Single Amino Acid Switch between a Flavin-Dependent Dehalogenase and Nitroreductase

Single-Electron Oxidation Triggered by Visible-Light-Excited Enzymes for Asymmetric Biocatalysis

By integrating enzymatic catalysis with photocatalysis, photoenzymatic catalysis emerges as a powerful strategy to enhance enzyme catalytic capabilities and provide superior stereocontrol in reactions involving reactive intermediates. Repurposing naturally occurring enzymes using visible light is among the most active directions of photoenzymatic catalysis. This Minireview focuses on a cutting-edge strategy in this direction, namely single-electron-oxidation-triggered non-natural biotransformations catalyzed by photoexcited enzymes. These straightforward transformations feature a unique radical mechanism initiated by single-electron oxidation, achieving redox-neutral non-natural C-C, C-O, and C-S bond formation, and expanding the chemical toolbox of enzymes. By highlighting recent advances in this field and emphasizing their catalytic mechanisms and synthetic potential, innovative approaches for photobiomanufacturing are anticipated.

Flavin-Mediated Reductive Deiodination: Conformational Events and Reactivity Pattern in the Active Site of Human Iodotyrosine Deiodinase

Human iodotyrosine deiodinase (hIYD) catalyzes the reductive deiodination of iodotyrosine using a flavin mononucleotide cofactor to maintain the iodine concentration in the body. Mutations in the hIYD gene are linked to human hypothyroidism, emphasizing its role in thyroid function regulation. The present work employs microsecond-scale molecular dynamics simulations and quantum chemical calculations to elucidate the conformational dynamics and reactivity in the active site at various stages of hIYD enzymatic cycle. The flavin is found to employ a unique butterfly motion of its isoalloxazine ring accompanied by a novel active-and-resting state of its ribose 2'-OH group at different stages of the enzymatic cycle. The flavin dynamics are found to control substrate binding affinity, the active site lid closure, and NADPH recognition. The predicted hIYD model shows enhanced stabilization of NADPH due to additional interactions with the N-terminal and intermediate domains. The enzyme uses a group of basic residues (R100, R101, R104, K182, and R279) to stabilize flavin in different stages of catalysis, suggesting potential mutations to control enzyme activity. The reactivity descriptors and stereoelectronic analysis predict the N5 nitrogen of flavin as a proton source during the reductive deiodination, while the anisotropic charge distribution on the halogen atom has negligible structural and electronic effects. The present findings provide key insights into the molecular basis of hIYD activity and lay the groundwork for future research aimed at therapeutic interventions and industrial applications.

Nitroreductase-Based "Turn-On" Fluorescent Probe for Bacterial Identification with Visible Features

Among pathogenic bacteria, Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa were the six leading causes for the deaths associated with antibiotic resistance in 2019. Although new treatment options are urgently needed, the precise identification of the bacterial species remains pivotal for an accurate diagnosis and effective treatment. Clinically, mass spectrometry is used to distinguish these bacteria based on their protein mass pattern at the genus and species level. Herein, we report an alternative approach to identify these bacteria using the nitroreductase-based "turn-on" fluorescent probes (ETH1-NO2 and ETH2-NO2), with potential visual indicators for the six individual bacteria species. The limits of detection (LODs) of the probes for NTRs are 0.562 (ETH1-NO2) and 0.153 μg/mL (ETH2-NO2), respectively. They respond effectively to both Gram-positive and Gram-negative bacteria, with the lowest LOD at 1.2 × 106 CFU/mL for E. coli. In particular, different bacteria show noticeable difference in the apparent color of ETH1-NO2 samples, allowing possible identification of these bacteria visually. In addition, ETH1-NO2 also has potential applications in bacterial fluorescence imaging. Thus, our study provides an alternative approach for bacteria identification and new reagents for bacteria imaging.

Polar Interactions between Substrate and Flavin Control Iodotyrosine Deiodinase Function

Flavin cofactors offer a wide range of chemical mechanisms to support a great diversity in catalytic function. As a corollary, such diversity necessitates careful control within each flavoprotein to limit its function to an appropriate subset of possible reactions and substrates. This task falls to the protein environment surrounding the flavin in most enzymes. For iodotyrosine deiodinase that catalyzes a reductive dehalogenation of halotyrosines, substrates can dictate the chemistry available to the flavin. Their ability to stabilize the necessary one-electron reduced semiquinone form of flavin strictly depends on a direct coordination between the flavin and α-ammonium and carboxylate groups of its substrates. While perturbations to the carboxylate group do not significantly affect binding to the resting oxidized form of the deiodinase, dehalogenation (kcat/Km) is suppressed by over 2000-fold. Lack of the α-ammonium group abolishes detectable binding and dehalogenation. Substitution of the ammonium group with a hydroxyl group does not restore measurable binding but does support dehalogenation with an efficiency greater than those of the carboxylate derivatives. Consistent with these observations, the flavin semiquinone does not accumulate during redox titration in the presence of inert substrate analogues lacking either the α-ammonium or carboxylate groups. As a complement, a nitroreductase activity based on hydride transfer is revealed for the appropriate substrates with perturbations to their zwitterion.

