Reverse engineering to suggest biologically relevant redox activities of phenolic materials

Multiplexed assessment of engineered bacterial constructs for intracellular β-galactosidase expression by redox amplification on catechol-chitosan modified nanoporous gold

Synthetic biology approaches for rewiring of bacterial constructs to express particular intracellular factors upon induction with the target analyte are emerging as sensing paradigms for applications in environmental and in vivo monitoring. To aid in the design and optimization of bacterial constructs for sensing analytes, there is a need for lysis-free intracellular detection modalities that monitor the signal level and kinetics of expressed factors within different modified bacteria in a multiplexed manner, without requiring cumbersome surface immobilization. Herein, an electrochemical detection system on nanoporous gold that is electrofabricated with a biomaterial redox capacitor is presented for quantifying β-galactosidase expressed inside modified Escherichia coli constructs upon induction with dopamine. This nanostructure-mediated redox amplification approach on a microfluidic platform allows for multiplexed assessment of the expressed intracellular factors from different bacterial constructs suspended in distinct microchannels, with no need for cell lysis or immobilization. Since redox mediators present over the entire depth of the microchannel can interact with the electrode and with the E. coli construct in each channel, the platform exhibits high sensitivity and enables multiplexing. We envision its application in assessing synthetic biology-based approaches for comparing specificity, sensitivity, and signal response time upon induction with target analytes of interest.

Mediated electrochemistry for redox-based biological targeting: entangling sensing and actuation for maximizing information transfer

Biology and electronics are both expert at receiving, analyzing, and responding to information, yet they use entirely different information processing paradigms. Biology processes information using networks that are intrinsically molecular while electronics process information through circuits that control the flow of electrons. There is great interest in coupling the molecular logic of biology with the electronic logic of technology, and we suggest that redox (reduction-oxidation) is a uniquely suited modality for interfacing biology with electronics. Specifically, redox is a native biological modality and is accessible to electronics through electrodes. We summarize recent advances in mediated electrochemistry to direct information transfer into biological systems intentionally altering function, exposing it for more advanced interpretation, which can dramatically expand the biotechnological toolbox.

Redox Electrochemistry to Interrogate and Control Biomolecular Communication

Cells often communicate by the secretion, transport, and perception of molecules. Information conveyed by molecules is encoded, transmitted, and decoded by cells within the context of the prevailing microenvironments. Conversely, in electronics, transmission reliability and message validation are predictable, robust, and less context dependent. In turn, many transformative advances have resulted by the formal consideration of information transfer. One way to explore this potential for biological systems is to create bio-device interfaces that facilitate bidirectional information transfer between biology and electronics. Redox reactions enable this linkage because reduction and oxidation mediate communication within biology and can be coupled with electronics. By manipulating redox reactions, one is able to combine the programmable features of electronics with the ability to interrogate and modulate biological function. In this review, we examine methods to electrochemically interrogate the various components of molecular communication using redox chemistry and to electronically control cell communication using redox electrogenetics.

Catechol-Based Capacitor for Redox-Linked Bioelectronics

A common bioelectronics goal is to enable communication between biology and electronics, and success is critically dependent on the communication modality. When a biorelevant modality aligns with instrumentation capabilities, remarkable successes have been observed (e.g., electrodes provide a powerful tool to observe and actuate biology through its ion-based electrical modality). Emerging biological research demonstrates that redox is another biologically relevant modality, and recent research has shown that advanced electrochemical methods enable biodevice communication through this redox modality. Here, we briefly summarize the biological relevance of this redox modality and the use of redox mediators to enable access to this modality through electrochemical measurements. Next, we describe the fabrication of a catechol-chitosan redox capacitor that is redox-active but nonconducting and thus offers a unique set of molecular electronic properties that enhance access to redox-based information. Finally, we cite several recent studies that demonstrate the broad potential for this capacitor to access redox-based biological information. In summary, we envision the redox capacitor will become a vital component in the integrated circuitry of redox-linked bioelectronics.

