Kinetics of the urea–urease clock reaction with urease immobilized in hydrogel beads

Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises

Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.

Specific anion effects on urease activity: A Hofmeister study

The effects of a range of electrolytes on the hydrolysis of urea by the enzyme urease is explored. The autocatalytic behavior of urease in unbuffered solutions and its pH clock reactions are studied. The concentration dependence of the experimental variables is analyzed in terms of specific ion-enzyme interactions and hydration. The results offer insights into the molecular mechanisms of the enzyme, and on the nature of its interactions with the electrolytes. We found that urease can tolerate mild electrolytes in its environment, while it is strongly inhibited by both strong kosmotropic and strong chaotropic anions. This study may cast light on an alternative therapy for Helicobacter pylori infections and contribute to the design of innovative materials and provide new approaches for the modulation of the enzymatic activity.

Poly(acrylamide)-co-poly(hydroxyethyl)methacrylate-co-poly(cyclohexyl methacrylate) hydrogel platform for stability, storage and biocatalytic applications of urease

In our present work, an explicit crosslinked thermo-responsive hydrogel platform has been developed, by using polyacrylamide (PAAm), poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(cyclohexyl methacrylate) (PCHMA), and then coupled with urease to yield bioconjugates (BCs). Synergic effect of these polymer units provides thermoresponsive nature, optimum crosslinking with desired swelling behaviour, and stability and improved catalytic to Urease in the resultant BCs. Synthesis of the terpolymer has been achieved by employing HEMA (monomer as well as crosslinker), instead of using the conventional crosslinkers, through free radical solution polymerization technique. Various grades of TRPUBs have been fabricated by varying HEMA and CHMA contents while keeping fixed amounts of AAm. Further, the structural analysis of BCs has been done by fourier transform infra-red spectroscopic study and their thermal stabilities have been studied by thermogravimetric analysis. Urea present in TRPUBs has beenanalysed for its hydrolysis atdifferent temperatures viz., 25 °C, 45 °C and 70 °C. Further, the effect of crosslinking, temperature and reaction time on catalytic activities of TRPUBs has been studied. TRPUBs grades have showna maximum swelling capacity up to 5200 %; excellent catalytic activity even at 70 °C; and 85 % activity retention after 18 days storage in buffer medium.

Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.

4D-printed needle panel meters coupled with enzymatic derivatization for reading urea and glucose concentrations in biological samples

On-site analytical techniques continue being developed with advances in modern technology. To demonstrate the applicability of four-dimensional printing (4DP) technologies in the direct fabrication of stimuli-responsive analytical devices for on-site determination of urea and glucose, we used digital light processing three-dimensional printing (3DP) and 2-carboxyethyl acrylate (CEA)-incorporated photocurable resins to fabricate all-in-one needle panel meters. When adding a sample having a value of pH above the pKa of CEA (ca. 4.6-5.0) into the fabricated needle panel meter, the [H+]-responsive layer of the needle, printed using the CEA-incorporated photocurable resins, swelled as a result of electrostatic repulsion among the dissociated carboxyl groups of the copolymer, leading to [H+]-dependent bending of the needle. When coupled with a derivatization reaction (urease-mediated hydrolysis of urea to decrease [H+]; glucose oxidase-mediated oxidization of glucose to increase [H+]), the bending of the needle allowed reliable quantification of urea or glucose when referencing pre-calibrated concentration scales. After method optimization, the method's detection limits for urea and glucose were 4.9 and 7.0 μM, respectively, within a working concentration range from 0.1 to 10 mM. We verified the reliability of this analytical method by determining the concentrations of urea and glucose in samples of human urine, fetal bovine serum, and rat plasma with spike analyses and comparing the results with those obtained using commercial assay kits. Our results confirm that 4DP technologies can allow the direct fabrication of stimuli-responsive devices for quantitative chemical analysis, and that they can advance the development and applicability of 3DP-enabling analytical methods.

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.

