Efficient bio-remediation of multiple aromatic hydrocarbons using different types of thermotolerant, ring-cleaving dioxygenases derived from Aeribacillus pallidus HB-1

As toxic contaminants, aromatic compounds are widespread in most environmental matrices, and bioenzymatic catalysis plays a critical role in the degradation of xenobiotics. Here, a thermophillic aromatic hydrocarbon degrader Aeribacillus pallidus HB-1 was found. Bioinformatic analysis of the HB-1 genome revealed two ring-cleaving extradiol dioxygenases (EDOs), among which, EDO-0418 was assigned to a new subfamily of type I.1 EDOs and exhibited a broad substrate specificity, particularly towards biarylic substrate. Both EDOs exhibited optimal activities at elevated temperatures (55 and 65 °C, respectively) and showed remarkable thermostability, pH stability, metal ion resistance and tolerance to chemical reagents. Most importantly, simulated wastewater bioreactor experiments demonstrated efficient and uniform degradation performance of mixed aromatic substrates under harsh environments by the two enzymes combined for potential industrial applications. The unveiling of two thermostable dioxygenases with broad substrate specificities and stress tolerance provides a novel approach for highly efficient environmental bioremediation using composite enzyme systems.

Structural determination and characterisation of the CYP105Q4 cytochrome P450 enzyme from Mycobacterium marinum

The cytochrome P450 family of heme metalloenzymes (CYPs) catalyse important biological monooxygenation reactions. Mycobacterium marinum contains a gene encoding a CYP105Q4 enzyme of unknown function. Other members of the CYP105 CYP family have key roles in bacterial metabolism including the synthesis of secondary metabolites. We produced and purified the cytochrome P450 enzyme CYP105Q4 to enable its characterization. Several nitrogen-donor atom-containing ligands were found to bind to CYP105Q4 generating type II changes in the UV-vis absorbance spectrum. Based on the UV-vis absorbance spectra none of the potential substrate ligands we tested with CYP105Q4 were able to displace the sixth distal aqua ligand from the heme, though there was evidence for binding of oleic acid and amphotericin B. The crystal structure of CYP105Q4 in the substrate-free form was determined in an open conformation. A computational structural similarity search (Dali) was used to find the most closely related characterized relatives within the CYP105 family. The structure of CYP105Q4 enzyme was compared to the GfsF CYP enzyme from Streptomyces graminofaciens which is involved in the biosynthesis of a macrolide polyketide. This structural comparison to GfsF revealed conformational changes in the helices and loops near the entrance to the substrate access channel. A disordered B/C loop region, usually involved in substrate recognition, was also observed.

In vitro Production of Hemin-Based Artificial Metalloenzymes

Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.

The oxidation of steroid derivatives by the CYP125A6 and CYP125A7 enzymes from Mycobacterium marinum

The members of the bacterial cytochrome P450 (CYP) monooxygenase family CYP125, catalyze the oxidation of steroid derivatives including cholesterol and phytosterols, as the initial activating step in their catabolism. However, several bacterial species contain multiple genes encoding CYP125 enzymes and other CYP enzymes which catalyze cholesterol/cholest-4-en-3-one hydroxylation. An important question is why these bacterium have more than one enzyme with overlapping substrate ranges capable of catalyzing the terminal oxidation of the alkyl chain of these sterols. To further understand the role of these enzymes we investigated CYP125A6 and CYP125A7 from Mycobacterium marinum with various cholesterol analogues. These have modifications on the A and B rings of the steroid and we assessed the substrate binding and catalytic activity of these with each enzyme. CYP125A7 gave similar results to those reported for the CYP125A1 enzyme from M. tuberculosis. Differences in the substrate binding and catalytic activity with the cholesterol analogues were observed with CYP125A6. For example, while cholesteryl sulfate could bind to both enzymes it was only oxidized by CYP125A6 and not by CYP125A7. CYP125A6 generated higher levels of metabolites with the majority of C-3 and C-7 substituted cholesterol analogues such 7-ketocholesterol. However, 5α-cholestan-3β-ol was only oxidized by CYP125A7 enzyme. The cholest-4-en-3-one and 7-ketocholesterol-bound forms of the CYP125A6 and CYP125A7 enzymes were modelled using AlphaFold. The structural models highlighted differences in the binding modes of the steroid derivatives within the same enzyme. Significant changes in the binding mode of the steroids between these CYP125 enzymes and other bacterial cholesterol oxidizing enzymes, CYP142A3 and CYP124A1, were also seen. Despite this, all these models predicted the selectivity for terminal methyl hydroxylation, in agreement with the experimental data.

