Stable and functionally diverse versatile peroxidases by computational design directly from sequence

White-rot fungi secrete a repertoire of high-redox potential oxidoreductases to efficiently decompose lignin. Of these enzymes, versatile peroxidases (VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes for research and industrial use, but their recombinant production is extremely challenging. To date, only a single VP has been structurally characterized and optimized for recombinant functional expression, stability and activity. Computational enzyme optimization methods can be applied to many enzymes in parallel, but they require accurate structures. Here, we demonstrate that model structures computed by deep-learning based ab initio structure prediction methods are reliable starting points for one-shot PROSS stability-design calculations. Four designed VPs encoding as many as 43 mutations relative to the wild type enzymes are functionally expressed in yeast whereas their wild type parents are not. Three of these designs exhibit substantial and useful diversity in reactivity profile and tolerance to environmental conditions. The reliability of the new generation of structure predictors and design methods increases the scale and scope of computational enzyme optimization, enabling efficient discovery and exploitation of the functional diversity in natural enzyme families.

Nanozyme-Natural Enzymes Cascade Catalyze Cholesterol Consumption and Reverse Cancer Multidrug Resistance

Multidrug resistance is still a major obstacle to cancer treatment. The most studies are to inhibit the activity of the drug transporter P-glycoprotein (P-gp), but the effect is not ideal. Herein, a nanosystem was built based on cascade catalytic consumption of cholesterol. Cholesterol oxidase (natural enzyme, COD) was immobilized on the carrier (NH2-MIL-88B, MOF) through amide reaction, COD catalyzed the consumption of cholesterol, the reaction product H2O2 was further produced by the MOF with its peroxidase-like activity to produce hydroxyl radicals (•OH) with killing effect. Due to the high expression of CD44 receptor on the surface of tumor cells, we encapsulated chondroitin sulfate gel shell (CS-shell) with CD44 targeting and apoptosis promoting effect on the surface of DOX@MOF-COD nanoparticles, which can accurately and efficiently deliver the drugs to the tumor site and improve the effect of reversing drug resistance. Taking drug-resistant cell membrane as "breakthrough", this paper will provide a new idea for reversing multidrug resistance of tumor.

Deep learning allows genome-scale prediction of Michaelis constants from structural features

The Michaelis constant KM describes the affinity of an enzyme for a specific substrate and is a central parameter in studies of enzyme kinetics and cellular physiology. As measurements of KM are often difficult and time-consuming, experimental estimates exist for only a minority of enzyme–substrate combinations even in model organisms. Here, we build and train an organism-independent model that successfully predicts KM values for natural enzyme–substrate combinations using machine and deep learning methods. Predictions are based on a task-specific molecular fingerprint of the substrate, generated using a graph neural network, and on a deep numerical representation of the enzyme’s amino acid sequence. We provide genome-scale KM predictions for 47 model organisms, which can be used to approximately relate metabolite concentrations to cellular physiology and to aid in the parameterization of kinetic models of cellular metabolism.

Potentiality of Nanoenzymes for Cancer Treatment and Other Diseases: Current Status and Future Challenges

Studies from past years have observed various enzymes that are artificial, which are issued to mimic naturally occurring enzymes based on their function and structure. The nanozymes possess nanomaterials that resemble natural enzymes and are considered an innovative class. This innovative class has achieved a brilliant response from various developments and researchers owing to this unique property. In this regard, numerous nanomaterials are inspected as natural enzyme mimics for multiple types of applications, such as imaging, water treatment, therapeutics, and sensing. Nanozymes have nanomaterial properties occurring with an inheritance that provides a single substitute and multiple platforms. Nanozymes can be controlled remotely via stimuli including heat, light, magnetic field, and ultrasound. Collectively, these all can be used to increase the therapeutic as well as diagnostic efficacies. These nanozymes have major biomedical applications including cancer therapy and diagnosis, medical diagnostics, and bio sensing. We summarized and emphasized the latest progress of nanozymes, including their biomedical mechanisms and applications involving synergistic and remote control nanozymes. Finally, we cover the challenges and limitations of further improving therapeutic applications and provide a future direction for using engineered nanozymes with enhanced biomedical and diagnostic applications.

