracellular delivery of ADI and combination therapy seem to be the future strategies in the treatment of arginine auxotrophic cancers. Applying ADIs with optimum features from different sources and or ADI engineering, are promising strategies to improve the clinical application of ADI.

Thermostability and Specific-Activity Enhancement of an Arginine Deiminase from Enterococcus faecalis SK23.001 via Semirational Design for l-Citrulline Production

l-Citrulline is a nonessential amino acid with a variety of physiological functions and can be enzymatically produced by arginine deiminase (ADI, EC 3.5.3.6). The enzymatic-production approach is of immense interest because of its mild conditions, high yield, low cost, and environmental benignity. However, the major hindrances of l-citrulline industrialization are the poor thermostability and enzyme activity of ADI. Hence, in this work, directed evolution and site-directed mutagenesis aided with in silico screening, including the use of b-factor values and HoTMuSiC, were applied to a previously identified ADI from Enterococcus faecalis SK23.001 ( EfADI), and a triple-site variant R15K-F269Y-G292P was obtained. The triple-site variant displays a 2.5-fold higher specific enzyme activity (333 U mg^-1), a lower K_m value of 6.4 mM, and a 6.1-fold longer half-life ( t_1/2,45°C = 86.7 min) than wild-type EfADI. This work provides a protein-engineering strategy to improve enzyme activity and thermostability, which might be transferrable to other ADIs and enzymes.