Characterisation of the heme aqua-ligand coordination environment in an engineered peroxygenase cytochrome P450 variant

The cytochrome P450 enzymes (CYPs) are heme-thiolate monooxygenases that catalyse the insertion of an oxygen atom into the C-H bonds of organic molecules. In most CYPs, the activation of dioxygen by the heme is aided by an acid-alcohol pair of residues located in the I-helix of the enzyme. Mutation of the threonine residue of this acid-alcohol pair of CYP199A4, from the bacterium Rhodospeudomonas palustris HaA2, to a glutamate residue induces peroxygenase activity. In the X-ray crystal structures of this variant an interaction of the glutamate side chain and the distal aqua ligand of the heme was observed and this results in this ligand not being readily displaced in the peroxygenase mutant on the addition of substrate. Here we use a range of bulky hydrophobic and nitrogen donor containing ligands in an attempt to displace the distal aqua ligand of the T252E mutant of CYP199A4. Ligand binding was assessed by UV-visible absorbance spectroscopy, native mass spectrometry, electron paramagnetic resonance and X-ray crystallography. None of the ligands tested, even the nitrogen donor ligands which bind directly to the iron in the wild-type enzyme, resulted in displacement of the aqua ligand. Therefore, modification of the I-helix threonine residue to a glutamate residue results in a significant strengthening of the ferric distal aqua ligand. This ligand was not displaced using any of the ligands during this study and this provides a rationale as to why this mutant can shutdown the monooxygenase pathway of this enzyme and switch to peroxygenase activity.

Discovery of a novel series of potent carbonic anhydrase inhibitors with selective affinity for μ Opioid receptor for Safer and long-lasting analgesia

In this study, we investigated the development of dual-targeted ligands that bind to both μ-opioid receptor (MOR) and carbonic anhydrase (CA) enzymes, using fentanyl structure as a template. We synthesized and evaluated 21 novel compounds with dual-targeted affinity identifying the lead candidate compound 8, showing selective affinity for MOR and potent inhibition of several cytosolic CA isoforms. By means of repeated treatment of 3 daily administrations for 17 days, fentanyl (0.1 mg/kg, subcutaneously) led to tolerance development, pain threshold alterations and withdrawal symptoms in CD-1 mice, as well as astrocyte and microglia activation in the dorsal horn of the lumbar spinal cord. In contrast, compound 8 (0.32 mg/kg s.c.) maintained stable during days its analgesic effect at the higher dose tested with fewer withdrawal symptoms, allodynia development and glial cells activation. Our results suggest that targeting both MOR and CA enzymes can lead to the development of new class of potent analgesic agents with fewer side effects and reduced tolerance development. Further studies are needed to explore the potential mechanisms underlying these effects and to further optimize the therapeutic potential of these compounds.

Effect of zero-valent iron nanoparticles on taxonomic composition and hydrogen production from kitchen waste

This study investigated the effects of varying zero-valent iron (ZVI) (0 to 5,000 mg/L) on fermentative hydrogen (H2) production, metabolic pattern, and taxonomic profile by using kitchen waste as substrate. The study demonstrated that the supplementation of 500 mg ZVI/L resulted in the highest H2 yield (219.68 ± 11.19 mL H2/g-volatile solids (VS)added), which was 19% higher than the control. The metabolic pattern analysis showed that acetic and butyric acid production primarily drove the H2 production. The taxonomic analysis further revealed that Firmicutes (relative abundance (RA): 80-96%) and Clostridium sensu stricto 1 (RA: 68-88%) were the dominant phyla and genera, respectively, during the exponential gas production phase, supporting the observation of accumulation of acetic and butyric acids. These findings suggest that supplementation of ZVI can enhance H2 production from organic waste and significantly influence the metabolic pattern and taxonomic profile, including the metalloenzymes.