Evidence for an N-halohistidyl Intermediate in the Catalytic Cycle of Vanadium Chloroperoxidase (VCPO) and an Artificial Enzyme derived from VCPO: A Computational Investigation

Vanadium haloperoxidases play an important catalytic role in the natural production of antibiotics which are difficult to make in the laboratory. Understanding the catalytic mechanism of these enzymes will aide in the production of artificial enzymes useful in bioengineering the synthesis of drugs and useful chemicals. However, the catalytic mechanism remains not fully understood yet. In this paper, we investigate one of the key steps of the catalytic mechanism using QM/MM. Our investigation reveals a new N-haloxy histidyl intermediate in the catalytic cycle of vanadium chloroperoxidase (VCPO). This new intermediate, in turn, yields an explanation for the known inhibition of the enzyme by substrate under acidic conditions (pH<4). Additionally, we examine the possibility of replacing V in VCPO by Nb or Ta using QM modeling. We report the new result that the Gibbs free energy barrier of several steps of the catalytic cycle are lower in the case of artificial enzymes, incorporating NbO43- or TaO43- instead of VO43-. Our results suggest that these new artificial enzymes may catalyze the oxidation of halide faster than the natural enzyme.

Entrapment of glucose oxidase within gold converts it to a general monosaccharide-oxidase

We report that entrapping glucose oxidase (GOx) within metallic gold, expands its activity to become an oxidase for monosaccharides that do not have a natural enzyme with that activity—fructose and xylose—and that this entrapment also removes the enantioselectivity, rendering this enzyme capable of oxidizing the “wrong” l-enantiomer of glucose. These observations suggest that in this biomaterial adsorptive interactions of the outer regions of the protein with the gold cage, pull apart and widen the tunnel between the two monomeric units of GOx, to a degree that its stereoselectivity is compromised; then, the active sites which are more versatile than currently attributed to, are free and capable of acting on the foreign sugars. To test this proposition, we entrapped in gold l-asparaginase, which is also a dimeric enzyme (a dimer of tight dimers), and found, again, that this metallic biomaterial widens the activity of that enzyme, to include the D-amino acid counter enantiomer as well. Detailed kinetic analyses for all substrates are provided for the gold bio-composites, including determination of the difference between the activation energies towards two opposite enantiomers.

Carbon nanomaterial hybrids via laser writing for high-performance non-enzymatic electrochemical sensors: a critical review

Non-enzymatic electrochemical sensors possess superior stability and affordability in comparison to natural enzyme-based counterparts. A large variety of nanomaterials have been introduced as enzyme mimicking with appreciable sensitivity and detection limit for various analytes of which glucose and H2O2 have been mostly investigated. The nanomaterials made from noble metal, non-noble metal, and metal composites, as well as carbon and their derivatives in various architectures, have been extensively proposed over the past years. Three-dimensional (3D) transducers especially realized from the hybrids of carbon nanomaterials either with metal-based nanocatalysts or heteroatom dopants are favorable owing to low cost, good electrical conductivity, and stability. In this critical review, we evaluate the current strategies to create such nanomaterials to serve as non-enzymatic transducers. Laser writing has emerged as a powerful tool for the next generation of devices owing to their low cost and resultant remarkable performance that are highly attractive to non-enzymatic transducers. So far, only few works have been reported, but in the coming years, more and more research on this topic is foreseeable. Graphical abstract

Coding Synthetic Chemistry Strategies into Bacterial Designer Cells

<p>Following a synthetic chemistry blueprint for the valorization of lignocellulosic platform chemicals, this study showcases a so far unprecedented approach to implement non-natural enzyme modules in vivo. For the design of a novel functional whole cell tool, two purely abiotic transformations were incorporated into a recombinant bacterial host that allows production of complex lactone building blocks. This whole cell system streamlines the synthetic cascade, eliminates isolation and purification steps, and provides a high degree stereoselectivity that has so far been elusive in the chemical methodology.</p>

Coding Synthetic Chemistry Strategies into Bacterial Designer Cells

<p>Following a synthetic chemistry blueprint for the valorization of lignocellulosic platform chemicals, this study showcases a so far unprecedented approach to implement non-natural enzyme modules in vivo. For the design of a novel functional whole cell tool, two purely abiotic transformations were incorporated into a recombinant bacterial host that allows production of complex lactone building blocks. This whole cell system streamlines the synthetic cascade, eliminates isolation and purification steps, and provides a high degree stereoselectivity that has so far been elusive in the chemical methodology.</p>