Structure and function of the cytochrome P450 peroxygenase enzymes

In-vitro optimization and active-site mutagenesis of CYP105D18 peroxygenase enhance the production of indigo

Practical implementation of efficient biocatalysts for large-scale production of indigo remains challenging. Microbial cytochrome P450s may be useful for indigo production, but this has been rarely reported. We discovered that CYP105D18 catalysed H2O2-mediated C-3 hydroxylation of indole to synthesize indigo. A cell-free lysate from Escherichia coli containing CYP105D18 peroxygenase obtained after cell disruption was optimized for in vitro reaction. Next, 250 µM hydroxylamine was added to the cell-free lysate to inhibit other H2O2-utilizing enzymes that interfere with the CYP105D18 function. Furthermore, the active-site residues of CYP105D18, namely L87, A235, A282, and I386, involved in indole binding were mutated. L87F resulted in an approximately 12-fold increase in CYP105D18 activity. The catalytic efficiencies of the wild-type and L87F mutant were 0.01 and 0.12 mM-1min-1, respectively. Fed-batch fermentation using enriched autoinduction medium was used for higher production of E. coli cells containing CYP105D18 peroxygenase. The Cell-free lysate of disrupted cells yielded 710 mg/L of indigo in 20 min. This represents a simple enzymatic approach for indigo biosynthesis using cell-free lysate of E. coli overexpressing CYP105D18, H2O2, and catalase inhibitor without the need for multi enzyme systems and expensive cofactors. This single-enzyme system, used in a rapid process for indigo formation, could serve as an efficient approach for commercial bio-indigo production.

Insights into the Imidaclothiz Biodegradation by the White-Rot Fungus Phanerochaete sordida YK-624 under Ligninolytic Conditions

Imidaclothiz (IMZ), an innovative neonicotinoid insecticide, has attracted significant interest due to its environmental persistence and consequent ecological implications. In this research, the white-rot fungus Phanerochaete sordida YK-624 was used to degrade IMZ, unveiling a novel fungal degradation mechanism. The results demonstrated that IMZ was efficiently degraded by P. sordida YK-624. Transcriptomic analysis revealed that IMZ-induced stress triggered a cascade of enzymatic and cellular defense responses that are instrumental in facilitating its biodegradation. Through inhibitor experiments and enzyme activity profiling, cytochrome P450 and manganese peroxidase (MnP) were identified to play crucial roles in IMZ biodegradation. Additionally, three metabolites were isolated and identified by NMR, and two innovative degradation pathways involving hydroxylation and nitro reduction were proposed. Toxicity assessment suggested the reduced environmental risk of IMZ after its degradation by P. sordida YK-624. These findings provided insights into the IMZ degradation mechanism and highlighted the potential of white-rot fungi in neonicotinoid bioremediation.

Oxidovanadium(IV) Porphyrin-Imidazole Complex-Catalyzed One-Pot, Three-Component Green Synthesis of Biologically Active Pyrano[2,3-d]pyrimidine and 4H-Chromene Heterocycles

A β-functionalized porphyrin ligand {H2TPP(Phen)}, has been synthesized and subsequently employed as a dibasic tetradentate ligand in synthesizing its vanadyl complex 2-(1H-imidazo[4,5-f][1,10]phenanthroline-2-yl)-5,10,15,20-tetraphenylporphyrinatooxido-vanadium(IV)[VIVOTPP(Phen)] (1). Comprehensive characterization of the ligand {H2TPP(Phen)} and its vanadyl(IV) complex (1) was achieved through various analytical and spectroscopic techniques, including NMR, ultraviolet-visible (UV-vis), EPR, and MALDI-TOF mass spectrometry and elemental analysis. Electrochemical studies indicated that the free base porphyrin {H2TPP(Phen)} tends to four successive reduction peaks and two oxidation peaks observed in cyclic voltammetry. In contrast, the metalated complex [VIVOTPP(Phen)] displayed two successive reversible reductions and two oxidation peaks. The synthesized vanadyl(IV)-porphyrin complex (1) was further employed as an efficient and reusable catalyst in an environmentally friendly, one-pot, three-component synthesis of biologically and clinically relevant pyrano[2,3-d]pyrimidine (Ca-Ch, Da-Dg) and 4H-chromene (Ga-Gj, Ha-Hj) heterocycles. Based on the current literature regarding one-pot, multicomponent reactions, two distinct and plausible mechanistic pathways are postulated for these transformations. A detailed mechanistic investigation, including the isolation of intermediates and stepwise reaction analysis, revealed that the type of 1,3-dicarbonyl compound used is pivotal in determining the operative mechanistic pathway in these reactions. The current catalytic protocol developed for the synthesis of pyrano[2,3-d]pyrimidine and 4H-chromene heterocycles presents several advantages over existing methodologies, including the use of an eco-friendly solvent (ethanol), high product yields (up to 97%), shorter reaction time scale (30 min), high turnover frequency (TOF) values (up to 14.7 min-1), and excellent catalyst reusability over five catalytic cycles.

Computing pathogenicity of mutations in human cytochrome P450 superfamily

Cytochrome P450 (CYPs) are crucial heme-containing enzymes that metabolize drugs and endogenous compounds. In humans, 57 CYP isoforms have been identified, with over 200 mutations linked to severe disorders. Our comprehensive computational study assessed the reason for the pathogenicity of mutations by comparing pathogenic and non-pathogenic variants. We analyzed 25,94,151 mutations across 26 CYP structures using structure- and sequence-based methods, revealing a meaningful stability pattern: non-pathogenic > all > pathogenic mutation datasets. Notably, pathogenic mutations were predominantly buried within CYP structures, indicating a higher potential for pathogenesis. We identified three key amino acid properties affected by mutations: Gibbs free energy, isoelectric point, and volume. Furthermore, diseased mutations significantly reduced positive residue content, particularly due to arginine mutations, which directly influenced the isoelectric point. Our findings indicate a greater likelihood of pathogenic mutations occurring at conserved sites, disrupting CYP function. A higher frequency of pathogenic mutations was observed in heme sites, primarily involving arginine, which may interfere with arginine-heme interactions. Molecular docking revealed a differential binding of heme in wild-type and pathogenic CYPs. This study provides a foundational analysis of mutation effects across multiple CYPs. It models the chemical basis of CYP-related pathogenicity, facilitating the development of a semi-quantitative disease prediction model.

Heme-Aβ compound 0: a common intermediate in ROS generation and peroxidase activity

Oxidative stress is a key factor in neurodegenerative diseases, particularly in Alzheimer's disease (AD) which is the leading cause of dementia. A hallmark of AD is the accumulation of amyloid β (Aβ) peptides, along with redox-active metal ions and heme cofactors, all of which significantly contribute to disease progression. When heme binds to Aβ, it can drive oxidative stress through two primary pathways: firstly, reduced high-spin ferrous heme-Aβ active sites may generate H2O2 through oxygen reduction, leading to the oxidation of biomolecules and lipid membranes; secondly, this H2O2 can react with the oxidised form of high-spin ferric heme-Aβ, initiating peroxidase-like activity that can catalyse the oxidation of neurotransmitters. These pathways converge at a crucial intermediate i.e. the heme-Aβ-peroxo complex, which serves as the final intermediate in the ROS cycle and the first in the peroxidase cycle. Although, we have previously characterized other intermediates in these pathways, compound 0 resulting from the reaction of a high-spin heme-Aβ species with peroxides has remained elusive due to its rapid hydrolysis in an aqueous environment. In this study, we report the oxidation of dopamine by peroxides catalyzed by ferric heme-Aβ species and successfully stabilised and characterized compound 0 of high-spin heme-Aβ in dimethylformamide, an organic aprotic solvent. This stabilization enables detection through stopped-flow, EPR and resonance Raman spectroscopy, thereby facilitating a deeper understanding of the oxidative stress caused by high-spin heme-Aβ.