Room temperature crystallography and X-ray spectroscopy of metalloenzymes

The ultrashort (10s of femtoseconds) X-ray pulses generated by X-ray free electron lasers enable the measurement of X-ray diffraction and spectroscopic data from radiation-sensitive metalloenzymes at room temperature while mostly avoiding the effects of radiation damage usually encountered when performing such experiments at synchrotron sources. Here we discuss an approach to measure both X-ray emission and X-ray crystallographic data at the same time from the same sample volume. The droplet-on-tape setup described allows for efficient sample use and the integration of different reaction triggering options in order to conduct time-resolved studies with limited sample amounts. The approach is illustrated by two examples, photosystem II that catalyzes the light-driven oxidation of water to oxygen, and isopenicillin N synthase, an enzyme that catalyzes the double ring cyclization of a tripeptide precursor into the β-lactam isopenicillin and can be activated by oxygen exposure. We describe the necessary steps to obtain microcrystals of both proteins as well as the operation procedure for the drop-on-tape setup and details of the data acquisition and processing involved in this experiment. At the end, we present how the combination of time-resolved X-ray emission spectra and diffraction data can be used to improve the knowledge about the enzyme reaction mechanism.

Carboxysome-Inspired Electrocatalysis using Enzymes for the Reduction of CO2 at Low Concentrations

The electrolysis of dilute CO2 streams suffers from low concentrations of dissolved substrate and its rapid depletion at the electrolyte-electrocatalyst interface. These limitations require first energy-intensive CO2 capture and concentration, before electrolyzers can achieve acceptable performances. For direct electrocatalytic CO2 reduction from low-concentration sources, we introduce a strategy that mimics the carboxysome in cyanobacteria by utilizing microcompartments with nanoconfined enzymes in a porous electrode. A carbonic anhydrase accelerates CO2 hydration kinetics and minimizes substrate depletion by making all dissolved carbon available for utilization, while a highly efficient formate dehydrogenase reduces CO2 cleanly to formate; down to even atmospheric concentrations of CO2 . This bio-inspired concept demonstrates that the carboxysome provides a viable blueprint for the reduction of low-concentration CO2 streams to chemicals by using all forms of dissolved carbon.

In situ H2O2 Generation by Choline Oxidase and Its Application in Amino Polysaccharide Degradation by Coupling to Lytic Polysaccharide Monooxygenase

Chitin, the most abundant amino polysaccharide in Nature, has many applications in different fields. However, processing of this recalcitrant biopolymer in an environmentally friendly manner remains a major challenge. In this context, lytic polysaccharide monooxygenases (LPMOs) are of interest, as they can act on the most recalcitrant parts of chitin and related insoluble biopolymers such as cellulose. Efficient LPMO catalysis can be achieved by feeding reactions with H2O2, but careful control of H2O2 is required to avoid autocatalytic enzyme inactivation. Herein, we present a coupled enzyme system in which a choline oxidase from Arthrobacter globiformis is employed for controlled in situ generation of H2O2 that fuels LPMO-catalyzed oxidative degradation of chitin. We show that the rate, stability and extent of the LPMO reaction can be manipulated by varying the amount of choline oxidase and/or its substrate, choline chloride, and that efficient peroxygenase reactions may be achieved using sub-μM concentrations of the H2O2-generating enzyme. This coupled system requires only sub-stoichiometric amounts of the reductant that is needed to keep the LPMO in its active, reduced state. It is conceivable that this enzyme system may be used for bioprocessing of chitin in choline-based natural deep eutectic solvents.

