Cross-Regulation of an Artificial Metalloenzyme

Lewis acid-driven self-assembly of diiridium macrocyclic catalysts imparts substrate selectivity and glutathione tolerance

Molecular inorganic catalysts (MICs) tend to have solvent-exposed metal centers that lack substrate specificity and are easily inhibited by biological nucleophiles. Unfortunately, these limitations exclude many MICs from being considered for in vivo applications. To overcome this challenge, a strategy to spatially confine MICs using Lewis acid-driven self-assembly is presented. It was shown that in the presence of external cations (e.g., Li+, Na+, K+, or Cs+) or phosphate buffered saline, diiridium macrocycles spontaneously formed supramolecular iridium-cation species, which were characterized by X-ray crystallography and dynamic light scattering. These nanoassemblies selectively reduced sterically unhindered C[double bond, length as m-dash]O groups via transfer hydrogenation and tolerated up to 1 mM of glutathione. In contrast, when non-coordinating tetraalkylammonium cations were used, the diiridium catalysts were unable to form higher-ordered structures and discriminate between different aldehyde substrates. This work suggests that in situ coordination self-assembly could be a versatile approach to enable or enhance the integration of MICs with biological hosts.

pH-feedback systems to program autonomous self-assembly and material lifecycles

pH-responsive systems have gained importance for the development of smart materials and for biomedical applications because they can switch between different states by simple acid/base triggers. However, such equilibrium systems lack the autonomous behaviour that is so ubiquitous in living systems that self-regulate out of equilibrium. As a contribution to the emerging field of autonomous chemical systems, we have developed pH-feedback systems (pH-FS) based on the coupling of acid- and base-producing steps in chemical reaction networks. The resulting autonomous nonlinear pH curves can be coupled with a variety of pH-sensitive building blocks to program the lifecycles of the associated transient state at the level of self-assemblies and material systems. In this article, we discuss the different generations of such pH-feedback systems, the principles of their coupling to self-assemblies with lifecycles and highlight emerging concepts for the design of autonomous functional materials. The specificity, robustness, and flexible operation of such pH-FS can also be used to realize chemo-structural and chemo-mechanical feedbacks that extend the behaviour of such materials systems toward complex and functional life-like systems.

Dissipative operation of pH-responsive DNA-based nanodevices

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the fuel acids to a water solution initially causes a rapid transient pH decrease, which is then followed by a slower pH increase. We have employed such low-to-high pH cycles to control in a dissipative way the operation of two model DNA-based nanodevices: a DNA nanoswitch undergoing time-programmable open–close–open cycles of motion, and a DNA-based receptor able to release-uptake a DNA cargo strand. The kinetics of the transient operation of both systems can be easily modulated by varying the concentration of the acid fuel added to the solution and both acid fuels show an efficient reversibility which further supports their versatility.

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices.

Time-programmable pH: decarboxylation of nitroacetic acid allows the time-controlled rising of pH to a definite value

In this report it is shown that nitroacetic acid 1 (O2NCH2CO2H) can be conveniently used to control the pH of a water solution over time. Time-programmable sequences of the kind pH1(high)-pH2(low)-pH3(high) can be achieved, where both the extent of the initial pH jump (pH1(high)-pH2(low)) and the time required for the subsequent pH rising (pH2(low)-pH3(high)) can be predictably controlled by a judicious choice of the absolute and relative concentrations of the reagents (acid 1 and NaOH). Successive pH1(high)-pH2(low)-pH3(high) sequences can be obtained by subsequent additions of acid 1. As a proof of concept, the method is applied to control over time the pH-dependent host-guest interaction between alpha-cyclodextrin and p-aminobenzoic acid.

Intracellular Unnatural Catalysis Enabled by an Artificial Metalloenzyme

Artificial metalloenzymes, constructed by incorporating a synthetic catalyst into the internal spaces of a protein scaffold, can perform noncanonical chemical transformations that are not possible using natural enzymes. The addition of cell-permeable modules to artificial metalloenzymes allows for noncanonical catalysis to be implemented as a function of mammalian cells. In this chapter, we describe a protocol for controlling cellular function through a cascade consisting of an artificial metalloenzyme and a gene-circuit engineered via synthetic biology.

Evolution of strept(avidin)-based artificial metalloenzymes in organometallic catalysis

Artificial metalloenzymes have been recently established as efficient alternatives to traditional transition metal catalysts. The presence of a secondary coordination sphere in artificial metalloenzymes makes them advantageous over transition metal catalysts, which rely essentially on their first coordination sphere to exhibit their catalytic activity. Recent developments on streptavidin- and avidin-based artificial metalloenzymes have made them highly chemically and genetically evolved for selective organometallic transformations. In this review, we discuss the chemo-genetic optimization of streptavidin- and avidin-based artificial metalloenzymes for the enhancement of their catalytic activities towards a wide range of synthetic transformations. Considering the high impact in vivo applications of artificial metalloenzymes, their catalytic efficacies to promote abiological reactions in intracellular as well as periplasmic environment are also discussed. Overall, this review can provide an insight to readers regarding the design and systematic optimization of strept(avidin)-based artificial metalloenzymes for specific reactions.

