Effect of surface charge alteration on stability of l-asparaginase II from Escherichia sp

Prediction of peptide hormones using an ensemble of machine learning and similarity-based methods

Peptide hormones serve as genome-encoded signal transduction molecules that play essential roles in multicellular organisms, and their dysregulation can lead to various health problems. In this study, we propose a method for predicting hormonal peptides with high accuracy. The dataset used for training, testing, and evaluating our models consisted of 1174 hormonal and 1174 non-hormonal peptide sequences. Initially, we developed similarity-based methods utilizing BLAST and MERCI software. Although these similarity-based methods provided a high probability of correct prediction, they had limitations, such as no hits or prediction of limited sequences. To overcome these limitations, we further developed machine and deep learning-based models. Our logistic regression-based model achieved a maximum AUROC of 0.93 with an accuracy of 86% on an independent/validation dataset. To harness the power of similarity-based and machine learning-based models, we developed an ensemble method that achieved an AUROC of 0.96 with an accuracy of 89.79% and a Matthews correlation coefficient (MCC) of 0.8 on the validation set. To facilitate researchers in predicting and designing hormone peptides, we developed a web-based server called HOPPred. This server offers a unique feature that allows the identification of hormone-associated motifs within hormone peptides. The server can be accessed at: https://webs.iiitd.edu.in/raghava/hoppred/.

Thermostable bacterial L-asparaginase for polyacrylamide inhibition and in silico mutational analysis

The L-asparaginase (ASPN) enzyme has received recognition in various applications including acrylamide degradation in the food industry. The synthesis and application of thermostable ASPN enzymes is required for its use in the food sector, where thermostable enzymes can withstand high temperatures. To achieve this goal, the bacterium Bacillus subtilis was isolated from the hot springs of Tapovan for screening the production of thermostable ASPN enzyme. Thus, ASPN with a maximal specific enzymatic activity of 0.896 U/mg and a molecular weight of 66 kDa was produced from the isolated bacteria. The kinetic study of the enzyme yielded a Km value of 1.579 mM and a Vmax of 5.009 µM/min with thermostability up to 100 min at 75 °C. This may have had a positive indication for employing the enzyme to stop polyacrylamide from being produced. The current study has also been extended to investigate the interaction of native and mutated ASPN enzymes with acrylamide. This concluded that the M10 (with 10 mutations) has the highest protein and thermal stability compared to the wild-type ASPN protein sequence. Therefore, in comparison to a normal ASPN and all other mutant ASPNs, M10 is the most favorable mutation. This research has also demonstrated the usage of ASPN in food industrial applications.

Rational engineering and insight for a L-glutaminase activity reduced type II L-asparaginase from Bacillus licheniformis and its antileukemic activity in vitro

Type II L-asparaginase (ASNase) has been approved by the FDA for treating acute lymphoid leukemia (ALL), but its therapeutic effect is limited by low catalytic efficiency and L-glutaminase (L-Gln) activity. This study utilized free energy based molecular dynamics calculations to identify residues associated with substrate binding in Bacillus licheniformis L-asparaginase II (BLASNase) with high catalytical activity. After saturation and combination mutagenesis, the mutant LGT (74 L/75G/111 T) with intensively reduced l-glutamine catalytic activity was generated. The l-glutamine/L-asparagine activity (L-Gln/L-Asn) of LGT was only 6.6 % of parent BLASNase, whereas the L-asparagine (L-Asn) activity was preserved >90 %. Furthermore, structural comparison and molecular dynamics calculations indicated that the mutant LGT had reduced binding ability and affinity towards l-glutamine. To evaluate its effect on acute leukemic cells, LGT was supplied in treating MOLT-4 cells. The experimental results demonstrated that LGT was more cytotoxic and promoted apoptosis compared with commercial Escherichia coli ASNase. Overall, our findings firstly provide insights into reducing l-glutamine activity without impacting L-asparagine activity for BLASNase to possess remarkable potential for anti-leukemia therapy.