Regulation of ferryl reactivity by the cytochrome P450 decarboxylase OleT

The cytochrome P450 OleT catalyzes the decarboxylation of long-chain fatty acid substrates to produce terminal alkenes using hydrogen peroxide as a co-substrate. The facile activation of peroxide to form Compound I in the first step of the reaction, and subsequent CC bond cleavage mediated by Compound II, provides a unique opportunity to visualize both ferryl intermediates using transient kinetic approaches. Analysis of the Arrhenius behavior yields activation barriers of ∼6 kcal/mol and ∼ 18 kcal/mol for the decay of Compound I and Compound II respectively. The influence of the secondary coordination sphere, probed through site-directed mutagenesis approaches, suggests that restriction of the donor-acceptor distance contributes to the reactivity of Compound I. The reactivity of Compound II was further probed using kinetic solvent isotope effect approaches, confirming that the large barrier owes to a proton-gated mechanism in the decarboxylation reaction coordinate. Hydrogen-bonding to an active-site histidine (H85) in the distal pocket plays a key role in this process.

Evaluation of stabilizing additives to protect activities of cytochrome P450 enzymes for in vitro drug testing and pharmacogenetic studies: Focus on CYP2D6

In vitro and ex vivo studies on drug metabolism and stability are vital for drug development and pre-clinical safety assessment. Traditional in vitro models, such as liver enzyme (S9) fractions and microsomes, often fail to account for individual variability. Personalized models, including 3D cell models and organoids, offer promising alternatives but may not fully replicate physiological processes, especially for Cytochrome P450 (CYP) families involved in extrahepatic metabolism. A major challenge in these studies is the low stability and expression of CYP enzymes. This study aimed to stabilize native CYP activity in vitro by developing an optimized buffer formulation. Initial experiments using recombinant CYP supersomes and liver microsomes identified 45 μM cysteine, 4 mM dithiothreitol (DTT), and 300 μM phosphocholine (PC) as the most effective stabilizers. The applicability of these stabilizers was subsequently confirmed in primary human brain tissue, where they enabled the successful determination of CYP2D6 activity. This highlights the stabilizing buffer's utility for enhancing CYP functionality in diverse tissue types, including the brain, which plays a critical role in cerebral detoxification and drug metabolism. These findings suggest that specific enzyme stabilization can enable comprehensive evaluations of CYP function in ex vivo tissue samples, advancing the development of organoid human tissue models and supporting drug metabolism research.

Molecular detection of novel Glutamate-gated chloride channel mutations in field collected human head lice (Phthiraptera: Pediculidae) from Iran

OBJECTIVE

Recently, insecticides such as ivermectin, which targets glutamate-gated chloride channel (GluCl) channels in the nervous system of invertebrates, have gained attention for the treatment of head lice. However, resistance to this insecticide threatens the effectiveness of head louse control programs.

RESULTS

Molecular bioinformatics sequence analysis revealed that the most common mutations were R37K and E50K with a frequency of 85.71%, followed by D93N (64.28%), M101R (35.71%), and R100Q (28.57%). These mutations are reported here for the first time. The identification of these novel mutations in head louse populations raises concerns about the potential emergence of ivermectin resistance. Further research is needed to explore the functional implications of these mutations and their impact on the effectiveness of insecticide treatments.

Metabolomic and genomic insights into Micromonospora carbonacea subsp. caeruleus for anti-colorectal compound

Cancer is a predominant contributor to global morbidity and mortality, affecting populations worldwide. Marine Micromonospora species have been identified as significant sources of anticancer compounds. This work aimed to perform a polyphasic approach of isolated strain and conduct comparative metabolomic and genomic analyses to identify compounds with anticancer activity. The study utilized a polyphasic approach on isolated strains for anticancer compound identification. Taxonomic analysis of strain 2MTK254 revealed unique pigment and fatty acid patterns, designating it as a novel Micromonospora carbonacea subsp. caeruleus. Its crude extract displayed significant anti-colorectal activity (66.03% inhibition). Molecular network analysis classified metabolites into eight classes, highlighting a polycyclic tetramate macrolactams (PTMs) compound (P1, C29H38N2O4) with 99.31% inhibitory activity against HCT-116 cell lines (IC50 at 0.125 µM). Genome analysis identified 32 biosynthetic gene clusters (BGCs), including unique PTMs BGCs (83% similarity) linked to the P1 compound. Thus, M. carbonacea subsp. caeruleus 2MTK254 holds promise as a source of novel PTMs with anti-colorectal cancer potential. KEY POINTS: • A novel strain of Micromonospora carbonacea subsp. caeruleus 2MTK254 was isolated in Thailand • A new polycyclic tetramate macrolactam (PTM) with anticancer activity was identified in 2MTK254 • The genome of 2MTK254 has unique secondary metabolite gene clusters.

Structural insights into S-lignin O-demethylation via a rare class of heme peroxygenase enzymes

The O-demethylation of lignin aromatics is a rate-limiting step in their bioconversion to higher-value compounds. A recently discovered cytochrome P450, SyoA, demethylates the S-lignin aromatic syringol. In this work, we solve high-resolution X-ray crystal structures of substrate-free and substrate-bound SyoA and evaluate demethylation of para-substituted S-lignin aromatics via monooxygenase and peroxide shunt pathways. We find that SyoA demethylates S-lignin aromatics exclusively using the peroxide shunt pathway. The atomic-resolution structures reveal the position of non-canonical residues in the I-helix (Gln252, Glu253). Mutagenesis of this amide-acid pair in SyoA shows they are critical for catalytic activity. This work expands the enzymatic toolkit for improving the capacity to funnel lignin derived aromatics towards higher value compounds and defines the chemistry within the active site of the enzyme that enables peroxygenase activity. These insights provide a framework for engineering peroxygenase activity in other heme enzymes to generate easier to use biocatalysts.

Flash Communication: Flexibility of a Biologically Inspired Ligand Framework for Intramolecular C-H Activation

High-valent iron complexes play a crucial role in the oxidation of organic substrates, especially in C-H bond functionalization reactions in biology. This paper investigates the reactivity of nonporphyrin tripodal ligands featuring a secondary coordination sphere, focusing on their prospective ability to stabilize high-valent iron-oxo species. Using NMR spectroscopy and X-ray crystallography, we detail the formation of an Fe(III)-alkoxide complex through intramolecular C-H bond activation, providing insight into the potential transient formation of a high-valent iron-oxo intermediate. While attempts to observe an Fe(IV)-oxo complex were unsuccessful, our findings underscore the significance of the ligand electronic environment in stabilizing reactive iron species for C-H bond activation.

Heme-thiolate monooxygenase cytochrome P450 1B1, an old dog with many new tricks

Cytochrome P450 CYP1B1 is a heme-thiolate monooxygenase traditionally recognized for its xenobiotic functions and extrahepatic expressions. Recent studies have suggested that CYP1B1 is also expressed in hepatic stellate cells, immune cells, endothelial cells, and fibroblasts within the tumor microenvironment, as well as tumor cells themselves. CYP1B1 is responsible for the metabolism of a wide range of substrates, including xenobiotics such as drugs, environmental chemicals, and endobiotics such as steroids, retinol, and fatty acids. Consequently, CYP1B1 and its associated exogenous and endogenous metabolites have been critically implicated in the pathogenesis of many diseases. Understanding the mode of action of CYP1B1 in different pathophysiological conditions and developing pharmacological inhibitors that allow for systemic or cell type-specific modulation of CYP1B1 may pave the way for novel therapeutic opportunities. This review highlights the significant role of CYP1B1 in maintaining physiological homeostasis and provides a comprehensive discussion of recent advancements in our understanding of CYP1B1's involvement in the pathogenesis of diseases such as fibrosis, cancer, glaucoma, and metabolic disorders. Finally, the review emphasizes the therapeutic potential of targeting CYP1B1 for drug development, particularly in the treatment and prevention of cancers and liver fibrosis. SIGNIFICANCE STATEMENT: CYP1B1 plays a critical role in various physiological processes. Dysregulation or genetic mutations of the gene encoding this enzyme can lead to health complications and may increase the risk of diseases such as cancer and liver fibrosis. In this review, we summarize recent preclinical and clinical evidence that underscores the potential of CYP1B1 as a therapeutic target.