19F NMR Reveals the Dynamics of Substrate Binding and Lid Closure for Iodotyrosine Deiodinase as a Complement to Steady-State Kinetics and Crystallography

Active site lids are common features of enzymes and typically undergo conformational changes upon substrate binding to promote catalysis. Iodotyrosine deiodinase is no exception and contains a lid segment in all of its homologues from human to bacteria. The solution-state dynamics of the lid have now been characterized using 19F NMR spectroscopy with a CF3-labeled enzyme and CF3O-labeled ligands. From two-dimensional 19F-19F NMR exchange spectroscopy, interconversion rates between the free and bound states of a CF3O-substituted tyrosine (45 ± 10 s-1) and the protein label (40 ± 3 s-1) are very similar and suggest a correlation between ligand binding and conformational reorganization of the lid. Both occur at rates that are ∼100-fold faster than turnover, and therefore these steps do not limit catalysis. A simple CF3O-labeled phenol also binds to the active site and induces a conformational change in the lid segment that was not previously detectable by crystallography. Exchange rates of the ligand (130 ± 20 s-1) and protein (98 ± 8 s-1) in this example are faster than those above but remain self-consistent to affirm a correlation between ordering of the lid and binding of the ligand. Both ligands also protect the protein from limited proteolysis, as expected from their ability to stabilize a compact lid structure. However, the minimal turnover of simple phenol substrates indicates that such stabilization may be necessary but is not sufficient for efficient catalysis.

A single-molecule fluorescent probe for visualizing viscosity and hypoxia in lysosomes and zebrafish embryos

Viscosity and hypoxia, as microenvironment parameters, play important roles in maintaining normal biological processes and homeostasis. Therefore, simultaneous and sensitive detection of these elements with simple and effective methods could offer precise information in biology. Here, we report a two-site lysosome-targeting fluorescent probe, NVP, for monitoring viscosity and nitroreductase with dual emission channels (emission shift is 86 nm). The NVP probe has displayed highly sensitive and selective responses towards viscosity and nitroreductase, respectively. Significantly, the fluctuations of viscosity and NTR have been detected in vitro and in vivo. We expect that the dual-responsive fluorescent NVP probe will become a potential molecular tool for the exploration of deeper functions of viscosity and hypoxia.

Nitroreductase-responsive nanoparticles for in situ fluorescence imaging and synergistic antibacterial therapy of bacterial keratitis

As bacterial keratitis progresses rapidly, prompt intervention is necessary. Current diagnostic processes are time-consuming and invasive, leading to improper antibiotics for treatment. Therefore, innovative strategies for diagnosing and treating bacterial keratitis are urgently needed. In this study, Cu2-xSe@BSA@NTRP nanoparticles were developed by loading nitroreductase-responsive probes (NTRPs) onto Cu2-xSe@BSA. These nanoparticles exhibited integrated fluorescence imaging and antibacterial capabilities. In vitro and in vivo experiments showed that the nanoparticles produced responsive fluorescence signals in bacteria within 30 min due to an interaction between the released NTRP and bacterial endogenous nitroreductase (NTR). When combined with low-temperature photothermal therapy (PTT), the nanoparticles effectively eliminated E. coli and S. aureus, achieved antibacterial efficacy above 95% and facilitated the re-epithelialization process at the corneal wound site in vivo. Overall, the Cu2-xSe@BSA@NTRP nanoparticles demonstrated potential for rapid, noninvasive in situ diagnosis, treatment, and visualization assessment of therapy effectiveness in bacterial keratitis.

The 2'-hydroxy group of flavin mononucleotide influences the catalytic function and promiscuity of the flavoprotein iodotyrosine dehalogenase