Effective mitigation in the amount of acrylamide through enzymatic approaches

Acrylamide (AA), as a food-borne toxicant, is created at some stages of thermal processing in the starchy food through Maillard reaction, fatty food via acrolein route, and proteinous food using free amino acids pathway. Maillard reaction obviously takes place in thermal-based products, being responsible for specific sensory attributes; AA formation, thereby, is unavoidable during the thermal processing. Additionally, AA can naturally occur in soil and water supply. In order to reduce the levels of acrylamide in cooked foods, mitigation techniques can be separated into three different types. Firstly, starting materials low in acrylamide precursors can be used to reduce the acrylamide in the final product. Secondly, process conditions may be modified in order to decrease the amount of acrylamide formation. Thirdly, post-process intervention could be used to reduce acrylamide. Conventional or emerging mitigation techniques might negatively influence the pleasant features of heated foods. The current study summarizes the effect of enzymatic reaction induced by asparaginase, glucose oxidase, acrylamidase, phytase, amylase, and protease to possibly inhibit AA formation or progressively hydrolyze formed AA. Not only enzyme-assisted AA reduction could dramatically maintain bio-active compounds, but also no damaging impact has been reported on the sensorial and rheological properties of the final heated products. The enzyme engineering can be applied to ameliorate enzyme functionality through altering the amino acid sequence like site-specific mutagenesis and directed evolution, chemical modifications by covalent conjugation of L-asparaginase onto soluble/insoluble biocompatible polymers and immobilization. Moreover, it would be possible to improve the enzyme's physical, chemical, and thermal stability, recyclability and prevent enzyme overuse by applying engineered ones. In spite of enzymes' cost-effective and eco-friendly, promoting their large-scale usages for AA reduction in food application and AA bioremediation in wastewater and soil resources.

L-Asparaginase as the gold standard in the treatment of acute lymphoblastic leukemia: a comprehensive review

L-Asparaginase is an antileukemic drug long approved for clinical use to treat childhood acute lymphoblastic leukemia, the most common cancer in this population worldwide. However, the efficacy and its use as a drug have been subject to debate due to the variety of adverse effects that patients treated with it present, as well as the prompt elimination in plasma, the need for multiple administrations, and high rates of allergic reactions. For this reason, the search for new, less immunogenic variants has long been the subject of study. This review presents the main aspects of the L-asparaginase enzyme from a structural, pharmacological, and clinical point of view, from the perspective of its use in chemotherapy protocols in conjunction with other drugs in the different treatment phases.

Anticancer Asparaginases: Perspectives in Using Filamentous Fungi as Cell Factories

The enzyme L-asparaginase (L-asparagine amidohydrolase) catalyzes the breakdown of L-asparagine into aspartate and ammonia, which leads to an anti-neoplastic activity stemming from its capacity to deplete L-asparagine concentrations in the bloodstream, and it is therefore used in cases of acute lymphoblastic leukemia (ALL) to inhibit malignant cell growth. Nowadays, this anti-cancer enzyme, largely produced by Escherichia coli, is well established on the market. However, E. coli L-asparaginase therapy has side effects such as anaphylaxis, coagulation abnormality, low plasma half-life, hepatotoxicity, pancreatitis, protease action, hyperglycemia, and cerebral dysfunction. This review provides a perspective on the use of filamentous fungi as alternative cell factories for L-asparaginase production. Filamentous fungi, such as various Aspergillus species, have superior protein secretion capacity compared to yeast and bacteria and studies show their potential for the future production of proteins with humanized N-linked glycans. This article explores the past and present applications of this important enzyme and discusses the prospects for using filamentous fungi to produce safe eukaryotic asparaginases with high production yields.