Transcriptomic analysis of Rhipicephalus microplus hemocytes from female ticks infected with Babesia bovis or Babesia bigemina

BACKGROUND

Tick hemolymph is a sterile fluid that carries nutrients to maintain tick health. The hemolymph creates a hostile environment for invaders including the destruction of microorganisms by its circulating hemocytes. However, Babesia parasites escape and disseminate to other organs through the hemolymph to continue their transmission life cycle. Still, it is unknown how tick hemocytes respond to B. bovis or B. bigemina infection. In this study, we conducted a transcriptomic analysis of hemocytes from female Rhipicephalus microplus ticks infected with Babesia parasites to understand how gene expression changes during parasite infection.

METHODS

During Babesia acute infection, female R. microplus ticks were fed on bovines to acquire parasites. Engorged females were collected and incubated to develop Babesia kinetes in tick hemolymph. The hemolymph was examined to identify ticks that were highly infected with Babesia kinetes. Hemocyte cells were collected from replete female ticks infected with Babesia bovis or Babesia bigemina to perform high-throughput RNA-sequencing (RNA-Seq) analysis.

RESULTS

This study identified major changes in the gene profile of tick hemocytes during Babesia infection. The main groups of hemocyte genes that were altered during Babesia infection were associated with metabolism, immunity, and cytoskeletal rearrangement. Upregulated genes were mainly involved in defense mechanisms, while downregulated genes were related to cell proliferation and apoptosis. However, the expression of hemocyte genes varied among Babesia species' infections, and it reflected the changes that occurred in the tick's physiology, including growth, reproduction, and skeletal muscle development.

CONCLUSIONS

The differential gene expression of R. microplus hemocytes revealed that genes highly regulated upon Babesia infection were related to metabolism, tick immunity, cell growth, apoptosis, development, metabolism, and reproduction. Additional research is necessary to further define the genes that exhibited varying expression levels in hemocytes during the infection. The findings of this study will enhance our understanding on how Babesia parasites survive in the hostile environment of ticks and perpetuate their transmission cycle, ultimately contributing to the spread of bovine babesiosis.

Characterisation of the Cytochrome P450 Monooxygenase CYP116B46 from Tepidiphilus thermophilus as a Homogentisic Acid Generating Enzyme and its Conversion to a Peroxygenase

The heme enzymes of the cytochrome P450 superfamily (CYPs) catalyse the selective hydroxylation of unactivated C-H bonds in organic molecules. There is great interest in applying these enzymes as biocatalysts with a focus on self-sufficient CYP 'fusion' enzymes, comprising a single polypeptide chain with the electron transfer components joined to the heme domain. Here we elucidate the function of the self-sufficient CYP116B46 fusion enzyme, from the thermophilic bacterium Tepidiphilus thermophilus. We demonstrate that it efficiently hydroxylates aromatic organic acids, exemplified by oxidation of 2-hydroxyphenylacetic acid to homogentisic acid (2,5-dihydroxyphenylacetic acid), an important metabolite in bacterial catabolism. In line with the thermophilic nature of the source bacterium, activity increased at higher temperatures, (50 °C), with a catalytic preference for NADPH over NADH. While self-sufficient fusion enzymes simplify biocatalysis; engineered peroxygenase activity is also a key advance in the application of these enzymes as biocatalysts as it eliminates the need for electron transfer partner proteins and nicotinamide cofactors. We demonstrate that a T278E mutation in the heme domain of CYP116B46, confers peroxygenase activity. This engineered peroxygenase enzyme is stable to elevated temperatures and catalytic concentrations of hydrogen peroxide, with an observed optimal activity resulting in a total turnover number of ~650.

Differentially spliced mitochondrial CYP419A1 contributes to ethiprole resistance in Nilaparvata lugens

The brown planthopper Nilaparvata lugens is one of the most economically important pests of cultivated rice in Southeast Asia. Extensive use of insecticide treatments, such as imidacloprid, fipronil and ethiprole, has resulted in the emergence of multiple resistant strains of N. lugens. Previous investigation of the mechanisms of resistance to imidacloprid and ethiprole demonstrated that overexpression and qualitative changes in the cytochrome P450 gene CYP6ER1 lead to enhanced metabolic detoxification of these compounds. Here, we present the identification of a secondary mechanism enhancing ethiprole resistance mediated by differential splicing and overexpression of CYP419A1, a planthopper-specific, mitochondrial P450 gene. Although metabolic resistance to insecticides is usually mediated by overexpression of P450 genes belonging to either CYP 3 or 4 clades, we validate the protective effect of over-expression of CYP419A1, in vivo, using transgenic Drosophila melanogaster. Additionally, we report some unusual features of both the CYP419A1 gene locus and protein, which include, altered splicing associated with resistance, a non-canonical heme-binding motif and an extreme 5' end extension of the open reading frame. These results provide insight into the molecular mechanisms underpinning resistance to insecticides and have applied implications for the control of a highly damaging crop pest.

Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament

Cyclic dipeptides are produced by organisms across all domains of life, with many exhibiting anticancer and antimicrobial properties. Oxidations are often key to their biological activities, particularly C-C bond oxidation catalysed by tailoring enzymes including cyclodipeptide oxidases. These flavin-dependent enzymes are underexplored due to their intricate three-dimensional arrangement involving multiple copies of two distinct small subunits, and mechanistic details underlying substrate selection and catalysis are lacking. Here, we determined the structure and mechanism of the cyclodipeptide oxidase from the halophile Nocardiopsis dassonvillei (NdasCDO), a component of the biosynthetic pathway for nocazine natural products. We demonstrated that NdasCDO forms filaments in solution, with a covalently bound flavin mononucleotide (FMN) cofactor at the interface between three distinct subunits. The enzyme exhibits promiscuity, processing various cyclic dipeptides as substrates in a distributive manner. The reaction is optimal at high pH and involves the formation of a radical intermediate. Pre-steady-state kinetics, a significant solvent kinetic isotope effect, and the absence of viscosity effects suggested that a step linked to FMN regeneration controlled the reaction rate. Our work elucidates the complex mechanistic and structural characteristics of this dehydrogenation reaction, positioning NdasCDO as a promising biocatalyst and expanding the FMN-dependent oxidase family to include enzyme filaments.

Coordinated conformational changes in P450 decarboxylases enable hydrocarbons production from renewable feedstocks

Fatty acid peroxygenases have emerged as promising biocatalysts for hydrocarbon biosynthesis due to their ability to perform C-C scission, producing olefins - key building blocks for sustainable materials and fuels. These enzymes operate through non-canonical and complex mechanisms that yield a bifurcated chemoselectivity between hydroxylation and decarboxylation. In this study, we elucidate structural features in P450 decarboxylases that enable the catalysis of unsaturated substrates, expanding the mechanistic pathways for decarboxylation reaction. Combining X-ray crystallography, molecular dynamics simulations, and machine learning, we have identified intricate molecular rearrangements within the active site that enable the Cβ atom of the substrate to approach the heme iron, thereby promoting oleate decarboxylation. Furthermore, we demonstrate that the absence of the aromatic residue in the Phe-His-Arg triad preserves chemoselectivity for alkenes, providing a distinct perspective on the molecular determinants of decarboxylation activity. Ultimately, these findings enable the sustainable production of biohydrocarbons from industrial feedstocks.