The oxidation of cholesterol derivatives by the CYP124 and CYP142 enzymes from Mycobacterium marinum

The CYP124 and CYP142 families of bacterial cytochrome P450 monooxygenases (CYPs), catalyze the oxidation of methyl branched lipids, including cholesterol, as one of the initial activating steps in their catabolism. Both enzymes are reported to supplement the CYP125 family of P450 enzymes. These CYP125 enzymes are found in the same bacteria, and are the primary cholesterol/cholest-4-en-3-one metabolizing enzymes. To further understand the role of the CYP124 and CYP142 cytochrome P450s we investigated the Mycobacterium marinum enzymes, MmarCYP124A1 and CYP142A3, with various cholesterol analogues with modifications on the A and B rings of the steroid. We assessed the substrate binding and catalytic activity of each enzyme. Neither enzyme could bind or oxidize cholesteryl acetate or 3,5-cholestadiene, which have modifications at the C3 hydroxyl moiety of cholesterol. The CYP142 enzyme was better able to accommodate and oxidize cholesterol analogues which have changes on the A/B rings including cholesterol-5α,6α-epoxide and diastereomers of 5-cholestan-3-ol. The CYP124 enzyme was more tolerant of changes at C7 of the cholesterol B ring, e.g., 7-ketocholesterol than in the A ring. The selectivity for oxidation at the ω-carbon of a branched chain was observed in all steroids that were oxidized. The 7-ketocholesterol-bound MmarCYP124A1 enzyme from M. marinum, was structurally characterized by X-ray crystallography to 1.81Å resolution. The 7-ketocholesterol-bound X-ray crystal structure of the MmarCYP124A1 enzyme revealed that the substrate binding mode of this cholesterol derivative was altered compared to those observed with other non-steroidal ligands. The structure provided an explanation for the selectivity of the enzyme for terminal methyl hydroxylation.

Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases"

The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.

The [4Fe-4S]-Cluster of HydF is not Required for the Binding and Transfer of the diiron site of [FeFe]-Hydrogenases

The active site of [FeFe]-hydrogenases contains a cubane [4Fe-4S]-cluster and a unique diiron cluster with biologically unusual CO and CN- ligands. The biogenesis of this diiron site, termed [2FeH], requires the maturation proteins HydE, HydF and HydG. During the maturation process HydF serves as a scaffold protein for the final assembly steps and the subsequent transfer of the [2FeH] precursor, termed [2FeP], to the [FeFe]-hydrogenase. The binding site of [2FeP] in HydF has not been elucidated, however, the [4Fe-4S]-cluster of HydF was considered as a possible binding partner of [2FeP]. By targeting individual amino acids in HydF from Thermosipho melanesiensis using site directed mutagenesis, we examined the postulated binding mechanism as well as the importance and putative involvement of the [4Fe-4S]-cluster for binding and transferring [2FeP]. Surprisingly, our results suggest that binding or transfer of [2FeP] does not involve the proposed binding mechanism or the presence of a [4Fe-4S]-cluster at all.

The catalytic activity and structure of the lipid metabolizing CYP124 cytochrome P450 enzyme from Mycobacterium marinum

The CYP124 family of cytochrome P450 enzymes, as exemplified by CYP124A1 from Mycobacterium tuberculosis, is involved in the metabolism of methyl branched lipids and cholesterol derivatives. The equivalent enzyme from Mycobacterium marinum was investigated to compare the degree of functional conservation between members of this CYP family from closely related bacteria. We compared substrate binding of each CYP124 enzyme using UV-vis spectroscopy and the catalytic oxidation of methyl branched lipids, terpenes and cholesterol derivatives was investigated. The CYP124 enzyme from M. tuberculosis displayed a larger shift to the ferric high-spin state on binding cholesterol derivatives compared to the equivalent enzyme from M. marinum. The biggest difference was observed with cholesteryl sulfate which induced distinct UV-vis spectra in each CYP124 enzyme. The selectivity for oxidation at the ω-carbon of a branched chain was maintained for all substrates, except cholesteryl sulfate which was not oxidized by either enzyme. The CYP124A1 enzyme from M. marinum, in combination with farnesol and farnesyl acetate, was structurally characterized by X-ray crystallography. These ligand-bound structures of the CYP124 enzyme revealed that the polar component of the substrates bound in a different manner to that of phytanic acid in the structure of CYP124A1 from M. tuberculosis. However, closer to the heme the structures were similar providing an explanation for the high selectivity of the enzyme for terminal methyl C-H bond oxidation. The work here demonstrates that there were differences in the biochemistry of the CYP124 enzymes from these closely related bacteria.