Enhanced Thermostability and Molecular Insights for l-Asparaginase from Bacillus licheniformis via Structure- and Computation-Based Rational Design

l-Asparaginase has gained much attention for effectively treating acute lymphoblastic leukemia (ALL) and mitigating carcinogenic acrylamide in fried foods. Due to high-dose dependence for clinical treatment and low mitigation efficiency for thermal food processes caused by poor thermal stability, a method to achieve thermostable l-asparaginase has become a critical bottleneck. In this study, a rational design including free energy combined with structural and conservative analyses was applied to engineer the thermostability of l-asparaginase from Bacillus licheniformis (BlAsnase). Two enhanced thermostability mutants D172W and E207A were screened out by site-directed saturation mutagenesis. The double mutant D172W/E207A exhibited highly remarkable thermostability with a 65.8-fold longer half-life at 55 °C and 5 °C higher optimum reaction temperature and melting temperature (T_m) than those of wild-type BlAsnase. Further, secondary structure, sequence, molecular dynamics (MD), and 3D-structure analysis revealed that the excellent thermostability of the mutant D172W/E207A was on account of increased hydrophobicity and decreased flexibility, highly rigid structure, hydrophobic interactions, and favorable electrostatic potential. As the first report of rationally designing l-asparaginase with improved thermostability from B. licheniformis, this study offers a facile and efficient process to improve the thermostability of l-asparaginase for industrial applications.

Enhancing the Catalytic Activity of Type II L-Asparaginase from Bacillus licheniformis through Semi-Rational Design

Low catalytic activity is a key factor limiting the widespread application of type II L-asparaginase (ASNase) in the food and pharmaceutical industries. In this study, smart libraries were constructed by semi-rational design to improve the catalytic activity of type II ASNase from Bacillus licheniformis. Mutants with greatly enhanced catalytic efficiency were screened by saturation mutations and combinatorial mutations. A quintuple mutant ILRAC was ultimately obtained with specific activity of 841.62 IU/mg and kcat/Km of 537.15 min−1·mM−1, which were 4.24-fold and 6.32-fold more than those of wild-type ASNase. The highest specific activity and kcat/Km were firstly reported in type II ASNase from Bacillus licheniformis. Additionally, enhanced pH stability and superior thermostability were both achieved in mutant ILRAC. Meanwhile, structural alignment and molecular dynamic simulation demonstrated that high structure stability and strong substrate binding were beneficial for the improved thermal stability and enzymatic activity of mutant ILRAC. This is the first time that enzymatic activity of type II ASNase from Bacillus licheniformis has been enhanced by the semi-rational approach, and results provide new insights into enzymatic modification of L-asparaginase for industrial applications.

Construction of L-Asparaginase Stable Mutation for the Application in Food Acrylamide Mitigation

Acrylamide, a II A carcinogen, widely exists in fried and baked foods. L-asparaginase can inhibit acrylamide formation in foods, and enzymatic stability is the key to its application. In this study, the Escherichia coli L-asparaginase (ECA) stable variant, D60W/L211R/L310R, was obtained with molecular dynamics (MD) simulation, saturation mutation, and combinatorial mutation, the half-life of which increased to 110 min from 60 min at 50 °C. Furthermore, the working temperature (maintaining the activity above 80%) of mutation expanded from 31 °C–43 °C to 35 °C–55 °C, and the relative activity of mutation increased to 82% from 65% at a pH range of 6–10. On treating 60 U/mL and 100 U/g flour L-asparaginase stable mutant (D60W/L211R/L310R) under uncontrolled temperature and pH, the acrylamide content of potato chips and bread was reduced by 66.9% and 51.7%, which was 27% and 49.9% higher than that of the wild type, respectively. These results demonstrated that the mutation could be of great potential to reduce food acrylamide formation in practical applications.

Molecular Analysis of L-Asparaginases for Clarification of the Mechanism of Action and Optimization of Pharmacological Functions

L-asparaginases (EC 3.5.1.1) are a family of enzymes that catalyze the hydrolysis of L-asparagine to L-aspartic acid and ammonia. These proteins with different biochemical, physicochemical and pharmacological properties are found in many organisms, including bacteria, fungi, algae, plants and mammals. To date, asparaginases from E. coli and Dickeya dadantii (formerly known as Erwinia chrysanthemi) are widely used in hematology for the treatment of lymphoblastic leukemias. However, their medical use is limited by side effects associated with the ability of these enzymes to hydrolyze L-glutamine, as well as the development of immune reactions. To solve these issues, gene-editing methods to introduce amino-acid substitutions of the enzyme are implemented. In this review, we focused on molecular analysis of the mechanism of enzyme action and to optimize the antitumor activity.