Obesity alters the fitness of peritumoral adipose tissue, exacerbating tumor invasiveness in renal cancer through the induction of ADAM12 and CYP1B1

Obesity exacerbates the risk and aggressiveness of many types of cancer. Adipose tissue (AT) represents a prevalent component of the tumor microenvironment (TME) and contributes to cancer development and progression. Reciprocal communication between cancer and adipose cells leads to the generation of cancer-associated adipocytes (CAAs), which in turn foster tumor invasiveness by producing paracrine metabolites, adipocytokines, and growth factors. Interfering with the crosstalk between CAAs and cancer cells is of key relevance in the prevention of tumor progression. The present study aimed to analyze the contribution of peritumoral AT in renal cell carcinoma (RCC) progression in lean versus overweight or obese patients. By isolating human adipose-derived stromal/stem cells from the three groups of patients and performing conditioned medium studies with RCC cells along with in vivo xenograft experiments, we found that peritumoral adipocytes from the three groups show a distinct expression profile of genes. In particular, ADAM metallopeptidase domain 12 (ADAM12) and cytochrome P450 family 1 subfamily B member 1 (CYP1B1) were found to be upregulated in obesity and their silencing reduced RCC cell invasiveness. In conclusion, high ADAM12 and CYP1B1 expressions in the peritumoral adipocytes boost tumor invasiveness and may serve as an indicator of poor prognosis in RCC.

Efficient sex hormone biosensors in Saccharomyces cerevisiae cells to evaluate human aromatase activity and inhibition

Yeast sex-hormone whole-cell biosensors are analytical tools characterized by long-time storage and low production cost. We engineered compact β-estradiol biosensors in S. cerevisiae cells by leveraging short (20-nt long) operators bound by the fusion protein LexA-ER-VP64-where ER is the human estrogen receptor and VP64 a strong viral activation domain. Our best biosensors showed high accuracy since their recovery concentration ranged between 97.13% and 104.69%. As a novelty, we built on top of them testosterone biosensors that exploit the conversion of testosterone into β-estradiol by the human aromatase enzyme-expressed in S. cerevisiae together with its co-factor CPR. We used our engineered yeast strains to evaluate aromatase activity through fluorescence measurements without the need for protein purification. Besides, we set up an aromatase-inhibitors evaluation assay to measure the IC50 (half-maximal inhibitory concentration) of candidate inhibitory compounds and developed a screening assay for enzymes that metabolize β-estradiol that demands only to measure fluorescence. These two assays allow the screening of a large number of chemicals and proteins in a fast and economic fashion. We think that our work will facilitate considerably high throughput screening for the discovery of new drugs and unknown metabolic processes.

Comprehensive analysis of mRNA and miRNA differential expression profiles in the hypothalamus-pituitary-gonadal axis in laying and broodiness period of Wanxi white geese

The hypothalamus-pituitary-gonadal (HPG) axis is an important neuroendocrine regulatory center involved in egg-laying process in poultry. However, its mechanism of regulating broodiness behavior and laying performance in geese remains unclear. This study explored the molecular mechanism by which the HPG axis regulates brooding behavior in Wanxi white geese (WWG). The hypothalamus, pituitary, and ovarian tissues of Wanxi white geese were collected at laying and brooding periods for transcriptome sequencing analysis. A total of 240 (BH vs. LH), 319 (BP vs. LP), and 445 (BO vs. LO) differentially expressed genes, and 56 (BH vs. LH), 82 (BP vs. LP), and 48 (BO vs. LO) differentially expressed miRNAs were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis showed that differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were significantly enriched in hormone level regulation, cell communication, calcium signaling pathway, GnRH signaling pathway, MAPK signaling pathway, Wnt signaling pathway, and other processes. Six DEGs and four DEMs were randomly selected for real-time fluorescence quantitative reverse transcription PCR (RT-qPCR). The results showed that the transcriptome sequencing data were accurate and reliable. In addition, 22 potential hub miRNAs were screened. Dual luciferase reporter assays confirmed the targeting relationship between miR-144-y and DIO3. The results showed that the miRNAs mainly regulated the laying performance and brooding behavior of WWG by mediating the expression of target genes. In this study, we systematically elucidated the mechanisms by which the HPG axis regulates the broodiness behavior and laying performance of WWG at the post-transcriptional level. Several miRNAs and mRNAs associated with the reproductive performance of WWG were identified, providing a crucial reference for the subsequent use of gene editing technologies to breed new varieties and advance the development of WWG breeding industry.

Role of Fatty Acids β-Oxidation in the Metabolic Interactions Between Organs

In recent decades, several discoveries have been made that force us to reconsider old ideas about mitochondria and energy metabolism in the light of these discoveries. In this review, we discuss metabolic interaction between various organs, the metabolic significance of the primary substrates and their metabolic pathways, namely aerobic glycolysis, lactate shuttling, and fatty acids β-oxidation. We rely on the new ideas about the supramolecular structure of the mitochondrial respiratory chain (respirasome), the necessity of supporting substrates for fatty acids β-oxidation, and the reverse electron transfer via succinate dehydrogenase during β-oxidation. We conclude that ATP production during fatty acid β-oxidation has its upper limits and thus cannot support high energy demands alone. Meanwhile, β-oxidation creates conditions that significantly accelerate the cycle: glucose-aerobic glycolysis-lactate-gluconeogenesis-glucose. Therefore, glycolytic ATP production becomes an important energy source in high energy demand. In addition, lactate serves as a mitochondrial substrate after converting to pyruvate + H+ by the mitochondrial lactate dehydrogenase. All coupled metabolic pathways are irreversible, and the enzymes are organized into multienzyme structures.

Understanding Cytochrome P450 Enzyme Substrate Inhibition and Prospects for Elimination Strategies

Cytochrome P450 (CYP450) enzymes, which are widely distributed and pivotal in various biochemical reactions, catalyze diverse processes such as hydroxylation, epoxidation, dehydrogenation, dealkylation, nitrification, and bond formation. These enzymes have been applied in drug metabolism, antibiotic production, bioremediation, and fine chemical synthesis. Recent research revealed that CYP450 catalytic kinetics deviated from the classic Michaelis-Menten model. A notable substrate inhibition phenomenon that affects the catalytic efficiency of CYP450 at high substrate concentrations was identified. However, the substrate inhibition of various reactions catalyzed by CYP450 enzymes have not been comprehensively reviewed. This review describes CYP450 substrate inhibition examples and atypical Michaelis-Menten kinetic models, and provides insight into mechanisms of these enzymes. We also reviewed 3D structure and dynamics of CYP450 with substrate binding. Outline methods for alleviating substrate inhibition in CYP450 and other enzymes, including traditional fermentation approaches and protein engineering modifications. The comprehensive analysis presented in this study lays the foundation for enhancing the catalytic efficiency of CYP450 by deregulating substrate inhibition.

Immobilization of Membrane-Associated Protein Complexes on SERS-Active Nanomaterials for Structural and Dynamic Characterization

Exploring the structural basis of membrane proteins is significant for a deeper understanding of protein functions. In situ analysis of membrane proteins and their dynamics, however, still challenges conventional techniques. Here we report the first attempt to immobilize membrane protein complexes on surface-enhanced Raman scattering (SERS)-active supports, titanium dioxide-coated silver (Ag@TiO2) nanoparticles. Biocompatible immobilization of microsomal monooxygenase complexes is achieved through lipid fission and fusion. SERS activity of the Ag@TiO2 nanoparticles enables in situ monitoring of protein-protein electron transfer and enzyme catalysis in real time. Through SERS fingerprints of the monooxygenase redox centers, the correlations between these protein-ligand interactions and reactive oxygen species generation are revealed, providing novel insights into the molecular mechanisms underlying monooxygenase-mediated apoptotic regulation. This study offers a novel strategy to explore structure-function relationships of membrane protein complexes and has the potential to advance the development of novel reactive oxygen species-inducing drugs for cancer therapy.

Progress and challenges of developing volatile metabolites from exhaled breath as a biomarker platform

BACKGROUND

The multitude of metabolites generated by physiological processes in the body can serve as valuable biomarkers for many clinical purposes. They can provide a window into relevant metabolic pathways for health and disease, as well as be candidate therapeutic targets. A subset of these metabolites generated in the human body are volatile, known as volatile organic compounds (VOCs), which can be detected in exhaled breath. These can diffuse from their point of origin throughout the body into the bloodstream and exchange into the air in the lungs. For this reason, breath VOC analysis has become a focus of biomedical research hoping to translate new useful biomarkers by taking advantage of the non-invasive nature of breath sampling, as well as the rapid rate of collection over short periods of time that can occur. Despite the promise of breath analysis as an additional platform for metabolomic analysis, no VOC breath biomarkers have successfully been implemented into a clinical setting as of the time of this review.