Newly designed acrylamide derivative-based pH-responsive hydrogel-urease bioconjugates: synthesis and catalytic urea hydrolysis

Jack bean urease, the first nickel metalloenzyme, and crystallized enzymes have historical significance due to their several applications in the biomedical and other fields. For the first time, cross-linker free pH-responsive hydrogel-urease bioconjugates have been reported. Without the use of divinyl benzene or divinyl acrylamide derivatives, urease was immobilized inside the hydrogel matrix and various grades of bioconjugates were synthesized. The hydrogel-urease bioconjugate exhibits excellent swelling-deswelling and pH-responsive characteristics without affecting the urease enzyme. The pH-responsive bioconjugates were characterized by FT-IR, powder XRD, SEM, TGA, and UV-vis spectroscopy. Urea hydrolysis and enzyme affinity have been investigated at pH 4, pH 7, and pH 11 using bioconjugates and free urease. At basic pH, BCs showed excellent enzyme activity. In summary, this technique is effective for stabilizing biomacromolecules at different pHs for a variety of real applications.

Inhibition of the urea-urease reaction by the components of the zeolite imidazole frameworks-8 and the formation of urease-zinc-imidazole hybrid compound

In the past decade, much effort has been devoted to using chemical clock-type reactions in material design and driving the self-assembly of various building blocks. Urea-urease enzymatic reaction has chemical pH clock behavior in an unbuffered medium, in which the induction time and the final pH can be programmed by the concentrations of the reagents. The urea-urease reaction can offer a new alternative in material synthesis, where the pH and its course in time are crucial factors in the synthesis. However, before using it in any synthesis method, it is important to investigate the possible effects of the reagents on the enzymatic reaction. Here we investigate the effect of the reagents of the zeolite imidazole framework-8 (zinc ions and 2-methylimidazole) on the urea-urease reaction. We have chosen the zeolite imidazole framework-8 because its formation serves as a model reaction for the formation of other metal–organic frameworks. We found that, besides the inhibition effect of the zinc ions which is well-known in the literature, 2-methylimidazole inhibits the enzymatic reaction as well. In addition to the observed inhibition effect, we report the formation of a hybrid urease-zinc-2-methylimidazole hybrid material. To support the inhibition effect, we developed a kinetic model which reproduced qualitatively the experimentally observed kinetic curves.

Stochastic pH Oscillations in a Model of the Urea-Urease Reaction Confined to Lipid Vesicles

The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators.

Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures

Compartmentalized reaction networks regulating signal processing, communication and pattern formation are central to living systems. Towards achieving life-like materials, we compartmentalized urea-urease and more complex urea-urease/ester-esterase pH-feedback reaction networks into hydrogel spheres and investigate how fuel-driven pH fronts can be sent out from these spheres and regulated by internal reaction networks. Membrane characteristics are installed by covering urease spheres with responsive hydrogel shells. We then encapsulate the two networks (urea-urease and ester-esterase) separately into different hydrogel spheres to devise communication, pattern formation and attraction. Moreover, these pH fronts and patterns can be used for self-growing hydrogels, and for developing complex geometries from non-injectable hydrogels without 3D printing tools. This study opens possibilities for compartmentalized feedback reactions and their use in next generation materials fabrication.

pH-Sensitive Oscillatory Motion of a Urease Motor on the Urea Aqueous Phase

A self-propelled object coupled with an enzyme reaction between urease and urea was investigated at the air/aqueous interface. A plastic object that was fixed to a urease-immobilized filter paper was used as a self-propelled object, termed a urease motor, placed on an aqueous urea solution. The driving force of the urease motor is the difference in the surface tension around the object. Oscillatory motion or no motion was triggered depending on the initial pH of the urea solution. Both the frequency and maximum speed of the oscillatory motion varied depending on the initial pH of the water phase. The mechanisms underlying the oscillatory motion and no motion were discussed in relation to the bell-shaped enzyme activity of urease in the enzyme reaction and the surface tension around the urease motor.

Hydrogels and Their Role in Biosensing Applications

Hydrogels play an important role in the field of biomedical research and diagnostic medicine. They are emerging as a powerful tool in the context of bioanalytical assays and biosensing. In this context, this review gives an overview of different hydrogels and the role they adopt in a range of applications. Not only are hydrogels beneficial for the immobilization and embedding of biomolecules, but they are also used as responsive material, as wearable devices, or as functional material. In particular, the scientific and technical progress during the last decade is discussed. The newest hydrogel types, their synthesis, and many applications are presented. Advantages and performance improvements are described, along with their limitations.