Heterologous Expression and Rational Design of l-asparaginase from Rhizomucor miehei to Improve Thermostability

Simple Summary

l-asparaginase has been extensively applied in food industries. However, the application of l-asparaginase from non-thermophilic sources is greatly limited due to the poor thermostability and the complex environments typically encountered in food industries. Therefore, improving the thermostability of l-asparaginase is essential for its industrial application. In this work, the thermostability and enzyme activity of heterologously expressed l-asparaginase from Rhizomucor miehei was greatly improved by rational design and molecular modification. Moreover, we further characterized the mechanism underlying improved thermostability in detail. A high-yield l-asparaginase B. subtilis recombinant was constructed by 5′ untranslated region (UTR) modification. These results demonstrate that rational design can be an efficient approach for enhancing the thermostability of l-asparaginase from non-thermophilic sources.

Abstract

l-asparaginase (EC 3.5.1.1) hydrolyzes l-asparagine to produce l-aspartate and ammonia and is widely found in microorganisms, plants, and some rodent sera. l-asparaginase used for industrial production should have good thermostability. We heterologously expressed l-asparaginase from Rhizomucor miehei, selected nine loci for site-directed mutagenesis by rational design, and obtained two mutants with significantly improved thermostability. The optimal temperature of mutants S302I and S302M was 50 °C. After incubating the mutant and wild-type enzymes at 45 °C for 35 h, the residual activity of the wild-type enzyme (WT) was only about 10%. In contrast, the residual activity of S302I and S302M was more than 50%. After combination mutagenesis, Bacillus subtilis 168-pMA5-A344E/S302I was constructed using the food-safe host strain B. subtilis 168. Additionally, a 5′ untranslated region (UTR) modification strategy was adopted to enhance the expression level of R. miehei-derived l-asparaginase in B. subtilis. In a 5-L fermenter scale-up experiment, the enzyme activity of recombinant B. subtilis 168-pMA5-UTR-A344E/S302I reached 521.9 U·mL⁻¹ by fed-batch fermentation.

Microbial production, molecular modification, and practical application of l-Asparaginase: A review

L-Asparaginase (L-ASNase, EC 3.5.1.1), an antitumor drug for acute lymphoblastic leukemia (ALL) therapy, is widely used in the clinical field. Similarly, L-ASNase is also a powerful and significant biological tool in the food industry to inhibit acrylamide (AA) formation. This review comprehensively summarizes the latest achievements and improvements in the production, modification, and application of microbial L-ASNase. To date, the expression levels and optimization of expression hosts such as Escherichia coli, Bacillus subtilis, and Pichia pastoris, have made significant progress. In addition, examples of successful modification of L-ASNase such as decreasing glutaminase activity, increasing the in vivo stability, and enhancing thermostability have been presented. Impressively, the application of L-ASNase as a food addition aid, as well as its commercialization in the pharmaceutical field, and cutting-edge biosensor application developments have been summarized. The presented results and proposed ideas could be a good guide for other L-ASNase researchers in both scientific and practical fields.

Circumventing the side effects of L-asparaginase

L-asparaginase is an enzyme that catalyzes the degradation of asparagine and successfully used in the treatment of acute lymphoblastic leukemia. L-asparaginase toxicity is either related to hypersensitivity to the foreign protein or to a secondary L-glutaminase activity that causes inhibition of protein synthesis. PEGylated versions have been incorporated into the treatment protocols to reduce immunogenicity and an alternative L-asparaginase derived from Dickeya chrysanthemi is used in patients with anaphylactic reactions to the E. coli L-asparaginase. Alternative approaches commonly explore new sources of the enzyme as well as the use of protein engineering techniques to create less immunogenic, more stable variants with lower L-glutaminase activity. This article reviews the main strategies used to overcome L-asparaginase shortcomings and introduces recent tools that can be used to create therapeutic enzymes with improved features.