AIM OF REVIEW

This review aims to summarize the progress made to address the major methodological challenges, including standardization, that have historically limited the translation of breath VOC biomarkers into the clinic. We highlight what steps can be taken to improve these issues within new and ongoing breath research to promote the successful development of the VOCs in breath as a robust source of candidate biomarkers. We also highlight key recent papers across select fields, critically reviewing the progress made in the past few years to advance breath research.

KEY SCIENTIFIC CONCEPTS OF REVIEW

VOCs are a set of metabolites that can be sampled in exhaled breath to act as advantageous biomarkers in a variety of clinical contexts.

Decoding the Role of CYP450 Enzymes in Metabolism and Disease: A Comprehensive Review

Cytochrome P450 (CYP450) is a group of enzymes that play an essential role in Phase I metabolism, with 57 functional genes classified into 18 families in the human genome, of which the CYP1, CYP2, and CYP3 families are prominent. Beyond drug metabolism, CYP enzymes metabolize endogenous compounds such as lipids, proteins, and hormones to maintain physiological homeostasis. Thus, dysregulation of CYP450 enzymes can lead to different endocrine disorders. Moreover, CYP450 enzymes significantly contribute to fatty acid metabolism, cholesterol synthesis, and bile acid biosynthesis, impacting cellular physiology and disease pathogenesis. Their diverse functions emphasize their therapeutic potential in managing hypercholesterolemia and neurodegenerative diseases. Additionally, CYP450 enzymes are implicated in the onset and development of illnesses such as cancer, influencing chemotherapy outcomes. Assessment of CYP450 enzyme expression and activity aids in evaluating liver health state and differentiating between liver diseases, guiding therapeutic decisions, and optimizing drug efficacy. Understanding the roles of CYP450 enzymes and the clinical effect of their genetic polymorphisms is crucial for developing personalized therapeutic strategies and enhancing drug responses in diverse patient populations.

Engineering Electron Transfer Pathway of Cytochrome P450s

Cytochrome P450s (P450s), a superfamily of heme-containing enzymes, existed in animals, plants, and microorganisms. P450s can catalyze various regional and stereoselective oxidation reactions, which are widely used in natural product biosynthesis, drug metabolism, and biotechnology. In a typical catalytic cycle, P450s use redox proteins or domains to mediate electron transfer from NAD(P)H to heme iron. Therefore, the main factors determining the catalytic efficiency of P450s include not only the P450s themselves but also their redox-partners and electron transfer pathways. In this review, the electron transfer pathway engineering strategies of the P450s catalytic system are reviewed from four aspects: cofactor regeneration, selection of redox-partners, P450s and redox-partner engineering, and electrochemically or photochemically driven electron transfer.

Vital role of CYP450 in the biodegradation of antidiabetic drugs in the aerobic activated sludge system and the mechanisms

The extensive use of antidiabetic drugs (ADDs) and their detection in high concentrations in the environment have been extensively documented. However, the mechanism of ADDs dissipation in aquatic environments is still not well understood. This study thoroughly investigates the dissipation behavior of ADDs and the underlying mechanisms in the aerobic activated sludge system. The results indicate that the removal efficiencies of ADDs range from 3.98% to 100% within 48 h, largely due to the biodegradation process. Additionally, the gene expression of cytochrome P450 (CYP450) is shown to be significantly upregulated in most ADDs-polluted samples (P < 0.05), indicating the vital role of CYP450 enzymes in the biodegradation of ADDs. Enzyme inhibition experiments validated this hypothesis. Moreover, molecular docking and simulation results indicate that a strong correlation between the biodegradation of ADDs and the interactions between ADDs and CYP450 (Ebinding). The differences in dissipation behavior among the tested ADDs are possibly due to their electrophilic characteristics. Overall, this study makes the initial contribution to a more profound comprehension of the crucial function of CYP450 enzymes in the dissipation behavior of ADDs in a typical aquatic environment.

Overexpressing CYP81D11 enhances 2,4,6-trinitrotoluene tolerance and removal efficiency in Arabidopsis

Phytoremediation is a promising technology for removing the high-toxic explosive 2,4,6-trinitrotoluene (TNT) pollutant from the environment. Mining dominant genes is the key research direction of this technology. Most previous studies have focused on the detoxification of TNT rather than plants' TNT tolerance. Here, we conducted a transcriptomic analysis of wild type Arabidopsis plants under TNT stress and found that the Arabidopsis cytochrome P450 gene CYP81D11 was significantly induced in TNT-treated plants. Under TNT stress, the root length was approximately 1.4 times longer in CYP81D11-overexpressing transgenic plants than in wild type plants. The half-removal time for TNT was much shorter in CYP81D11-overexpressing transgenic plants (1.1 days) than in wild type plants (t1/2 = 2.2 day). In addition, metabolic analysis showed no difference in metabolites in transgenic plants compared to wild type plants. These results suggest that the high TNT uptake rates of CYP81D11-overexpressing transgenic plants were most likely due to increased tolerance and biomass rather than TNT degradation. However, CYP81D11-overexpressing plants were not more tolerant to osmotic stresses, such as salt or drought. Taken together, our results indicate that CYP81D11 is a promising target for producing bioengineered plants with high TNT removing capability.

Uncoupling of Cytochrome P450 2B6 and stimulation of reactive oxygen species production in pharmacogenomic alleles affected by interethnic variability

Cytochrome P450 mediated substrate metabolism is generally characterized by the formation of reactive intermediates. In vitro and in vivo reaction uncoupling, results in the accumulation and dissociation of reactive intermediates, leading to increased ROS formation. The susceptibility towards uncoupling and altered metabolic activity is partly modulated by pharmacogenomic alleles resulting in amino acid substitutions. A large variability in the prevalence of these alleles has been demonstrated in CYP2B6, with some being predominantly unique to African populations. The aim of this study is to characterize the uncoupling potential of recombinant CYP2B6*1, CYP2B6*6 and CYP2B6*34 metabolism of specific substrates. Therefore, functional effects of these alterations on enzyme activity were determined by quantification of bupropion, efavirenz and ketamine biotransformation using HPLC-MS/MS. Determination of H2O2 levels was performed by the AmplexRed/horseradish peroxidase assay. Our studies of the amino acid substitutions Q172H, K262R and R487S revealed an exclusive use of the peroxide shunt for the metabolism of bupropion and ketamine by CYP2B6*K262R. Ketamine was also identified as a trigger for the peroxide shunt in CYP2B6*1 and all variants. Concurrently, ketamine acted as an uncoupler for all enzymes. We further showed that the expressed CYP2B6*34 allele results in the highest H2O2 formation. We therefore conclude that the reaction uncoupling and peroxide shunt are directly linked and can be substrate specifically induced with K262R carriers being most likely to use the peroxide shunt and R487S carrier being most prone to reaction uncoupling. This elucidates the functional diversity of pharmacogenomics in drug metabolism and safety.

Assessment of new hydrogen peroxide activators in water and comparison of their active species toward contaminants of emerging concern

Advanced oxidation processes are the most efficient tool to thwart the overaccumulation of harmful organic compounds in the environment. In this direction bioinspired metal complexes may be a viable solution for oxidative degradations in water. However, their synthesis is often elaborated and their scalability consequently low. This study presents alternative easy-to-synthesize bioinspired metal complexes to promote degradations in water. The metals employed were iron and manganese ions, hence cheap and highly accessible ions. The complexes were tested toward Phenol, Estrone, Triclosan, Oxybenzone, Diclofenac, Carbamazepine, Erythromycin, Aspartame, Acesulfame K, Anisole and 2,4-Dinitrotoluene. The reaction favoured electron-rich compounds reaching a removal efficiency of over 90%. The central ion plays a crucial role. Specifically, Mn(II) induces a non-radical pathway while iron ions a predominant radical one (⋅OH is predominant). The iron systems resulted more versatile toward contaminants, while the manganese ones showed a higher turn-over number, hence higher catalytic behaviour.