Electrochemical Kinetics Support a Second Coordination Sphere Mechanism in Metal-Based Formate Dehydrogenase

Metal-based formate dehydrogenases are molybdenum or tungsten-dependent enzymes that catalyze the interconversion between formate and CO₂ . According to the current consensus, the metal ion of the catalytic center in its active form is coordinated by 6 S (or 5 S and 1 Se) atoms, leaving no free coordination sites to which formate could bind to the metal. Some authors have proposed that one of the active site ligands decoordinates during turnover to allow formate binding. Another proposal is that the oxidation of formate takes place in the second coordination sphere of the metal. Here, we have used electrochemical steady-state kinetics to elucidate the order of the steps in the catalytic cycle of two formate dehydrogenases. Our results strongly support the "second coordination sphere" hypothesis.

Design and synthesis of benzothiazole-based SLC-0111 analogues as new inhibitors for the cancer-associated carbonic anhydrase isoforms IX and XII

In this work, different series of benzothiazole-based sulphonamides 8a-c, 10, 12, 16a-b and carboxylic acids 14a-c were developed as novel SLC-0111 analogues with the goal of generating potent carbonic anhydrase (CA) inhibitors. The adopted strategy involved replacing the 4-fluorophenyl tail in SLC-0111 with a benzothiazole motif that attached to the ureido linker to produce compounds 8c and its regioisomers 8a-b. In addition, the ureido spacer was elongated by methylene or ethylene groups to afford the counterparts 10 and 12. In turn, the primary sulfamoyl zinc binding group (ZBG) was either substituted or replaced by carboxylic acid functionality in order to provide the secondary sulphonamide-based SLC-0111 analogues 16a-b, and the carboxylic acid derivatives 14a-c, respectively. All compounds (8a-c, 10, 12, 14a-c and 16a-b) were tested for their ability to inhibit CA isoforms CA I, II, IX and XII. Additionally, the in vitro anticancer properties of the developed CAIs were evaluated.

Discovery of the First Selective Nanomolar Inhibitors of ERAP2 by Kinetic Target-Guided Synthesis

Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a key enzyme involved in the trimming of antigenic peptides presented by Major Histocompatibility Complex class I. It is a target of growing interest for the treatment of autoimmune diseases and in cancer immunotherapy. However, the discovery of potent and selective ERAP2 inhibitors is highly challenging. Herein, we have used kinetic target-guided synthesis (KTGS) to identify such inhibitors. Co-crystallization experiments revealed the binding mode of three different inhibitors with increasing potency and selectivity over related enzymes. Selected analogues engage ERAP2 in cells and inhibit antigen presentation in a cellular context. 4 d (BDM88951) displays favorable in vitro ADME properties and in vivo exposure. In summary, KTGS allowed the discovery of the first nanomolar and selective highly promising ERAP2 inhibitors that pave the way of the exploration of the biological roles of this enzyme and provide lead compounds for drug discovery efforts.