The isoalloxazine ring system of the flavin cofactor is responsible for much of the catalytic power and diversity associated with flavoproteins. While the specificity of these enzymes is greatly influenced by the surrounding protein environment, the ribityl group of the cofactor may also participate in stabilizing transient intermediates formed by substrates and flavin. A conserved interaction between the phenolate oxygen of l-iodotyrosine and the 2'-hydroxy group of flavin mononucleotide (FMN) bound to iodotyrosine deiodianase (IYD) implied such a contribution to catalysis. Reconstitution of this deiodinase with 2'-deoxyflavin mononucleotide (2'-deoxyFMN) decreased the overall catalytic efficiency of l-iodotyrosine dehalogenation (kcat/Km) by more than 5-fold but increased kcat by over 2-fold. These affects are common to human IYD and its homolog from Thermotoga neapolitana and are best explained by an ability of the 2'-hydroxy group of FMN to stabilize association of the substrate in its phenolate form. Loss of this 2'-hydroxy group did not substantially affect the formation of the one electron reduced semiquinone form of FMN but its absence released constraints that otherwise suppresses the ability of IYD to promote hydride transfer as measured by a competing nitroreductase activity. Generation of IYD containing 2'-deoxyFMN also removed steric constraints that had previously limited the use of certain mechanistic probes. For example, l-O-methyl iodotyrosine could be accommodated in the active site lacking the 2'-hydroxy of FMN and shown to be inert to dehalogenation as predicted from a mechanism requiring ketonization of the phenolic oxygen. In the future, ancillary sites within a cofactor should now be considered when engineering new functions within existing protein architectures as demonstrated by the ability of IYD to promote nitroreduction after loss of the 2'-hydroxy group of FMN.

Substrate Electronics Dominate the Rate of Reductive Dehalogenation Promoted by the Flavin-Dependent Iodotyrosine Deiodinase

Iodotyrosine deiodinase (IYD) is unusual in its reliance on flavin to promote reductive dehalogenation of halotyrosines under aerobic conditions. Applications of this activity can be envisioned for bioremediation, but expansion of its specificity requires an understanding of the mechanistic steps that limit the rate of turnover. Key processes capable of controlling steady-state turnover have now been evaluated and described in this study. While proton transfer is necessary for converting the electron-rich substrate into an electrophilic intermediate suitable for reduction, kinetic solvent deuterium isotope effects suggest that this process does not contribute to the overall efficiency of catalysis under neutral conditions. Similarly, reconstituting IYD with flavin analogues demonstrates that a change in reduction potential by as much as 132 mV affects kcat by less than 3-fold. Furthermore, kcat/Km does not correlate with reduction potential and indicates that electron transfer is also not rate determining. Catalytic efficiency is most sensitive to the electronic nature of its substrates. Electron-donating substituents on the ortho position of iodotyrosine stimulate catalysis and conversely electron-withdrawing substituents suppress catalysis. Effects on kcat and kcat/Km range from 22- to 100-fold and fit a linear free-energy correlation with a ρ ranging from -2.1 to -2.8 for human and bacterial IYD. These values are consistent with a rate-determining process of stabilizing the electrophilic and nonaromatic intermediate poised for reduction. Future engineering can now focus on efforts to stabilize this electrophilic intermediate over a broad series of phenolic substrates that are targeted for removal from our environment.

Two-Photon Small-Molecule Fluorogenic Probes for Visualizing Endogenous Nitroreductase Activities from Tumor Tissues of a Cancer Patient

Nitroreductase (NTR), a common enzymatic biomarker of hypoxia, is widely used to evaluate tumor microenvironments. To date, numerous optical probes have been reported for NTRs detection. Approaches capable of concisely guiding the probe design of NTRs suitable for deep-tissue imaging, however, are still lacking. As such, direct optical imaging of endogenous NTR activities from tumors derived from cancer patients is thus far not possible. Herein, aided by computational calculations, the authors have successfully developed a series of two-photon (TP) small-molecule fluorogenic probes capable of sensitively detecting general NTR activities from various biological samples; by optimizing the distance between the recognition moiety and the reactive site of NTRs from different sources, the authors have discovered and experimentally proven that X4 displays the best performance in both sensitivity and selectivity. Furthermore, X4 shows excellent TP excited fluorescence properties capable of directly monitoring/imaging endogenous NTR activities from live mammalian cells, growing zebrafish, and tumor-bearing mice. Finally, with an outstanding TP tissue-penetrating imaging property, X4 is used, for the first time, to successfully detect endogenous NTR activities from the liver lysates and cardia tissues of a cancer patient. The work may provide a universal strategy to design novel TP small-molecule enzymatic probes in future clinical applications.

Sequence Conservation Does Not Always Signify a Functional Imperative as Observed in the Nitroreductase Superfamily

Consensus sequences have the potential to help classify the structure and function of proteins and highlight key regions that may contribute to their biological properties. Often, the level of significance will track with the extent of sequence conservation, but this should not be considered universal. Arg and Lys dominate a position adjacent to the N1 and C2 carbonyl of flavin mononucleotide (FMN) bound in the proteins of the nitroreductase superfamily. Although this placement satisfies expectations for stabilizing the reduced form of FMN, the substitution of these residues in three subfamilies promoting distinct reactions demonstrates their importance to catalysis as only modest. Replacing Arg34 with Lys, Gln, or Glu enhances FMN binding to a flavin destructase (BluB) by twofold and diminishes FMN turnover by no more than 25%. Similarly, replacing Lys14 with Arg, Gln, or Glu in a nitroreductase (NfsB) does not perturb the binding of the substrate nitrofurazone. The catalytic efficiency does decrease by 21-fold for the K14Q variant, but no change in the midpoint potential of FMN was observed with any of the variants. Equivalent substitution at Arg38 in iodotyrosine deiodinase (IYD) affects catalysis even more modestly (<10-fold). While the Arg/Lys to Glu substitution inactivates NfsB and IYD, this change also stabilizes one-electron transfer in IYD contrary to predictions based on other classes of flavoproteins. Accordingly, functional correlations developed in certain structural superfamilies may not necessarily translate well to other superfamilies.