On the engineering of reductase-based-monooxygenase activity in CYP450 peroxygenases

Recent bioengineering of CYP450OleT shows that peroxide-based CYP450OleT can be converted to a reductase-based self-sufficient enzyme, which is capable of showing efficient hydroxylation and decarboxylation activity for a wide range of substrates. The so-generated enzyme creates several mechanistic puzzles: (A) as CYP450 peroxygenases lack the conventional acid-alcohol pair, what is the source of two protons that are required to create the ultimate oxidant Cpd I? (B) Why is it only CYP450OleT that shows the reductase-based activity but no other CYP members? The present study provides a mechanistic solution to these puzzles using comprehensive MD simulations and hybrid QM/MM calculations. We show that the fusion of the reductase domain to the heme-binding domain triggers significant conformational rearrangement, which is gated by the propionate side chain, which constitutes a new water aqueduct via the carboxylate end of the substrate that ultimately participates in Cpd I formation. Importantly, such well-synchronized choreographies are controlled by remotely located Tyr359, which senses the fusion of reductase and communicates to the heme domain via non-covalent interactions. These findings provide crucial insights and a broader perspective which enables us to make a verifiable prediction: thus, the catalytic activity is not only limited to the first or second catalytic shell of an enzyme. Furthermore, it is predicted that reinstatement of tyrosine at a similar position in other members of CYP450 peroxygenases can convert these enzymes to reductase-based monooxygenases.

Reagent Engineering for Group Transfer Biocatalysis

Biocatalysis has become a major driver in the innovation of preparative chemistry. Enzyme discovery, engineering and computational design have matured to reliable strategies in the development of biocatalytic processes. By comparison, substrate engineering has received much less attention. In this Minireview, we highlight the idea that the design of synthetic reagents may be an equally fruitful and complementary approach to develop novel enzyme-catalysed group transfer chemistry. This Minireview discusses key examples from the literature that illustrate how synthetic substrates can be devised to improve the efficiency, scalability and sustainability, as well as the scope of such reactions. We also provide an opinion as to how this concept might be further developed in the future, aspiring to replicate the evolutionary success story of natural group transfer reagents, such as adenosine triphosphate (ATP) and S-adenosyl methionine (SAM).

An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase

The cytochrome P450 monooxygenases (CYPs) are a class of heme-thiolate enzymes that insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering, which enables their activity to occur using hydrogen peroxide (H2 O2 ) without the requirement for additional nicotinamide co-factors or partner proteins. Here, we demonstrate that soaking crystals of an engineered P450 peroxygenase with H2 O2 enables the enzymatic reaction to occur within the crystal. Crystals of the designed P450 peroxygenase, the T252E mutant of CYP199A4, in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2 O2 for varying times to initiate the in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid. A new X-ray crystal structure of this enzyme with the 4-hydroxybenzoic acid product was obtained to enable comparison alongside the existing substrate-bound structure. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to initiate the reactions of P450 enzymes, in crystallo by simply soaking crystals with H2 O2 will enable new structural biology methods and techniques to be applied to study their mechanism of action.

Emerging Strategies for Modifying Cytochrome P450 Monooxygenases into Peroxizymes

ConspectusCytochrome P450 monooxygenase is a versatile oxidizing enzyme with great potential in synthetic chemistry and biology. However, the dependence of its catalytic function on the nicotinamide cofactor NAD(P)H and redox partner proteins limits the practical catalytic application of P450 in vitro. An alternative to expensive cofactors is low-cost H2O2, which can be used directly to exploit the catalytic potential of P450s. However, the peroxide shunt pathway is generally inefficient at driving P450 catalysis compared to normal NAD(P)H-dependent activity. Over the last few decades, the scientific community has made continuous efforts to use directed evolution or site-directed mutagenesis to modify P450 monooxygenases into their peroxizyme modes─peroxygenase and peroxidase. Despite significant progress, obtaining efficient P450 peroxizymes remains a huge challenge. Here, we summarize our efforts to modulate peroxizyme activity in P450 monooxygenases and exploit their catalytic applications in challenging selective C-H oxidation, oxygenation, and oxyfunctionalization over the past seven years. We first developed a dual-functional small molecule (DFSM) strategy for transforming P450BM3 monooxygenase into peroxygenase. In this strategy, the typical DFSM, such as N-(ω-imidazolyl)-hexanoyl-l-phenylalanine (Im-C6-Phe), binds to the P450BM3 protein with an anchoring group at one end and plays a general acid-base catalytic role in the activation of H2O2 with an imidazolyl group at the other end. Compared with the O-O homolysis mechanism in the absence of DFSM, the addition of DFSM efficiently enables the heterolytic O-O cleavage of the adduct Fe-O-OH, thus being favored for the formation of active species compound I, which has been demonstrated by combining crystallographic and theoretical calculations. Furthermore, protein engineering showed the unique catalytic performance of DFSM-facilitated P450 peroxygenase for the highly difficult selective oxidation of C-H bonds. This catalytic performance was demonstrated during the chemoselective hydroxylation of gaseous alkanes, regioselective O-demethylation of aryl ethers, highly (R)-enantioselective epoxidation of styrene, and regio- and enantiomerically diverse hydroxylation of alkylbenzenes. Second, we demonstrated that DFSM-facilitated P450BM3 peroxygenase could be effectively switched to an efficient peroxidase mode through mechanism-guided protein engineering of redox-sensitive residues. Utilizing the peroxidase function of P450 enabled the direct nitration of unsaturated hydrocarbons including phenols, aromatic amines, and styrene derivatives, which was not only the P450-catalyzed direct nitration of phenols and aromatic amines for the first time but also the first example of the direct biological nitration of olefins. Finally, we report an H2O2 tunnel engineering strategy to enable peroxygenase activity in several different P450 monooxygenases for the first time, providing a general approach for accessing engineered P450 peroxygenases. In this Account, we highlight the emerging strategies we have developed for producing practical P450 peroxizyme biocatalysts. Although the DFSM strategy is primarily applied to P450BM3 to date, both strategies of redox-sensitive residue engineering and H2O2 tunnel engineering show great potential to extend to other P450s. These strategies have expanded the scope of applications of P450 chemistry and catalysis. Additionally, they provide a unique solution to the challenging selective oxidation of inert C-H bonds in synthetic chemistry.

Abiotic stress tolerance in pearl millet: Unraveling molecular mechanisms via transcriptomics

Pearl millet (Pennisetum glaucum (L.)) is a vital cereal crop renowned for its ability to thrive in challenging environmental conditions; however, the molecular mechanisms governing its salt stress tolerance remain poorly understood. To address this gap, next-generation RNA sequencing was conducted to compare gene expression patterns in pearl millet seedlings exposed to salt stress with those grown under normal conditions. Our RNA sequencing analysis focused on shoots from 13-day-old pearl millet plants subjected to either salinity stress (150 mmol of NaCl for 3 days) or thermal stress (50°C for 60 s). Of 36,041 genes examined, 17,271 genes with fold changes ranging from 2.2 to 19.6 were successfully identified. Specifically, 2388 genes were differentially upregulated in response to heat stress, whereas 4327 genes were downregulated. Under salt stress conditions, 2013 genes were upregulated and 4221 genes were downregulated. Transcriptomic analysis revealed four common abiotic KEGG pathways that play crucial roles in the response of pearl millet to salt and heat stress: phenylpropanoid biosynthesis, photosynthesis-antenna proteins, photosynthesis, and plant hormone signal transduction. These metabolic pathways are necessary for pearl millet to withstand and adapt to abiotic stresses caused by salt and heat. Moreover, the pearl millet shoot heat stress group showed specific transcriptomics related to KEEG metabolic pathways such as cytochrome P450, cutin, suberine, and wax biosynthesis, zeatin biosynthesis, crocin biosynthesis, ginsenoside biosynthesis, saponin biosynthesis, and biosynthesis of various plant secondary metabolites. In contrast, pearl millet shoots exposed to salinity stress exhibited transcriptomic changes associated with KEEG metabolic pathways related to carbon fixation in photosynthetic organisms, mismatch repair, and nitrogen metabolism. Our findings underscore the remarkable cross-tolerance of pearl millet to simultaneous salt and heat stress, elucidated through the activation of shared abiotic KEGG pathways. This study emphasizes the pivotal role of transcriptomics analysis in unraveling the molecular responses of pearl millet under abiotic stress conditions.