Artificial Metalloenzymes: From Selective Chemical Transformations to Biochemical Applications

Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: 1) the newly reported ArMs, according to their type of reaction, and 2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/in vivo catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.

ATP-fuelled self-assembly to regulate chemical reactivity in the time domain

Here, we exploit a small biomolecule - ATP - to gain temporal control over chemical reactivity in a synthetic system composed of small self-assembling molecules and reactants. The approach relies on the capacity of ATP to template the formation of amphiphile-based assemblies. The presence of the enzyme alkaline phosphatase causes a gradual decrease in the ATP-concentration in time and, consequently, a spontaneous dissociation of the assemblies. The uptake of apolar reactants in the hydrophobic domain of the assemblies leads to an enhancement of the reaction rate. It is shown that ATP-triggered self-assembly causes the selective upregulation of one out of two hydrazone-bond formation reactions that take place concurrently in the system. This leads to an inversion in the product ratio, which, however, is transient in nature because the upregulated reaction spontaneously reverts to its basal low reaction rate once the ATP has been consumed by the enzyme. Overall, the results demonstrate the potential of chemically-fuelled self-assembly under dissipative conditions to gain temporal control over reactivity in complex chemical systems.

X-ray-Controlled Bilayer Permeability of Bionic Nanocapsules Stabilized by Nucleobase Pairing Interactions for Pulsatile Drug Delivery

The targeted and sustained drug release from stimuli-responsive nanodelivery systems is limited by the irreversible and uncontrolled disruption of the currently used nanostructures. Bionic nanocapsules are designed by cross-linking polythymine and photoisomerized polyazobenzene (PETAzo) with adenine-modified ZnS (ZnS-A) nanoparticles (NPs) via nucleobase pairing. The ZnS-A NPs convert X-rays into UV radiation that isomerizes the azobenzene groups, which allows controlled diffusion of the active payloads across the bilayer membranes. In addition, the nucleobase pairing interactions between PETAzo and ZnS-A prevent drug leakage during their in vivo circulation, which not only enhances tumor accumulation but also maintains stability. These nanocapsules with tunable permeability show prolonged retention, remotely controlled drug release, enhanced targeted accumulation, and effective antitumor effects, indicating their potential as an anticancer drug delivery system.

Artificial Metalloenzymes: Challenges and Opportunities

Artificial metalloenzymes (ArMs) result from the incorporation of an abiotic metal cofactor within a protein scaffold. From the earliest techniques of transition metals adsorbed on silk fibers, the field of ArMs has expanded dramatically over the past 60 years to encompass a range of reaction classes and inspired approaches: Assembly of the ArMs has taken multiple forms with both covalent and supramolecular anchoring strategies, while the scaffolds have been intuitively selected and evolved, repurposed, or designed in silico. Herein, we discuss some of the most prominent recent examples of ArMs to highlight the challenges and opportunities presented by the field.

Artificial Metalloenzymes Based on the Biotin-Streptavidin Technology: Enzymatic Cascades and Directed Evolution

Artificial metalloenzymes (ArMs) result from anchoring a metal-containing moiety within a macromolecular scaffold (protein or oligonucleotide). The resulting hybrid catalyst combines attractive features of both homogeneous catalysts and enzymes. This strategy includes the possibility of optimizing the reaction by both chemical (catalyst design) and genetic means leading to achievement of a novel degree of (enantio)selectivity, broadening of the substrate scope, or increased activity, among others. In the past 20 years, the Ward group has exploited, among others, the biotin–(strept)avidin technology to localize a catalytic moiety within a well-defined protein environment. Streptavidin has proven versatile for the implementation of ArMs as it offers the following features: (i) it is an extremely robust protein scaffold, amenable to extensive genetic manipulation and mishandling, (ii) it can be expressed in E. coli to very high titers (up to >8 g·L^–1 in fed-batch cultures), and (iii) the cavity surrounding the biotinylated cofactor is commensurate with the size of a typical metal-catalyzed transition state. Relying on a chemogenetic optimization strategy, varying the orientation and the nature of the biotinylated cofactor within genetically engineered streptavidin, 12 reactions have been reported by the Ward group thus far. Recent efforts within our group have focused on extending the ArM technology to create complex systems for integration into biological cascade reactions and in vivo.