The Role of Surface Exposed Lysine in Conformational Stability and Functional Properties of Lipase from Staphylococcus Family

Surface charge residues have been recognized as one of the stability determinants in protein. In this study, we sought to compare and analyse the stability and conformational dynamics of staphylococcal lipase mutants with surface lysine mutation using computational and experimental methods. Three highly mutable and exposed lysine residues (Lys91, Lys177, Lys325) were targeted to generate six mutant lipases in silico. The model structures were simulated in water environment at 25 °C. Our simulations showed that the stability was compromised when Lys177 was substituted while mutation at position 91 and 325 improved the stability. To illustrate the putative alterations of enzyme stability in the stabilising mutants, we characterized single mutant K325G and double mutant K91A/K325G. Both mutants showed a 5 °C change in optimal temperature compared to their wild type. Single mutant K325G rendered a longer half-life at 25 °C (T_1/2 = 21 h) while double mutant K91A/K325G retained only 40% of relative activity after 12 h incubation. The optimal pH for mutant K325G was shifted from 8 to 9 and similar substrate preference was observed for the wild type and two mutants. Our findings indicate that surface lysine mutation alters the enzymatic behaviour and, thus, rationalizes the functional effects of surface exposed lysine in conformational stability and activity of this lipase.

Effect of introducing disulfide bridges in C-terminal structure on the thermostability of xylanase XynZF-2 from Aspergillus niger

In this study, a mutant xylanase of high thermostability was obtained by site-directed mutagenesis. The homologous 3D structure of xylanase was successfully modeled and the mutation sites were predicted using bioinformatics software. Two amino acids of XynZF-2 were respectively substituted by cysteines (T205C and A52C) and a disulfide bridge was introduced into the C-terminal of XynZF-2. The mutant gene xynZFTA was cloned into pPIC9K and expressed in P. pastoris. The optimum temperature of the variant XynZFTA was improved from 45°C to 60°C, and XynZFTA retained greater than 90.0% activity (XynZF-2 retained only 50.0% activity) after treatment at 50°C for 5 min. The optimum pH of mutant xylanase was similar to XynZF-2 (pH = 5.0). The pH stability span (5.0~7.0) of the mutant xylanase was increased to 3.0~9.0. Overall, the results implied that the introduction of a disulfide bridge in the C-terminal structure improved the thermostability and pH stability of XynZF-2.

Development of L-Asparaginase Biobetters: Current Research Status and Review of the Desirable Quality Profiles

L-Asparaginase (ASNase) is a vital component of the first line treatment of acute lymphoblastic leukemia (ALL), an aggressive type of blood cancer expected to afflict over 53,000 people worldwide by 2020. More recently, ASNase has also been shown to have potential for preventing metastasis from solid tumors. The ASNase treatment is, however, characterized by a plethora of potential side effects, ranging from immune reactions to severe toxicity. Consequently, in accordance with Quality-by-Design (QbD) principles, ingenious new products tailored to minimize adverse reactions while increasing patient survival have been devised. In the following pages, the reader is invited for a brief discussion on the most recent developments in this field. Firstly, the review presents an outline of the recent improvements on the manufacturing and formulation processes, which can severely influence important aspects of the product quality profile, such as contamination, aggregation and enzymatic activity. Following, the most recent advances in protein engineering applied to the development of biobetter ASNases (i.e., with reduced glutaminase activity, proteolysis resistant and less immunogenic) using techniques such as site-directed mutagenesis, molecular dynamics, PEGylation, PASylation and bioconjugation are discussed. Afterwards, the attention is shifted toward nanomedicine including technologies such as encapsulation and immobilization, which aim at improving ASNase pharmacokinetics. Besides discussing the results of the most innovative and representative academic research, the review provides an overview of the products already available on the market or in the latest stages of development. With this, the review is intended to provide a solid background for the current product development and underpin the discussions on the target quality profile of future ASNase-based pharmaceuticals.