MicroPET imaging of bacterial infection with nitroreductase-specific responsive 18F-labelled nitrogen mustard analogues

PURPOSE

Bacterial infection and antibiotic resistance are serious threats to human health. This study aimed to develop two novel radiotracers, ¹⁸F-NTRP and ¹⁸F-NCRP, that possess a specific nitroreductase (NTR) response to image deep-seated bacterial infections using positron emission tomography (PET). This method can distinguish infection from sterile inflammation.

METHODS

¹⁸F-NTRP and ¹⁸F-NCRP were synthesized via a one-step method; all the steps usually involved in tracer radiosynthesis were successfully adapted in the All-In-One automated module. After the physiochemical properties of ¹⁸F-NTRP and ¹⁸F-NCRP were characterized, their specificity and selectivity for NTR were verified in E. coli and S. aureus. The ex vivo biodistribution of the tracers was evaluated in normal mice. MicroPET-CT imaging was performed in mouse models of bacterial infection and inflammation after the administration of ¹⁸F-NTRP or ¹⁸F-NCRP.

RESULTS

Fully automated radiosynthesis of ¹⁸F-NTRP and ¹⁸F-NCRP was achieved within 90-110 min with overall decay-uncorrected, isolated radiochemical yields of 21.24 ± 4.25% and 11.3 ± 3.78%, respectively. The molar activities of ¹⁸F-NTRP and ¹⁸F-NCRP were 320 ± 40 GBq/μmol and 275 ± 33 GBq/µmol, respectively. In addition, ¹⁸F-NTRP and ¹⁸F-NCRP exhibited high selectivity and specificity for NTR response. PET-CT imaging in bacteria-infected mouse models with ¹⁸F-NTRP or ¹⁸F-NCRP showed significant radioactivity uptake in either E. coli- or S. aureus-infected muscles. The uptake for E. coli-infected muscles, 2.4 ± 0.2%ID/g with ¹⁸F-NTRP and 4.05 ± 0.49%ID/g with ¹⁸F-NCRP, was up to three times greater than that for uninfected control muscles. Furthermore, for both ¹⁸F-NTRP and ¹⁸F-NCRP, the uptake in bacterial infection was 2.6 times higher than that in sterile inflammation, allowing an effective distinction of infection from inflammation.

CONCLUSION

¹⁸F-NTRP and ¹⁸F-NCRP are worth further investigation to verify their potential clinical application for distinguishing bacterial infection from sterile inflammation via their specific NTR responsiveness.

Tuning the Quantum Chemical Properties of Flavins via Modification at C8

Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH₂, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.

Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR

Proteins like NADH:ubiquinone oxidoreductase (NQR), an essential enzyme and ion pump in the physiology of several pathogenic bacteria, tightly regulate the redox properties of their cofactors. Although flavin mononucleotide (FMN) is fully reduced in aqueous solution, FMN in subunits B and C of NQR exclusively undergo one-electron transitions during its catalytic cycle. Here, we perform ab initio calculations and molecular dynamics simulations to elucidate the mechanisms that regulate the redox state of FMN in NQR. QM/MM calculations show that binding site electrostatics disfavor anionic forms of FMNH₂ , but permit a neutral form of the fully reduced flavin. The potential energy surface is unaffected by covalent bonding between FMN and threonine. Molecular dynamics simulations show that the FMN binding sites are inaccessible by water, suggesting that further reductions of the cofactors are limited or prohibited by the availability of water and other proton donors. These findings provide a deeper understanding of the mechanisms used by NQR to regulate electron transfer through the cofactors and perform its physiologic role. They also provide the first, to our knowledge, evidence of the simple concept that proteins regulate flavin redox states via water occlusion.