Essential metals in health and disease

In total, twenty elements appear to be essential for the correct functioning of the human body, half of which are metals and half are non-metals. Among those metals that are currently considered to be essential for normal biological functioning are four main group elements, sodium (Na), potassium (K), magnesium (Mg), and calcium (Ca), and six d-block transition metal elements, manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn) and molybdenum (Mo). Cells have developed various metallo-regulatory mechanisms for maintaining a necessary homeostasis of metal-ions for diverse cellular processes, most importantly in the central nervous system. Since redox active transition metals (for example Fe and Cu) may participate in electron transfer reactions, their homeostasis must be carefully controlled. The catalytic behaviour of redox metals which have escaped control, e.g. via the Fenton reaction, results in the formation of reactive hydroxyl radicals, which may cause damage to DNA, proteins and membranes. Transition metals are integral parts of the active centers of numerous enzymes (e.g. Cu,Zn-SOD, Mn-SOD, Catalase) which catalyze chemical reactions at physiologically compatible rates. Either a deficiency, or an excess of essential metals may result in various disease states arising in an organism. Some typical ailments that are characterized by a disturbed homeostasis of redox active metals include neurological disorders (Alzheimer's, Parkinson's and Huntington's disorders), mental health problems, cardiovascular diseases, cancer, and diabetes. To comprehend more deeply the mechanisms by which essential metals, acting either alone or in combination, and/or through their interaction with non-essential metals (e.g. chromium) function in biological systems will require the application of a broader, more interdisciplinary approach than has mainly been used so far. It is clear that a stronger cooperation between bioinorganic chemists and biophysicists - who have already achieved great success in understanding the structure and role of metalloenzymes in living systems - with biologists, will access new avenues of research in the systems biology of metal ions. With this in mind, the present paper reviews selected chemical and biological aspects of metal ions and their possible interactions in living systems under normal and pathological conditions.

Metalloenzymes for Fatty Acid-Derived Hydrocarbon Biosynthesis: Nature's Cryptic Catalysts

Waning resources, massive energy consumption, everdeepening global warming crisis, and climate change have raised grave concerns regarding continued dependence on fossil fuels as the predominant source of energy and generated tremendous interest for developing biofuels, which are renewable. Hydrocarbon-based 'drop-in' biofuels can be a proper substitute for fossil fuels such as gasoline or jet fuel. In Nature, hydrocarbons are produced by diverse organisms such as insects, plants, bacteria, and cyanobacteria. Metalloenzymes play a crucial role in hydrocarbons biosynthesis, and the past decade has witnessed discoveries of a number of metalloenzymes catalyzing hydrocarbon biosynthesis from fatty acids and their derivatives employing unprecedented mechanisms. These discoveries elucidated the enigma related to the divergent chemistries involved in the catalytic mechanisms of these metalloenzymes. There is substantial diversity in the structure, mode of action, cofactor requirement, and substrate scope among these metalloenzymes. Detailed structural analysis along with mutational studies of some of these enzymes have contributed significantly to identifying the key amino acid residues that dictate substrate specificity and catalytic intricacy. In this Review, we discuss the metalloenzymes that catalyze fatty acid-derived hydrocarbon biosynthesis in various organisms, emphasizing the active site architecture, catalytic mechanism, cofactor requirements, and substrate specificity of these enzymes. Understanding such details is essential for successfully implementing these enzymes in emergent biofuel research through protein engineering and synthetic biology approaches.

Stability of the H-cluster under whole-cell conditions-formation of an Htrans-like state and its reactivity towards oxygen

Hydrogenases are metalloenzymes that catalyze the reversible oxidation of molecular hydrogen into protons and electrons. For this purpose, [FeFe]-hydrogenases utilize a hexanuclear iron cofactor, the H-cluster. This biologically unique cofactor provides the enzyme with outstanding catalytic activities, but it is also highly oxygen sensitive. Under in vitro conditions, oxygen stable forms of the H-cluster denoted H_trans and H_inact can be generated via treatment with sulfide under oxidizing conditions. Herein, we show that an H_trans-like species forms spontaneously under intracellular conditions on a time scale of hours, concurrent with the cells ceasing H₂ production. Addition of cysteine or sulfide during the maturation promotes the formation of this H-cluster state. Moreover, it is found that formation of the observed H_trans-like species is influenced by both steric factors and proton transfer, underscoring the importance of outer coordination sphere effects on H-cluster reactivity.