Pro- and Anti-oxidant Properties of Redox-Active Catechol-Chitosan Films

Catechols are abundant in nature and are believed to perform diverse biological functions that include photoprotection (e.g., melanins), molecular signaling (e.g., catecholamine neurotransmitters), and mechanical adhesion (e.g., mussel glue). Currently, the structure-property-function relationships for catechols remain poorly resolved, and this is especially true for redox-based properties (e.g., antioxidant, pro-oxidant, and radical scavenging activities). Importantly, there are few characterization methods available to probe the redox properties of materials. In this review, we focus on recent studies with redox-active catechol-chitosan films. First, we describe film fabrication methods to oxidatively-graft catechols to chitosan through chemical, enzymatic, or electrochemical methods. Second, we discuss a new experimental characterization method to probe the redox properties of catechol-functionalized materials. This mediated electrochemical probing (MEP) method probes the redox-activities of catechol-chitosan films by: (i) employing diffusible mediators to shuttle electrons between the electrode and grafted catechols; (ii) imposing tailored sequences of input voltages to “tune” redox probing; and (iii) analyzing the output current response characteristics to infer properties. Finally, we demonstrate that the redox properties of catechol-chitosan films enable them to perform antioxidant radical scavenging functions, as well as a pro-oxidant (reactive oxygen-generation) antimicrobial functions. In summary, our increasing knowledge of catechol-chitosan films is enabling us to better-understand the functions of catechols in biology as well as enhancing our capabilities to create advanced functional materials.

The Analgesic Acetaminophen and the Antipsychotic Clozapine Can Each Redox-Cycle with Melanin

Melanins are ubiquitous but their complexity and insolubility has hindered characterization of their structures and functions. We are developing electrochemical reverse engineering methodologies that focus on properties and especially on redox properties. Previous studies have shown that melanins (i) are redox-active and can rapidly and repeatedly exchange electrons with diffusible oxidants and reductants, and (ii) have redox potentials in midregion of the physiological range. These properties suggest the functional activities of melanins will depend on their redox context. The brain has a complex redox context with steep local gradients in O₂ that can promote redox-cycling between melanin and diffusible redox-active chemical species. Here, we performed in vitro reverse engineering studies and report that melanins can redox-cycle with two common redox-active drugs. Experimentally, we used two melanin models: a convenient natural melanin derived from cuttlefish (Sepia melanin) and a synthetic cysteinyldopamine-dopamine core-shell model of neuromelanin. One drug, acetaminophen (APAP), has been used clinically for over a century, and recent studies suggest that low doses of APAP can protect the brain from oxidative-stress-induced toxicity and neurodegeneration, while higher doses can have toxic effects in the brain. The second drug, clozapine (CLZ), is a second generation antipsychotic with polypharmacological activities that remain incompletely understood. These in vitro observations suggest that the redox activities of drugs may be relevant to their modes-of-action, and that melanins may interact with drugs in ways that affect their activities, metabolism, and toxicities.

Review of Electrochemically Triggered Macromolecular Film Buildup Processes and Their Biomedical Applications

Macromolecular coatings play an important role in many technological areas, ranging from the car industry to biosensors. Among the different coating technologies, electrochemically triggered processes are extremely powerful because they allow in particular spatial confinement of the film buildup up to the micrometer scale on microelectrodes. Here, we review the latest advances in the field of electrochemically triggered macromolecular film buildup processes performed in aqueous solutions. All these processes will be discussed and related to their several applications such as corrosion prevention, biosensors, antimicrobial coatings, drug-release, barrier properties and cell encapsulation. Special emphasis will be put on applications in the rapidly growing field of biosensors. Using polymers or proteins, the electrochemical buildup of the films can result from a local change of macromolecules solubility, self-assembly of polyelectrolytes through electrostatic/ionic interactions or covalent cross-linking between different macromolecules. The assembly process can be in one step or performed step-by-step based on an electrical trigger affecting directly the interacting macromolecules or generating ionic species.

Catechol-Based Hydrogel for Chemical Information Processing

Catechols offer diverse properties and are used in biology to perform various functions that range from adhesion (e.g., mussel proteins) to neurotransmission (e.g., dopamine), and mimicking the capabilities of biological catechols have yielded important new materials (e.g., polydopamine). It is well known that catechols are also redox-active and we have observed that biomimetic catechol-modified chitosan films are redox-active and possess interesting molecular electronic properties. In particular, these films can accept, store and donate electrons, and thus offer redox-capacitor capabilities. We are enlisting these capabilities to bridge communication between biology and electronics. Specifically, we are investigating an interactive redox-probing approach to access redox-based chemical information and convert this information into an electrical modality that facilitates analysis by methods from signal processing. In this review, we describe the broad vision and then cite recent examples in which the catechol–chitosan redox-capacitor can assist in accessing and understanding chemical information. Further, this redox-capacitor can be coupled with synthetic biology to enhance the power of chemical information processing. Potentially, the progress with this biomimetic catechol–chitosan film may even help in understanding how biology uses the redox properties of catechols for redox signaling.

Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology

The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O₂ for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H₂O₂) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this electrochemical tool for in vitro redox-probing.

Using a Redox Modality to Connect Synthetic Biology to Electronics: Hydrogel-Based Chemo-Electro Signal Transduction for Molecular Communication

A hydrogel-based dual film coating is electrofabricated for transducing bio-relevant chemical information into electronical output. The outer film has a synthetic biology construct that recognizes an external molecular signal and transduces this input into the expression of an enzyme that converts redox-inactive substrate into a redox-active intermediate, which is detected through an amplification mechanism of the inner redox-capacitor film.

Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels

The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing.

Paraquat-Melanin Redox-Cycling: Evidence from Electrochemical Reverse Engineering

Parkinson's disease is a neurodegenerative disorder associated with oxidative stress and the death of melanin-containing neurons of the substantia nigra. Epidemiological evidence links exposure to the pesticide paraquat (PQ) to Parkinson's disease, and this link has been explained by a redox cycling mechanism that induces oxidative stress. Here, we used a novel electrochemistry-based reverse engineering methodology to test the hypothesis that PQ can undergo reductive redox cycling with melanin. In this method, (i) an insoluble natural melanin (from Sepia melanin) and a synthetic model melanin (having a cysteinyldopamine-melanin core and dopamine-melanin shell) were entrapped in a nonconducting hydrogel film adjacent to an electrode, (ii) the film-coated electrode was immersed in solutions containing PQ (putative redox cycling reductant) and a redox cycling oxidant (ferrocene dimethanol), (iii) sequences of input potentials (i.e., voltages) were imposed to the underlying electrode to systematically engage reductive and oxidative redox cycling, and (iv) output response currents were analyzed for signatures of redox cycling. The response characteristics of the PQ-melanin systems to various input potential sequences support the hypothesis that PQ can directly donate electrons to melanin. This observation of PQ-melanin redox interactions demonstrates an association between two components that have been individually linked to oxidative stress and Parkinson's disease. Potentially, melanin's redox activity could be an important component in understanding the etiology of neurological disorders such as Parkinson's disease.

Electrochemical Probing through a Redox Capacitor To Acquire Chemical Information on Biothiols

The acquisition of chemical information is a critical need for medical diagnostics, food/environmental monitoring, and national security. Here, we report an electrochemical information processing approach that integrates (i) complex electrical inputs/outputs, (ii) mediators to transduce the electrical I/O into redox signals that can actively probe the chemical environment, and (iii) a redox capacitor that manipulates signals for information extraction. We demonstrate the capabilities of this chemical information processing strategy using biothiols because of the emerging importance of these molecules in medicine and because their distinct chemical properties allow evaluation of hypothesis-driven information probing. We show that input sequences can be tailored to probe for chemical information both qualitatively (step inputs probe for thiol-specific signatures) and quantitatively. Specifically, we observed picomolar limits of detection and linear responses to concentrations over 5 orders of magnitude (1 pM–0.1 μM). This approach allows the capabilities of signal processing to be extended for rapid, robust, and on-site analysis of chemical information.

HyPer Family Probes: State of the Art

SIGNIFICANCE

Hydrogen peroxide (H2O2) is not only a key mediator of oxidative stress but also one of the most important cellular second messengers. This small short-lived molecule is involved in the regulation of a wide range of different biological processes, including regulation of cellular signaling pathways. Studying the role of H2O2 in living systems would be challenging without modern approaches. A genetically encoded fluorescent biosensor, HyPer, is one of the most effective tools for this purpose.

RECENT ADVANCES

HyPer has been used by many investigators of redox signaling in various models of different scales: from cytoplasmic subcompartments and single cells to tissues of whole organisms. In many studies, the results obtained using HyPer have enabled a better understanding of the roles of H2O2 in these biological processes. However, much remains to be learned.

CRITICAL ISSUES

In this review, we focus on the uses of HyPer. We provide a general description of HyPer and its improved versions. Separate chapters are devoted to the results obtained by various groups who have used this biosensor for their experiments in living cells and organisms.

FUTURE DIRECTIONS

HyPer is an effective tool for H2O2 imaging in living systems as indicated by the increasing numbers of publications each year since its development. However, this biosensor requires further improvements. In particular, much brighter and more pH-stable versions of HyPer are necessary for imaging in mammalian tissues. Antioxid. Redox Signal. 24, 731-751.