Enhanced trypsin thermostability in Pichia pastoris through truncating the flexible region

Background

High thermostability is required for trypsin to have wider industrial applications. Target mutagenesis at flexible regions has been proved to be an efficient protein engineering method to enhance the protein thermostability.

Results

The flexible regions in porcine trypsin were predicted using the methods including molecular dynamic simulation, FlexPred, and FoldUnfold. The amino acids 78–90 was predicted to be the highly flexible region simultaneously by the three methods and hence selected to be the mutation target. We constructed five variants (D3, D5, D7, D9, and D11) by truncating the region. And the variant D9 showed higher thermostability, with a 5 °C increase in T_opt, 5.8 °C rise in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$T_{50}^{10}$$\end{document}T5010, and a 4.5 °C rise in T_m, compared to the wild-type. Moreover, the half-life value of the variant D9 was also found to be dramatically improved by 46 min. Circular dichroism and intrinsic fluorescence indicated that the structures had no significant change between the variant D9 and the wild-type. The surface hydrophobicity of D9 was measured to be lower than that of wild-type, indicating the increased hydrophobic interaction, which could have contributed to the improved thermostability of D9.

Conclusions

These results showed that the thermostability of variant D9 was increased. The variant D9 could be expected to be a promising tool enzyme for its wider industrial applications. The method of truncating the flexible region used in our study has the potential to be used for enhancing the thermostability of other proteins.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1012-x) contains supplementary material, which is available to authorized users.

A protease-resistant Escherichia coli asparaginase with outstanding stability and enhanced anti-leukaemic activity in vitro

L-Asparaginases (ASNases) have been used as first line drugs for paediatric Acute Lymphoblastic Leukaemia (ALL) treatment for more than 40 years. Both the Escherichia coli (EcAII) and Erwinia chrysanthemi (ErAII) type II ASNases currently used in the clinics are characterized by high in vivo instability, short half-life and the requirement of several administrations to obtain a pharmacologically active concentration. Moreover, they are sensitive to proteases (cathepsin B and asparagine endopeptidase) that are over-expressed by resistant leukaemia lymphoblasts, thereby impairing drug activity and pharmacokinetics. Herein, we present the biochemical, structural and in vitro antiproliferative characterization of a new EcAII variant, N24S. The mutant shows completely preserved asparaginase and glutaminase activities, long-term storage stability, improved thermal parameters, and outstanding resistance to proteases derived from leukaemia cells. Structural analysis demonstrates a modification in the hydrogen bond network related to residue 24, while Normal Mode-based geometric Simulation and Molecular Dynamics predict a general rigidification of the monomer as compared to wild-type. These improved features render N24S a potential alternative treatment to reduce the number of drug administrations in vivo and to successfully address one of the major current challenges of ALL treatment: spontaneous, protease-dependent and immunological inactivation of ASNase.

A critical review on properties and applications of microbial l-asparaginases

l-Asparaginase is one of the main drugs used in the treatment of acute lymphoblastic leukemia (ALL), a commonly diagnosed pediatric cancer. Although several microorganisms are found to produce l-asparaginase, only the purified enzymes from E. coli and Erwinia chrysanthemi are employed in the clinical and therapeutic applications in humans. However, their therapeutic response seldom occurs without some evidence of hypersensitivity and other toxic side effects. l-Asparaginase is also of prospective use in food industry to reduce the formation of acrylamide in fried, roasted or baked food products. This review is an attempt to compile information on the properties of l-asparaginases obtained from different microorganisms. The complications involved with the therapeutic use of the currently available l-asparaginases, and the enzyme's potential application as a food processing aid to mitigate acrylamide formation have also been reviewed. Further, avenues for searching alternate sources of l-asparaginase have been discussed, highlighting the prospects of endophytic microorganisms as a possible source of l-asparaginases with varied biochemical and pharmacological properties.