Designed Local Electric Fields-Promising Tools for Enzyme Engineering

Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.

Analysis of critical residues for peroxygenation and improved peroxygenase activity via in situ H2O2 generation in CYP105D18

Limited numbers of CYPs have been reported to work naturally as peroxygenases. The peroxide shunt pathway can be efficiently used as an alternative for the NAD(P)H and reductase systems, particularly in high hydrogen peroxide (H2O2) resistance CYPs. We reported the structural and biochemical features of CYP105D18 peroxygenase for its high H2O2 tolerance capacity. Q348 was a crucial residue for the stability of CYP105D18 during the exposure to H2O2. In addition, the role of the hydrophilic amino acid T239 from the I helix for peroxygenation and regiospecificity toward testosterone was investigated. Interestingly, T239E differs in product formation from wild type, catalyzing testosterone to androstenedione in the presence of H2O2. The other variant, T239A, worked with the Pdx/Pdr system and was unable to catalyze testosterone conversion in the presence of H2O2, suggesting the transformation of peroxygenase into monooxygenase. CYP105D18 supported the alternative method of H2O2 used for the catalysis of testosterone. The use of the same concentration of urea hydrogen peroxide adducts in place of direct H2O2 was more efficient for 2β-hydroxytestosterone conversion. Furthermore, in situ H2O2 generation using GOx/glucose system enhanced the catalytic efficiency (kcat/Km) for wild type and F184A by 1.3- and 1.9-fold, respectively, compared to direct use of H2O2 The engineering of CYP105D18, its improved peroxygenase activity, and alteration in the product oxidation facilitate CYP105D18 as a potential candidate for biotechnological applications.

Enzymatic Oxy- and Amino-Functionalization in Biocatalytic Cascade Synthesis: Recent Advances and Future Perspectives

Biocatalytic cascades are a powerful tool for building complex molecules containing oxygen and nitrogen functionalities. Moreover, the combination of multiple enzymes in one pot offers the possibility to minimize downstream processing and waste production. In this review, we illustrate various recent efforts in the development of multi-step syntheses involving C-O and C-N bond-forming enzymes to produce high value-added compounds, such as pharmaceuticals and polymer precursors. Both in vitro and in vivo examples are discussed, revealing the respective advantages and drawbacks. The use of engineered enzymes to boost the cascades outcome is also addressed and current co-substrate and cofactor recycling strategies are presented, highlighting the importance of atom economy. Finally, tools to overcome current challenges for multi-enzymatic oxy- and amino-functionalization reactions are discussed, including flow systems with immobilized biocatalysts and cascades in confined nanomaterials.

Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications

RNA modifications found in most RNAs, particularly in tRNAs and rRNAs, reveal an abundance of chemical alterations of nucleotides. Over 150 distinct RNA modifications are known, emphasizing a remarkable diversity of chemical moieties in RNA molecules. These modifications play pivotal roles in RNA maturation, structural integrity, and the fidelity and efficiency of translation processes. The catalysts responsible for these modifications are RNA-modifying enzymes that use a striking array of chemistries to directly influence the chemical landscape of RNA. This diversity is further underscored by instances where the same modification is introduced by distinct enzymes that use unique catalytic mechanisms and cofactors across different domains of life. This phenomenon of convergent evolution highlights the biological importance of RNA modification and the vast potential within the chemical repertoire for nucleotide alteration. While shared RNA modifications can hint at conserved enzymatic pathways, a major bottleneck is to identify alternative routes within species that possess a modified RNA but are devoid of known RNA-modifying enzymes. To address this challenge, a combination of bioinformatic and experimental strategies proves invaluable in pinpointing new genes responsible for RNA modifications. This integrative approach not only unveils new chemical insights but also serves as a wellspring of inspiration for biocatalytic applications and drug design. In this Account, we present how comparative genomics and genome mining, combined with biomimetic synthetic chemistry, biochemistry, and anaerobic crystallography, can be judiciously implemented to address unprecedented and alternative chemical mechanisms in the world of RNA modification. We illustrate these integrative methodologies through the study of tRNA and rRNA modifications, dihydrouridine, 5-methyluridine, queuosine, 8-methyladenosine, 5-carboxymethylamino-methyluridine, or 5-taurinomethyluridine, each dependent on a diverse array of redox chemistries, often involving organic compounds, organometallic complexes, and metal coenzymes. We explore how vast genome and tRNA databases empower comparative genomic analyses and enable the identification of novel genes that govern RNA modification. Subsequently, we describe how the isolation of a stable reaction intermediate can guide the synthesis of a biomimetic to unveil new enzymatic pathways. We then discuss the usefulness of a biochemical "shunt" strategy to study catalytic mechanisms and to directly visualize reactive intermediates bound within active sites. While we primarily focus on various RNA-modifying enzymes studied in our laboratory, with a particular emphasis on the discovery of a SAM-independent methylation mechanism, the strategies and rationale presented herein are broadly applicable for the identification of new enzymes and the elucidation of their intricate chemistries. This Account offers a comprehensive glimpse into the evolving landscape of RNA modification research and highlights the pivotal role of integrated approaches to identify novel enzymatic pathways.

P450 fatty acid decarboxylase

P450 fatty acid decarboxylases are able to utilize hydrogen peroxide as the sole cofactor to decarboxylate free fatty acids to produce α-olefins with abundant applications as drop-in biofuels and important chemical precursors. In this chapter, we review diverse approaches for discovery, characterization, engineering, and applications of P450 fatty acid decarboxylases. Information gained from structural data has been advancing our understandings of the unique mechanisms underlying alkene production, and providing important insights for exploring new activities. To build an efficient olefin-producing system, various engineering strategies have been proposed and applied to this unusual P450 catalytic system. Furthermore, we highlight a select number of applied examples of P450 fatty acid decarboxylases in enzyme cascades and metabolic engineering.

Electrochemical transformations catalyzed by cytochrome P450s and peroxidases

Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active Fe^IVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.

Dimer-assisted mechanism of (un)saturated fatty acid decarboxylation for alkene production

The enzymatic decarboxylation of fatty acids (FAs) represents an advance toward the development of biological routes to produce drop-in hydrocarbons. The current mechanism for the P450-catalyzed decarboxylation has been largely established from the bacterial cytochrome P450 OleTJE. Herein, we describe OleTPRN, a poly-unsaturated alkene-producing decarboxylase that outrivals the functional properties of the model enzyme and exploits a distinct molecular mechanism for substrate binding and chemoselectivity. In addition to the high conversion rates into alkenes from a broad range of saturated FAs without dependence on high salt concentrations, OleTPRN can also efficiently produce alkenes from unsaturated (oleic and linoleic) acids, the most abundant FAs found in nature. OleTPRN performs carbon-carbon cleavage by a catalytic itinerary that involves hydrogen-atom transfer by the heme-ferryl intermediate Compound I and features a hydrophobic cradle at the distal region of the substrate-binding pocket, not found in OleTJE, which is proposed to play a role in the productive binding of long-chain FAs and favors the rapid release of products from the metabolism of short-chain FAs. Moreover, it is shown that the dimeric configuration of OleTPRN is involved in the stabilization of the A-A' helical motif, a second-coordination sphere of the substrate, which contributes to the proper accommodation of the aliphatic tail in the distal and medial active-site pocket. These findings provide an alternative molecular mechanism for alkene production by P450 peroxygenases, creating new opportunities for biological production of renewable hydrocarbons.