Reverse Engineering Applied to Red Human Hair Pheomelanin Reveals Redox-Buffering as a Pro-Oxidant Mechanism

Pheomelanin has been implicated in the increased susceptibility to UV-induced melanoma for people with light skin and red hair. Recent studies identified a UV-independent pathway to melanoma carcinogenesis and implicated pheomelanin's pro-oxidant properties that act through the generation of reactive oxygen species and/or the depletion of cellular antioxidants. Here, we applied an electrochemically-based reverse engineering methodology to compare the redox properties of human hair pheomelanin with model synthetic pigments and natural eumelanin. This methodology exposes the insoluble melanin samples to complex potential (voltage) inputs and measures output response characteristics to assess redox activities. The results demonstrate that both eumelanin and pheomelanin are redox-active, they can rapidly (sec-min) and repeatedly redox-cycle between oxidized and reduced states, and pheomelanin possesses a more oxidative redox potential. This study suggests that pheomelanin's redox-based pro-oxidant activity may contribute to sustaining a chronic oxidative stress condition through a redox-buffering mechanism.

Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery?

High-throughput biology has contributed a wealth of data on chemicals, including natural products (NPs). Recently, attention was drawn to certain, predominantly synthetic, compounds that are responsible for disproportionate percentages of hits but are false actives. Spurious bioassay interference led to their designation as pan-assay interference compounds (PAINS). NPs lack comparable scrutiny, which this study aims to rectify. Systematic mining of 80+ years of the phytochemistry and biology literature, using the NAPRALERT database, revealed that only 39 compounds represent the NPs most reported by occurrence, activity, and distinct activity. Over 50% are not explained by phenomena known for synthetic libraries, and all had manifold ascribed bioactivities, designating them as invalid metabolic panaceas (IMPs). Cumulative distributions of ∼200,000 NPs uncovered that NP research follows power-law characteristics typical for behavioral phenomena. Projection into occurrence–bioactivity–effort space produces the hyperbolic black hole of NPs, where IMPs populate the high-effort base.

Rapid and repeatable redox cycling of an insoluble dietary antioxidant: electrochemical analysis

There are many unresolved questions concerning the health benefits of dietary antioxidants due in part to the complexity of the materials and mechanisms of action. We applied a new electrochemical method and report new observations for one of the richest sources of dietary antioxidants. We observed that the insoluble fraction of clove is redox-active and can be rapidly and repeatedly switched between oxidized and reduced states. Also, the radical scavenging antioxidant properties of insoluble clove are largely independent of this reversible redox activity, which is similar to observations made with the natural phenolic melanin. In contrast to melanin, insoluble clove was observed to have little pro-oxidant activity (as measured by H2O2 generation) irrelevant to whether it was poised in an oxidized or reduced state. These results suggest that dietary antioxidants, even when insoluble and nonabsorbed, can undergo important redox interactions in the intestinal tract.

Information processing through a bio-based redox capacitor: signatures for redox-cycling

Redox-cycling compounds can significantly impact biological systems and can be responsible for activities that range from pathogen virulence and contaminant toxicities, to therapeutic drug mechanisms. Current methods to identify redox-cycling activities rely on the generation of reactive oxygen species (ROS), and employ enzymatic or chemical methods to detect ROS. Here, we couple the speed and sensitivity of electrochemistry with the molecular-electronic properties of a bio-based redox-capacitor to generate signatures of redox-cycling. The redox capacitor film is electrochemically-fabricated at the electrode surface and is composed of a polysaccharide hydrogel with grafted catechol moieties. This capacitor film is redox-active but non-conducting and can engage diffusible compounds in either oxidative or reductive redox-cycling. Using standard electrochemical mediators ferrocene dimethanol (Fc) and Ru(NH3)6Cl3 (Ru(3+)) as model redox-cyclers, we observed signal amplifications and rectifications that serve as signatures of redox-cycling. Three bio-relevant compounds were then probed for these signatures: (i) ascorbate, a redox-active compound that does not redox-cycle; (ii) pyocyanin, a virulence factor well-known for its reductive redox-cycling; and (iii) acetaminophen, an analgesic that oxidatively redox-cycles but also undergoes conjugation reactions. These studies demonstrate that the redox-capacitor can enlist the capabilities of electrochemistry to generate rapid and sensitive signatures of biologically-relevant chemical activities (i.e., redox-cycling).