Stimuli responsive dynamic transformations in supramolecular gels

Supramolecular gels are formed by the self-assembly of small molecules under the influence of various non-covalent interactions. As the interactions are individually weak and reversible, it is possible to perturb the gels easily, which in turn enables fine tuning of their properties. Synthetic supramolecular gels are kinetically trapped and usually do not show time variable changes in material properties after formation. However, such materials potentially become switchable when exposed to external stimuli like temperature, pH, light, enzyme, redox, and chemical analytes resulting in reconfiguration of gel matrix into a different type of network. Such transformations allow gel-to-gel transitions while the changes in the molecular aggregation result in alteration of physical and chemical properties of the gel with time. Here, we discuss various methods that have been used to achieve gel-to-gel transitions by modifying a pre-formed gel material through external perturbation. We also describe methods that allow time-dependent autonomous switching of gels into different networks enabling synthesis of next generation functional materials. Dynamic modification of gels allows construction of an array of supramolecular gels with various properties from a single material which eventually extend the limit of applications of the gels. In some cases, gel-to-gel transitions lead to materials that cannot be accessed directly. Finally, we point out the necessity and possibility of further exploration of the field.

Programming properties of transient hydrogels by an enzymatic reaction

Supramolecular gels are usually stable in time as they are formed under thermodynamic equilibrium or at least in a deep well of a kinetically trapped state. However, artificial construction of kinetically controlled transient supramolecular gels is an interesting challenge. In these systems, usually a kinetically trapped transient aggregate is formed by active building blocks that leads to gelation; the gel then typically returns to the solution state. In this work, we show that such transient aggregation can occur by successive formation of two distinctly different kinetically controlled metastable states. Control over the first metastable state allows us to achieve significant control over the stability and properties of the second metastable state.

Annealing Supramolecular Gels by a Reaction Relay

Supramolecular gels have potential in many areas. In many cases, a major drawback is that the gels are formed at a high rate. As a result, nonoptimal, kinetically trapped self-assembled structures are often formed, leading to gels that can be hard to reproduce and control. One method to get around kinetic trapping is annealing. Thermal annealing is one possibility, but it is not always desirable to heat the gels. Here, we describe a method to anneal pH-triggered gels after they are formed. We employ a reaction relay in a peptide-based hydrogel system to anneal the structures by a controlled and uniform pH change. Our method allows us to prepare gels with more controlled properties. We show that this can be used to enable homogeneous "molding and casting" of the hydrogels. This method of annealing is more effective in improving gel robustness than a conventional heat-cool cycle.

Immobilization adjusted clock reaction in the urea–urease–H+ reaction system

The bell-shaped reactivity-pH curve is the fundamental reason that the temporal programmable kinetic switch in clock reactions can be obtained in bio-competitive enzymatic reactions. In this work, urease was loaded on small resin particles through ionic binding. Experimental results reveal that the immobilization not only increased the stability of the enzyme and the reproducibility of the clock reaction, but also shifted the bell-shaped activity curve to lower pHs. The latter change enables the clock reaction to occur from an initial pH of 2.3, where the free enzyme had already lost its activity. Two mechanisms explain the influence of the immobilization on the clock reaction. Immobilization modified the pH sensitive functional groups on the enzyme, shifting the activity curve to a more acidic region, and reduced diffusion alters the enzyme dynamics.

The reported immobilization shifts the bell-shaped reactivity-pH curve to lower pHs and enables the clock reaction to occur from a very low initial pH, where the free enzyme had already lost its activity.

Developing potential Helicobacter pylori urease inhibitors from novel oxoindoline derivatives: Synthesis, biological evaluation and in silico study

By recruiting the important moiety from Shikonin, a series of novel oxoindoline derivatives S1-S20 have been synthesized for inhibiting H. pylori urease. The most potent compound S18 displayed better activity (IC₅₀ = 0.71 μM; MIC = 0.48 μM) than the positive controls AHA (IC₅₀ = 17.2 μM) and Metronidazole (MIC = 31.3 μM). With low cytotoxicity, it showed considerable potential for further development. Docking simulation revealed the possible binding pattern of this series. 3D QSAR model was built to discuss SAR and give useful hints for future modification.