Self-Calibrating Bipartite Fluorescent Sensor for Nitroreductase Activity and Its Application to Cancer and Hypoxic Cells

Aromatic nitro compounds are reduced to their corresponding amino derivatives by nitroreductases (NTR), while identification and characterization of the corresponding enzymes in mammalian systems are yet unrevealed. However, mammalian NTR activity has been considered as a favorable target in development of theranostic agents for cancer and hypoxia of solid tumors. Currently, small molecule-based fluorescent probes have emerged as a valuable assay tool for NTR activity. However, there has been a limit to comparing NTR activity between different cells, since most probes have relied on fluorescence changes that are affected by not only enzymatic activity but also nonenzymatic factors. Here, we developed a self-calibrating bipartite fluorescent probe, consisting of NTR-sensitive nitronaphthalimide and nonsensitive coumarin moieties. Thereby, it was possible to compare the relative NTR activity by monitoring fluorescence ratios in noncancerous and some cancerous cells and to demonstrate for certain that the elevated NTR activity is associated with cancer cells and hypoxia states.

Evolutionary aspects of the Viridiplantae nitroreductases

Background

Nitroreductases are a family of evolutionarily related proteins catalyzing the reduction of nitro-substituted compounds. Nitroreductases are widespread enzymes, but nearly all modern research and practical application have been concentrated on the bacterial proteins, mainly nitroreductases of Escherichia coli. The main aim of this study is to describe the phylogenic distribution of the nitroreductases in the photosynthetic eukaryotes (Viridiplantae) to highlight their structural similarity and areas for future research and application.

Results

This study suggests that homologs of nitroreductase proteins are widely presented also in Viridiplantae. Maximum likelihood phylogenetic tree reconstruction method and comparison of the structural models suggest close evolutional relation between cyanobacterial and Viridiplantae nitroreductases.

Conclusions

This study provides the first attempt to understand the evolution of nitroreductase protein family in Viridiplantae. Our phylogeny estimation and preservation of the chloroplasts/mitochondrial localization indicate the evolutional origin of the plant nitroreductases from the cyanobacterial endosymbiont. A defined high level of the similarity on the structural level suggests conservancy also for the functions. Directions for the future research and industrial application of the Viridiplantae nitroreductases are discussed.

The potential of bacterial cultures to degrade the mutagen 2-methyl-1,4-dinitro-pyrrole in a processed meat model

Processed meats are classified by the International Agency for Research on Cancer as category 1 because their consumption increase the incidence of colorectal and stomach cancers. Meat processing widely employs nitrite and sorbate as preservatives. When these preservatives are concomitantly used in non-compliant processes, they may react and produce the mutagen 2-methyl-1,4-dinitro-pyrrole (DNMP). This study aimed to evaluate the ability of different bacteria isolated from food matrices to biodegrade DNMP in in vitro reactions and in a processed meat model. A possible mechanism of biodegradation was also tested. In vitro experiments were performed in two steps. In the first one, only one strain out of 13 different species did not interact with DNMP. In the following step, an empirical conversion factor was calculated to assess the conversion of DNMP to 4-amino-2-methyl-1-nitro-pyrrole by the strains. The most efficient strains were Staphylococcus xylosus LYOCARNI SXH-01, Lactobacillus fermentum LB-UFSC 0017, and Lactobacillus casei LB-UFSC 0019, which yielded conversion factors of 0.62, 0.60, and 0.43, respectively. Thus, such strains were individually added to the processed meat model and completely degraded the DNMP. Moreover, S. xylosus degraded DNMP in less than 30 min. The enzymatic mechanism was evaluated using its cell-free extract. It showed that, in the aerobic system, reduction rates were 30.321 and 22.411 nmol/mg of protein/min using NADH and NADPH, respectively. A DNMP reductase was assigned to the extract and a potential presence of an oxygen insensitive nitroreductase type I B was considered. Thus, biotechnological processes may be an efficient strategy to eliminate the DNMP from meat products and to increase food safety.

An Activatable NIR Fluorescent Rosol for Selectively Imaging Nitroreductase Activity

Hypoxia (pO₂ ≤ ~1.5%) is an important characteristic of tumor microenvironments that directly correlates with resistance against first-line therapies and tumor proliferation/infiltration. The ability to accurately identify hypoxic tumor cells/tissue could afford tailored therapeutic regimens for personalized treatment, development of more-effective therapies, and discerning the mechanisms underlying disease progression. Fluorogenic constructs identifying aforesaid cells/tissue operate by targeting the bioreductive activity of primarily nitroreductases (NTRs), but collectively present photophysical and/or physicochemical shortcomings that could limit effectiveness. To overcome these limitations, we present the rational design, development, and evaluation of the first activatable ultracompact xanthene core-based molecular probe (NO ₂ -Rosol) for selectively imaging NTR activity that affords an "OFF-ON" near-infrared (NIR) fluorescence response (> 700 nm) alongside a remarkable Stokes shift (> 150 nm) via NTR activity-facilitated modulation to its energetics whose resultant interplay discontinues an intramolecular d-PET fluorescence-quenching mechanism transpiring between directly-linked electronically-uncoupled π-systems comprising its components. DFT calculations guided selection of a suitable fluorogenic scaffold and nitroaromatic moiety candidate that when adjoined could (i) afford such photophysical response upon bioreduction by upregulated NTR activity in hypoxic tumor cells/tissue and (ii) employ a retention mechanism strategy that capitalizes on an inherent physical property of the NIR fluorogenic scaffold for achieving signal amplification. NO ₂ -Rosol demonstrated 705 nm NIR fluorescence emission and 157 nm Stokes shift, selectivity for NTR over relevant bioanalytes, and a 28-/12-fold fluorescence enhancement in solution and between cells cultured under different oxic conditions, respectively. In establishing feasibility for NO ₂ -Rosol to provide favorable contrast levels in solutio/vitro, we anticipate NO ₂ -Rosol doing so in preclinical studies.