Theoretical Study of Hydroxylation of α- and β-Pinene by a Cytochrome P450 Monooxygenase Model

Previous studies on biocatalytic transformations of pinenes by cytochrome P450 (CYP) enzymes reveal the formation of different oxygenated products from a single substrate due to the multistate reactivity of CYP and the many reactive sites in the pinene scaffold. Up until now, the detailed mechanism of these biocatalytic transformations of pinenes have not been reported. Hereby, we report a systematic theoretical study of the plausible hydrogen abstraction and hydroxylation reactions of α- and β-pinenes by CYP using the density functional theory (DFT) method. All DFT calculations in this study were based on B3LYP/LAN computational methodology using the Gaussian09 software. We used the B3LYP functional with corrections for dispersive forces, BSSE, and anharmonicity to study the mechanism and thermodynamic properties of these reactions using a bare model (without CYP) and a pinene-CYP model. According to the potential energy surface and Boltzmann distribution for radical conformers, the major reaction products of CYP-catalyzed hydrogen abstraction from β-pinene are the doublet trans (53.4%) and doublet cis (46.1%) radical conformer at delta site. The formation of doublet cis/trans hydroxylated products released a total Gibbs free energy of about 48 kcal/mol. As for alpha pinene, the most stable radicals were trans-doublet (86.4%) and cis-doublet (13.6%) at epsilon sites, and their hydroxylation products released a total of ~50 kcal/mol Gibbs free energy. Our results highlight the likely C-H abstraction and oxygen rebounding sites accounting for the multi-state of CYP (doublet, quartet, and sextet spin states) and the formation of different conformers due to the presence of cis/trans allylic hydrogen in α-pinene and β-pinene molecules.

Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids

The hydroxylation of fatty acids is an appealing reaction in synthetic chemistry, although the lack of selective catalysts hampers its industrial implementation. In this study, we have engineered a highly regioselective fungal peroxygenase for the ω-1 hydroxylation of fatty acids with quenched stepwise over-oxidation. One single mutation near the Phe catalytic tripod narrowed the heme cavity, promoting a dramatic shift toward subterminal hydroxylation with a drop in the over-oxidation activity. While crystallographic soaking experiments and molecular dynamic simulations shed light on this unique oxidation pattern, the selective biocatalyst was produced by Pichia pastoris at 0.4 g L^-1 in a fed-batch bioreactor and used in the preparative synthesis of 1.4 g of (ω-1)-hydroxytetradecanoic acid with 95 % regioselectivity and 83 % ee for the S enantiomer.

H2O2-Driven Hydroxylation of Steroids Catalyzed by Cytochrome P450 CYP105D18: Exploration of the Substrate Access Channel

CYP105D18 supports H2O2 as an oxygen surrogate for catalysis well and shows high H2O2 resistance capacity. We report the hydroxylation of different steroids using H2O2 as a cosubstrate. Testosterone was regiospecifically hydroxylated to 2β-hydroxytestosterone. Based on the experimental data and molecular docking, we predicted that hydroxylation of methyl testosterone and nandrolone would occur at position 2 in the A-ring, while hydroxylation of androstenedione and adrenosterone was predicted to occur in the B-ring. Further, structure-guided rational design of the substrate access channel was performed with the mutagenesis of residues S63, R82, and F184. Among the mutants, S63A showed a marked decrease in product formation, while F184A showed a significant increase in product formation in testosterone, nandrolone, methyl testosterone, androstenedione, and adrenosterone. The catalytic efficiency (kcat/Km) toward testosterone was increased 1.36-fold in the F184A mutant over that in the wild-type enzyme. These findings might facilitate the potential use of CYP105D18 and further engineering to establish the basis of biotechnological applications. IMPORTANCE The structural modification of steroids is a challenging chemical reaction. Modifying the core ring and the side chain improves the biological activity of steroids. In particular, bacterial cytochrome P450s are used as promiscuous enzymes for the activation of nonreactive carbons of steroids. In the present work, we reported the H2O2-mediated hydroxylation of steroids by CYP105D18, which also overcomes the use of expensive cofactors. Further, exploring the substrate access channel and modifying the bulky amino acid F184A increase substrate conversion while modifying the substrate recognizing amino acid S63 markedly decreases product formation. Exploring the substrate access channel and the rational design of CYP105D18 can improve the substrate conversion, which facilitates the engineering of P450s for industrial application.

Construction of Biocatalysts Using the P450 Scaffold for the Synthesis of Indigo from Indole

With the increasing demand for blue dyes, it is of vital importance to develop a green and efficient biocatalyst to produce indigo. This study constructed a hydrogen peroxide-dependent catalytic system for the direct conversion of indole to indigo using P450BM3 with the assistance of dual-functional small molecules (DFSM). The arrangements of amino acids at 78, 87, and 268 positions influenced the catalytic activity. F87G/T268V mutant gave the highest catalytic activity with k_cat of 1402 min^-1 and with a yield of 73%. F87A/T268V mutant was found to produce the indigo product with chemoselectivity as high as 80%. Moreover, F87G/T268A mutant was found to efficiently catalyze indole oxidation with higher activity (k_cat/K_m = 1388 mM^-1 min^-1) than other enzymes, such as the NADPH-dependent P450BM3 (2.4-fold), the Ngb (32-fold) and the Mb (117-fold). Computer simulation results indicate that the arrangements of amino acid residues in the active site can significantly affect the catalytic activity of the protein. The DFSM-facilitated P450BM3 peroxygenase system provides an alternative, simple approach for a key step in the bioproduction of indigo.

Axial N Ligand-Modulated Ultrahigh Activity and Selectivity Hyperoxide Activation over Single-Atoms Nanozymes

Learning and studying the structure-activity relationship in the bio-enzymes is conducive to the design of nanozymes for energy and environmental application. Herein, Fe single-atom nanozymes (Fe-SANs) with Fe-N5 site, inspired by the structure of cytochromes P450 (CYPs), are developed and characterized. Similar to the CYPs, the hyperoxide can activate the Fe(III) center of Fe-SANs to generate Fe(IV)O intermediately, which can transfer oxygen to the substrate with ultrafast speed. Particularly, using the peroxymonosulfate (PMS)-activated Fe-SANs to oxidize sulfamethoxazole, a typical antibiotic contaminant, as the model hyperoxides activation reaction, the excellent activity within 284 min-1 g-1 (catalyst) mmol-1 (PMS) oxidation rate and 91.6% selectivity to the Fe(IV)O intermediate oxidation are demonstrated. More importantly, instead of promoting PMS adsorption, the axial N ligand modulates the electron structure of FeN5 SANs for the lower reaction energy barrier and promotes electron transfer to PMS to produce Fe(IV)O intermediate with high selectivity. The highlight of the axial N coordination in the nanozymes in this work provides deep insight to guide the design and development of nanozymes nearly to the bio-enzyme with excellent activity and selectivity.

The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes

Modeling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods. Since water molecules play a crucial role in all sorts of chemistry, the accurate modeling of water molecules is vital for such simulations. In cytochrome P450 (CYP450), in particular, water molecules play a key role in forming active oxidant that ultimately performs oxidation and metabolism. In the present study, we have highlighted the behavior of the three most widely used water models─TIP3P, SPC/E, and OPC─for three different CYP450 enzymes─CYP450_BM3, CYP450_OleT, and CYP450_BSβ─during MD simulations and QM/MM calculations. We studied the various properties, such as RMSD, RMSF, H-bond, water occupancy, and hydrogen atom transfer (HAT), using QM/MM calculations and compared them for all three water models. Our study shows that the stabilities of the enzyme complexes are well maintained in all three water models. However, the OPC water model performs well for the polar active sites, that is, in CYP450_OleT and CYP450_BSβ, while the TIP3P water model is superior for the hydrophobic site, such as CYP450_BM3.