With the long-term goal of complementing in vivo natural enzymes with ArMs, we summarize herein three complementary research lines: (i) With the aim of mimicking complex cross-regulation mechanisms prevalent in metabolism, we have engineered enzyme cascades, including cross-regulated reactions, that rely on ArMs. These efforts highlight the remarkable (bio)compatibility and complementarity of ArMs with natural enzymes. (ii) Additionally, multiple-turnover catalysis in the cytoplasm of aerobic organisms was achieved with ArMs that are compatible with a glutathione-rich environment. This feat is demonstrated in HEK-293T cells that are engineered with a gene switch that is upregulated by an ArM equipped with a cell-penetrating module. (iii) Finally, ArMs offer the fascinating prospect of “endowing organometallic chemistry with a genetic memory.” With this goal in mind, we have identified E. coli’s periplasmic space and surface display to compartmentalize an ArM, while maintaining the critical phenotype–genotype linkage. This strategy offers a straightforward means to optimize by directed evolution the catalytic performance of ArMs. Five reactions have been optimized following these compartmentalization strategies: ruthenium-catalyzed olefin metathesis, ruthenium-catalyzed deallylation, iridium-catalyzed transfer hydrogenation, dirhodium-catalyzed cyclopropanation and carbene insertion in C–H bonds. Importantly, >100 turnovers were achieved with ArMs in E. coli whole cells, highlighting the multiple turnover catalytic nature of these systems.

Feedback-Induced Temporal Control of "Breathing" Polymersomes To Create Self-Adaptive Nanoreactors

Here we present the development of self-regulated "breathing" polymersome nanoreactors that show temporally programmable biocatalysis induced by a chemical fuel. pH-sensitive polymersomes loaded with horseradish peroxidase (HRP) and urease were developed. Addition of an acidic urea solution ("fuel") endowed the polymersomes with a transient size increase and permeability enhancement, driving a temporal "ON" state of the HRP enzymatic catalysis; subsequent depletion of fuel led to shrinking of the polymersomes, resulting in the catalytic "OFF" state. Moreover, the nonequilibrium nanoreactors could be reinitiated several cycles as long as fuel was supplied. This feedback-induced temporal control of catalytic activity in polymersome nanoreactors provides a platform for functional nonequilibrium systems as well as for artificial organelles with precisely controlled adaptivity.

Scope and limitations of carbohydrate hydrolysis for de novo glycan sequencing using a hydrogen peroxide/metallopeptide-based glycosidase mimetic

Acidic hydrolysis is commonly used as a first step to break down oligo- and polysaccharides into monosaccharide units for structural analysis. While easy to set up and amenable to mass spectrometry detection, acid hydrolysis is not without its drawbacks. For example, ring-destruction side reactions and degradation products, along with difficulties in optimizing conditions from analyte to analyte, greatly limits its broad utility. Herein we report studies on a hydrogen peroxide/CuGGH metallopeptide-based glycosidase mimetic design for a more efficient and controllable carbohydrate hydrolysis. A library of methyl glycosides consisting of ten common monosaccharide substrates, along with oligosaccharide substrates, was screened with the artificial glycosidase for hydrolytic activity in a high-throughput format with a robotic liquid handling system. The artificial glycosidase was found to be active towards most screened linkages, including alpha- and beta-anomers, thus serving as a potential alternative method for traditional acidic hydrolysis approaches of oligosaccharides.

Catalytic Organic Reactions in Water toward Sustainable Society

Traditional organic synthesis relies heavily on organic solvents for a multitude of tasks, including dissolving the components and facilitating chemical reactions, because many reagents and reactive species are incompatible or immiscible with water. Given that they are used in vast quantities as compared to reactants, solvents have been the focus of environmental concerns. Along with reducing the environmental impact of organic synthesis, the use of water as a reaction medium also benefits chemical processes by simplifying operations, allowing mild reaction conditions, and sometimes delivering unforeseen reactivities and selectivities. After the "watershed" in organic synthesis revealed the importance of water, the development of water-compatible catalysts has flourished, triggering a quantum leap in water-centered organic synthesis. Given that organic compounds are typically practically insoluble in water, simple extractive workup can readily separate a water-soluble homogeneous catalyst as an aqueous solution from a product that is soluble in organic solvents. In contrast, the use of heterogeneous catalysts facilitates catalyst recycling by allowing simple centrifugation and filtration methods to be used. This Review addresses advances over the past decade in catalytic reactions using water as a reaction medium.

Artificial Metalloenzymes on the Verge of New-to-Nature Metabolism

Residing at the interface of chemistry and biotechnology, artificial metalloenzymes (ArMs) offer an attractive technology to combine the versatile reaction repertoire of transition metal catalysts with the exquisite catalytic features of enzymes. While earlier efforts in this field predominantly comprised studies in well-defined test-tube environments, a trend towards exploiting ArMs in more complex environments has recently emerged. Integration of these artificial biocatalysts in enzymatic cascades and using them in whole-cell biotransformations and in vivo opens up entirely novel prospects for both preparative chemistry and synthetic biology. We highlight selected recent developments with a particular focus on challenges and opportunities in the in vivo application of ArMs.

Cross-Regulation of an Artificial Metalloenzyme

Cross-regulation of complex biochemical reaction networks is an essential feature of living systems. In a biomimetic spirit, we report on our efforts to program the temporal activation of an artificial metalloenzyme via cross-regulation by a natural enzyme. In the presence of urea, urease slowly releases ammonia that reversibly inhibits an artificial transfer hydrogenase. Addition of an acid, which acts as fuel, allows to maintain the system out of equilibrium.