Engineering Escherichia coli NfsB To Activate a Hypoxia-Resistant Analogue of the PET Probe EF5 To Enable Non-Invasive Imaging during Enzyme Prodrug Therapy

Gene-directed enzyme prodrug therapy (GDEPT) uses tumor-tropic vectors to deliver prodrug-converting enzymes such as nitroreductases specifically to the tumor environment. The nitroreductase NfsB from Escherichia coli (NfsB_Ec) has been a particular focal point for GDEPT and over the past 25 years has been the subject of several engineering studies seeking to improve catalysis of prodrug substrates. To facilitate clinical development, there is also a need to enable effective non-invasive imaging capabilities. SN33623, a 5-nitroimidazole analogue of 2-nitroimidazole hypoxia probe EF5, has potential for PET imaging exogenously delivered nitroreductases without generating confounding background due to tumor hypoxia. However, we show here that SN33623 is a poor substrate for NfsB_Ec. To address this, we used assay-guided sequence and structure analysis to identify two conserved residues that block SN33623 activation in NfsB_Ec and close homologues. Introduction of the rational substitutions F70A and F108Y into NfsB_Ec conferred high levels of SN33623 activity and enabled specific labeling of E. coli expressing the engineered enzyme. Serendipitously, the F70A and F108Y substitutions also substantially improved activity with the anticancer prodrug CB1954 and the 5-nitroimidazole antibiotic prodrug metronidazole, which is a potential biosafety agent for targeted ablation of nitroreductase-expressing vectors.

Redox control of iodotyrosine deiodinase

The redox chemistry of flavoproteins is often gated by substrate and iodotyrosine deiodinase (IYD) has the additional ability to switch between reaction modes based on the substrate. Association of fluorotyrosine (F-Tyr), an inert substrate analog, stabilizes single electron transfer reactions of IYD that are not observed in the absence of this ligand. The co-crystal of F-Tyr and a T239A variant of human IYD have now been characterized to provide a structural basis for control of its flavin reactivity. Coordination of F-Tyr in the active site of this IYD closely mimics that of iodotyrosine and only minor perturbations are observed after replacement of an active site Thr with Ala. However, loss of the side chain hydroxyl group removes a key hydrogen bond from flavin and suppresses the formation of its semiquinone intermediate. Even substitution of Thr with Ser decreases the midpoint potential of human IYD between its oxidized and semiquinone forms of flavin by almost 80 mV. This decrease does not adversely affect the kinetics of reductive dehalogenation although an analogous Ala variant exhibits a 6.7-fold decrease in its kcat /Km . Active site ligands lacking the zwitterion of halotyrosine are not able to induce closure of the active site lid that is necessary for promoting single electron transfer and dehalogenation. Under these conditions, a basal two-electron process dominates catalysis as indicated by preferential reduction of nitrophenol rather than deiodination of iodophenol.

Oxidative dehalogenation and denitration by a flavin-dependent monooxygenase is controlled by substrate deprotonation

Enzymes that are capable of detoxifying halogenated phenols (HPs) and nitrophenols (NPs) are valuable for bioremediation and waste biorefining. HadA monooxygenase was found to perform dual functions of oxidative dehalogenation (hydroxylation plus halide elimination) and denitration (hydroxylation plus nitro elimination). Rate constants associated with individual steps of HadA reactions with phenol, halogenated phenols and nitrophenols were measured using combined transient kinetic approaches of stopped-flow absorbance/fluorescence and rapid-quench flow techniques. Density functional theory was used to calculate the thermodynamic and electronic parameters associated with hydroxylation and group elimination steps. These parameters were correlated with the rate constants of hydroxylation, group elimination, and overall product formation to identify factors controlling individual steps. The results indicated that the hydroxylation rate constant is higher when the pK a of the phenolic group is lower, i.e. it is more easily deprotonated, but not higher when the energy gap between the E LUMO of the C4a-hydroperoxy-FAD intermediate and the E HOMO of the phenolate substrate is lower. These data suggest that the substrate deprotonation has a higher energy barrier than the -OH transfer, and thus controls the hydroxylation step. For the group elimination, the process is controlled by the ability of the C-X bond to break. For the overall product formation (hydroxylation and group elimination combined), this analysis showed that the rate constant of product formation is dependent on the pK a value of the substrate, indicating that the overall reaction is controlled by substrate deprotonation. This step also likely has the highest energy barrier and thus controls the overall process of oxidative dehalogenation and denitration by HadA. This report is the first to identify a key mechanistic factor controlling the enzymatic processes of oxidative dehalogenation and denitration.