Photolytic properties of B12-dependent enzymes: A theoretical perspective

The biologically active vitamin B₁₂ derivates, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are ubiquitous organometallic cofactors. In addition to their key roles in enzymatic catalysis, B₁₂ cofactors have complex photolytic properties which have been the target of experimental and theoretical studies. With the recent discovery of B₁₂-dependent photoreceptors, there is an increased need to elucidate the underlying photochemical mechanisms of these systems. This book chapter summarizes the photolytic properties of MeCbl- and AdoCbl-dependent enzymes with particular emphasis on the effect of the environment of the cofactor on the excited state processes. These systems include isolated MeCbl and AdoCbl as well as the enzymes, ethanolamine ammonia-lyase (EAL), glutamate mutase (GLM), methionine synthase (MetH), and photoreceptor CarH. Central to determining the photodissociation mechanism of each system is the analysis of the lowest singlet excited state (S₁) potential energy surface (PES). Time-dependent density functional theory (TD-DFT), employing BP86/TZVPP, is widely used to construct such PESs. Regardless of the environment, the topology of the S₁ PES of AdoCbl or MeCbl is marked by characteristic features, namely the metal-to-ligand charge transfer (MLCT) and ligand field (LF) regions. Conversely, the relative energetics of these electronic states are affected by the environment. Applications and outlooks for Cbl photochemistry are also discussed.

Identification of Cyclopropane Formation in the Biosyntheses of Hormaomycins and Belactosins: Sequential Nitration and Cyclopropanation by Metalloenzymes

Hormaomycins and belactosins are peptide natural products that contain unusual cyclopropane moieties. Bioinformatics analysis of the corresponding biosynthetic gene clusters showed that two conserved genes, hrmI/belK and hrmJ/belL, were potential candidates for catalyzing cyclopropanation. Using in vivo and in vitro assays, the functions of HrmI/BelK and HrmJ/BelL were established. HrmI and BelK, which are heme oxygenase-like dinuclear iron enzymes, catalyze oxidation of the ϵ-amino group of l-lysine to afford l-6-nitronorleucine. Subsequently, HrmJ and BelL, which are iron- and α-ketoglutarate-dependent oxygenases, effectively convert l-6-nitronorleucine into 3-(trans-2-nitrocyclopropyl)-alanine through C4-C6 bond installation. These observations disclose a novel pathway of cyclopropane ring construction and exemplify the new chemistry involving metalloenzymes in natural product biosynthesis.

Identification of indole-based activators of insulin degrading enzyme

Insulin degrading enzyme (IDE) is a zinc metalloprotease that cleaves numerous substrates among which amyloid-β and insulin. It has been linked through genetic studies to the risk of type-2 diabetes (T2D) or Alzheimer's disease (AD). Pharmacological activation of IDE is an attractive therapeutic strategy in AD. While IDE inhibition gave paradoxal activity in glucose homeostasis, recent studies, in particular in the liver suggest that IDE activators could be also of interest in diabetes. Here we describe the discovery of an original series of IDE activators by screening and structure-activity relationships. Early cellular studies show that hit 1 decreases glucose-stimulating insulin secretion. Docking studies revealed it has an unprecedented extended binding to the polyanion-binding site of IDE. These indole-based pharmacological tools are activators of both Aβ and insulin hydrolysis by IDE and could be helpful to explore the multiple roles of IDE.

Emerging artificial metalloenzymes for asymmetric hydrogenation reactions

Artificial metalloenzymes (ArMs) utilize the best properties of homogenous transition metal catalysts and naturally occurring proteins. While synthetic metal complexes offer high tunability and broad-scope reactivity with a variety of substrates, enzymes further endow these complexes with enhanced aqueous stability and stereoselectivity. For these reasons, dozens of ArMs have been designed to perform catalytic asymmetric hydrogenation reactions, and hydrogenase ArMs are, in fact, the oldest class of ArMs. Herein, we report recent advances in the design of hydrogenase ArMs, including (i) the modification of natural [Fe]-hydrogenase by insertion of artificial metallocofactors, (ii) design of a novel ArM system from the tractable and inexpensive protein β-lactoglobulin to afford a high-performing transfer hydrogenase, and (iii) the design of chimeric streptavidin scaffolds that drastically alter the secondary coordination sphere of previously reported streptavidin/biotin transfer hydrogenase ArMs.