Chondroitinase as a therapeutic enzyme: Prospects and challenges

The chondroitinases (Chase) are bacterial lyases that specifically digest chondroitin sulfate and/or dermatan sulfate glycosaminoglycans via a β-elimination reaction and generate unsaturated disaccharides. In recent decades, these enzymes have attracted the attention of many researchers due to their potential applications in various aspects of medicine from the treatment of spinal cord injury to use as an analytical tool. In spite of this diverse spectrum, the application of Chase is faced with several limitations and challenges such as thermal instability and lack of a suitable delivery system. In the current review, we address potential therapeutic applications of Chase with emphasis on the challenges ahead. Then, we summarize the latest achievements to overcome the problems by considering the studies carried out in the field of enzyme engineering, drug delivery, and combination-based therapy.

Effects of synonymous mutations on kinetic properties and structure of firefly luciferase: Molecular dynamics simulation, molecular docking, RNA folding, and experimental study

Although synonymous mutations have long been thought to lack striking results, a growing body of research shows these mutations have highly variable effects. In this study, the impact of synonymous mutations in the development of thermostable luciferase was investigated using a combination of experimental and theoretical approaches. Using bioinformatics analysis, the codon usage features in the Lampyridae family's luciferases were studied and four synonymous mutations of Arg in luciferase were created. An exciting result was that the analysis of kinetic parameters showed a slight increase in the thermal stability of the mutant luciferase. AutoDock Vina, %MinMax algorithm, and UNAFold Server were used to perform molecular docking, folding rate, and RNA folding, respectively. Here, it was assumed that in the region (Arg337) with a moderate propensity for coil, synonymous mutation altered the rate of translation, which in turn may lead to a slight change in the structure of the enzyme. According to the molecular dynamics simulation data, local minor global flexibility is observed in the context of the protein conformation. A plausible explanation is that this flexibility may strengthen hydrophobic interactions due to its sensitivity to a molecular collision. Accordingly, thermostability originated mainly from hydrophobic interaction.

Enzyme Kinetics Features of the Representative Engineered Recombinants of Chondroitinase ABC I

Chondroitinase ABC I (cABC I) from Proteus vulgaris is an important enzyme in medicinal biotechnology due to its ability to help axon regeneration after spinal cord injury. Its practical application involves solving several problems at the molecular and cellular levels. Structurally, most residues at the C-terminal domain of cABC I are arranged as organized strands, and only a small fraction of residues have helical conformation. The structural and functional features of modified residues on two specific helix fragments have previously been reported. The single mutant M889K has been combined with L679S and L679D mutants to make enzyme variants containing simultaneously modified helix. Here, the pH stability and temperature-based analysis of the transition state structure for the catalysis reaction were investigated. We found that double mutant L679D/M889K is the better choice to use in physiological conditions due to its higher pH stability at physiological pH as well as its different optimum temperature as compared with the (wild-type) WT protein. According to Arrhenius's analysis, the values of the Gibbs free energy of the transition state (∆G^#) are not changed upon mutation. However, the relative contribution and absolute values of the enthalpy and entropy change to the total value of ∆G^#, varied between the WT and mutants.

Protein Stability: Enhancement and Measurement

This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.

Reengineering biocatalysts: Computational redesign of chondroitinase ABC improves efficacy and stability

Maintaining biocatalyst stability and activity is a critical challenge. Chondroitinase ABC (ChABC) has shown promise in central nervous system (CNS) regeneration, yet its therapeutic utility is severely limited by instability. We computationally reengineered ChABC by introducing 37, 55, and 92 amino acid changes using consensus design and forcefield-based optimization. All mutants were more stable than wild-type ChABC with increased aggregation temperatures between 4° and 8°C. Only ChABC with 37 mutations (ChABC-37) was more active and had a 6.5 times greater half-life than wild-type ChABC, increasing to 106 hours (4.4 days) from only 16.8 hours. ChABC-37, expressed as a fusion protein with Src homology 3 (ChABC-37-SH3), was active for 7 days when released from a hydrogel modified with SH3-binding peptides. This study demonstrates the broad opportunity to improve biocatalysts through computational engineering and sets the stage for future testing of this substantially improved protein in the treatment of debilitating CNS injuries.

Osmotic Swelling Responses Are Conserved Across Cartilaginous Tissues With Varied Sulfated-Glycosaminoglycan Contents

Determining the influence of tissue composition on the osmotic swelling stress of articular cartilage and meniscus fibrocartilage is important to enhance our understanding of physiology and disease. This osmotic swelling stress is critical for the load-bearing capability of both tissues and results in part due to the interactions between the negatively charged sulfated glycosaminoglycan (sGAG) chains and the ionic interstitial fluid. Changes in sGAG content, as those occurring during the progression of degenerative joint disease, alter such interactions. Here, we compare the time-varying effects of altered osmotic environments on the confined compression swelling behavior of bovine tissues spanning a range of sGAG concentrations: juvenile articular cartilage, juvenile and adult meniscus, and juvenile cartilage enzymatically degraded to reduce its sGAG content. The transient response to changes in bath conditions was evaluated for explants assigned to one of three compressive offsets (5%, 10%, or 15% strain) and one of three bath conditions (0.1X, 1X, or 10X phosphate-buffered saline). Our results show that relative responses to alterations to the osmotic environment are consistent across native tissues but differ for degraded juvenile cartilage, demonstrating that changes in sGAG do not completely recapitulate the native swelling behaviors. Further, we found a strong correlation between aggregate modulus and sGAG/collagen, as well as between sGAG and collagen contents across native tissue types, suggesting some conservation of composition-function relationships across a range of tissue types with varying sGAG concentrations. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:785-792, 2020.

Designing and construction of novel variants of Chondroitinase ABC I to reduce aggregation rate

Chondroitinase ABC I (cABC I) can degrade inhibitory molecules for axon regrowth at the site of damage after spinal cord injury (SCI). One of the main problems in the practical application is the possibility of structural changes that lead to the inactivation of the enzyme. In current work, three variants of cABC I was designed and constructed by manipulation of a short helix conformation (Gln⁶⁷⁸-Leu⁶⁷⁹-Ser⁶⁸⁰-Gln⁶⁸¹); where Gln residues were converted to Glu. According to the enzyme kinetics studies, the catalytic efficiency of the Q681E and double mutant (Q678E/Q681E) increases in comparison with WT enzyme; while that of Q678E decreases. It was also shown that the rate of the inactivation of the enzyme variants over time is greater in WT and Q678E variants than that of the Q681E and double mutant. Negative values of entropy change of thermal inactivation measurements; demonstrate that inactivation of the WT and Q678E variants are mainly originated from aggregation. These observations can be explained by considering the repulsive electrostatic interaction between enzyme molecules that prevents protein aggregation over time. It is concluded that increasing the solubility of the Q681E and double mutant via favorable interactions of surface-exposed charged residues with dipole momentum of water molecules accompanied by the presence of intermolecular repulsive electrostatic interaction leads to decreasing the rate of aggregation in both long-term storage and heat-induced structural changes.