Informing Efforts to Develop Nitroreductase for Amine Production

Nitroreductases (NRs) hold promise for converting nitroaromatics to aromatic amines. Nitroaromatic reduction rate increases with Hammett substituent constant for NRs from two different subgroups, confirming substrate identity as a key determinant of reactivity. Amine yields were low, but compounds yielding amines tend to have a large π system and electron withdrawing substituents. Therefore, we also assessed the prospects of varying the enzyme. Several different subgroups of NRs include members able to produce aromatic amines. Comparison of four NR subgroups shows that they provide contrasting substrate binding cavities with distinct constraints on substrate position relative to the flavin. The unique architecture of the NR dimer produces an enormous contact area which we propose provides the stabilization needed to offset the costs of insertion of the active sites between the monomers. Thus, we propose that the functional diversity included in the NR superfamily stems from the chemical versatility of the flavin cofactor in conjunction with a structure that permits tremendous active site variability. These complementary properties make NRs exceptionally promising enzymes for development for biocatalysis in prodrug activation and conversion of nitroaromatics to valuable aromatic amines. We provide a framework for identifying NRs and substrates with the greatest potential to advance.

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold.

The distribution and mechanism of iodotyrosine deiodinase defied expectations

Iodotyrosine deiodinase (IYD) is unusual for its reliance on flavin to promote reductive dehalogenation under aerobic conditions. As implied by the name, this enzyme was first discovered to catalyze iodide elimination from iodotyrosine for recycling iodide during synthesis of tetra- and triiodothyronine collectively known as thyroid hormone. However, IYD likely supports many more functions and has been shown to debrominate and dechlorinate bromo- and chlorotyrosines. A specificity for halotyrosines versus halophenols is well preserved from humans to bacteria. In all examples to date, the substrate zwitterion establishes polar contacts with both the protein and the isoalloxazine ring of flavin. Mechanistic data suggest dehalogenation is catalyzed by sequential one electron transfer steps from reduced flavin to substrate despite the initial expectations for a single two electron transfer mechanism. A purported flavin semiquinone intermediate is stabilized by hydrogen bonding between its N5 position and the side chain of a Thr. Mutation of this residue to Ala suppresses dehalogenation and enhances a nitroreductase activity that is reminiscent of other enzymes within the same structural superfamily.

Conversion of a Dehalogenase into a Nitroreductase by Swapping its Flavin Cofactor with a 5-Deazaflavin Analogue

Natural and engineered nitroreductases have rarely supported full reduction of nitroaromatics to their amine products, and more typically, transformations are limited to formation of the hydroxylamine intermediates. Efficient use of these enzymes also requires a regenerating system for NAD(P)H to avoid the costs associated with this natural reductant. Iodotyrosine deiodinase is a member of the same structural superfamily as many nitroreductases but does not directly consume reducing equivalents from NAD(P)H, nor demonstrate nitroreductase activity. However, exchange of its flavin cofactor with a 5-deazaflavin analogue dramatically suppresses its native deiodinase activity and leads to significant nitroreductase activity that supports full reduction to an amine product in the presence of the convenient and inexpensive NaBH₄ .

Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase

The minimal requirements for substrate recognition and turnover by iodotyrosine deiodinase were examined to learn the basis for its catalytic specificity. This enzyme is crucial for iodide homeostasis and the generation of thyroid hormone in chordates. 2-Iodophenol binds only very weakly to the human enzyme and is dehalogenated with a k_cat/K_m that is more than 4 orders of magnitude lower than that for iodotyrosine. This discrimination likely protects against a futile cycle of iodinating and deiodinating precursors of thyroid hormone biosynthesis. Surprisingly, a very similar catalytic selectivity was expressed by a bacterial homologue from Haliscomenobacter hydrossis. In this example, discrimination was not based on affinity since 4-cyano-2-iodophenol bound to the bacterial deiodinase with a K_d lower than that of iodotyrosine and yet was not detectably deiodinated. Other phenols including 2-iodophenol were deiodinated but only very inefficiently. Crystal structures of the bacterial enzyme with and without bound iodotyrosine are nearly superimposable and quite similar to the corresponding structures of the human enzyme. Likewise, the bacterial enzyme is activated for single electron transfer after binding to the substrate analogue fluorotyrosine as previously observed with the human enzyme. A cocrystal structure of bacterial deiodinase and 2-iodophenol indicates that this ligand stacks on the active site flavin mononucleotide (FMN) in a orientation analogous to that of bound iodotyrosine. However, 2-iodophenol association is not sufficient to activate the FMN chemistry required for catalysis, and thus the bacterial enzyme appears to share a similar specificity for halotyrosines even though their physiological roles are likely very different from those in humans.

A universal fluorometric assay strategy for glycosidases based on functional carbon quantum dots: β-galactosidase activity detection in vitro and in living cells

The development of highly sensitive assays for glycosidases is of critical significance to understand their functions, facilely detect associated diseases and screen potential new drugs. In this work, we develop a universal assay strategy for glycosidase enzymes and inhibitor screening based on functional carbon quantum dots through a combined host-guest recognition and specific static quenching-induced signal transduction mechanism. This detection strategy is established in terms of the following facts: (1) β-cyclodextrin as a perfect host can selectively associate with p-nitrophenol due to its hydrophobic character and right size match of the cavity, which renders specific binding between β-cyclodextrin and p-nitrophenol via a host-guest recognition. (2) The formation of an inclusion complex between β-cyclodextrin modified carbon quantum dots (β-CD-CQDs) and p-nitrophenol results in fluorescence quenching with a high quenching efficiency due to the static quenching mechanism. Glycoconjugates of p-nitrophenol as the substrates could be rapidly hydrolyzed to corresponding glycose and p-nitrophenol in the presence of specific glycosidase, and the resulting p-nitrophenol induces the following host-guest interaction and static quenching leading to a change in the fluorescence signal. The activity of different glycosidase enzymes could be evaluated in the same way as long as the glycosyl unit of glycosylated substrates was changed. Here we take β-galactosidase as an example to demonstrate the applicability of the proposed detection strategy because it can act as a molecular target for primary ovarian cancers. A highly sensitive assay for β-galactosidase activity in terms of linear correlation of the fluorescence change with the β-galactosidase level was established with a low detection limit of 0.6 U L^-1. Its function of inhibitor screening was also assessed by using d-galactal as the inhibitor for β-galactosidase, and the positive results indicated its feasibility to screen potential inhibitors. It is also illustrated that the nanoprobe possesses excellent biocompatibility, and can sensitively monitor the intracellular β-galactosidase level in ovarian cancer cells. This work provides a general detection method for glycosidase activity, demonstrates its applicability of monitoring the enzyme level in living cells, and broadens fluorogenic probes in fluorescence-guided diagnostics.

A two-photon fluorescent probe for nitroreductase imaging in living cells, tissues and zebrafish under hypoxia conditions

A two-photon fluorescent probe FNTR, constructed for nitroreductase by using a fluorine derivative as a TP fluorophore and a p-nitrobenzyl carbamate group as a recognition domain, was successfully applied to detect endogenous NTR in living cells, tissues and zebrafish.

A novel off–on fluorescent probe for sensitive imaging of mitochondria-specific nitroreductase activity in living tumor cells

We have developed a novel fluorescent probe of a benzoindocyanine probe (BICP), which is able to target mitochondria and realize sensitive and selective detection of NTR.

Functional analysis of iodotyrosine deiodinase from drosophila melanogaster

The flavoprotein iodotyrosine deiodinase (IYD) was first discovered in mammals through its ability to salvage iodide from mono- and diiodotyrosine, the by-products of thyroid hormone synthesis. Genomic information indicates that invertebrates contain homologous enzymes although their iodide requirements are unknown. The catalytic domain of IYD from Drosophila melanogaster has now been cloned, expressed and characterized to determine the scope of its potential catalytic function as a model for organisms that are not associated with thyroid hormone production. Little discrimination between iodo-, bromo-, and chlorotyrosine was detected. Their affinity for IYD ranges from 0.46 to 0.62 μM (K_d ) and their efficiency of dehalogenation ranges from 2.4 - 9 x 10³ M^-1 s^-1 (k_cat /K_m ). These values fall within the variations described for IYDs from other organisms for which a physiological function has been confirmed. The relative contribution of three active site residues that coordinate to the amino acid substrates was subsequently determined by mutagenesis of IYD from Drosophila to refine future annotations of genomic and meta-genomic data for dehalogenation of halotyrosines. Substitution of the active site glutamate to glutamine was most detrimental to catalysis. Alternative substitution of an active site lysine to glutamine affected substrate affinity to the greatest extent but only moderately affected catalytic turnover. Substitution of phenylalanine for an active site tyrosine was least perturbing for binding and catalysis.