A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization

The key role of cytochrome P450s in the biosynthesis of plant derived natural products

Cytochrome P450 (CYP450 or CYP450, abbreviated as CYP450) represents a large family of self-oxidizable heme proteins, belonging to the class of monooxygenases, and is named because of the specific absorption peak at 450 nm in its ferrous/CO-bound complex. Cytochrome P450 has a wide spectrum of substrates and a rich variety of catalytic reactions, plays an important role in drug metabolism, natural product biosynthesis, and biocatalysis industry. In the biosynthesis of plant natural products, it plays an important role, especially in the downstream synthesis pathway and structural modification after skeleton synthesis. There are abundant natural products from plants, including terpenes, alkaloids, flavonoids, steroidal saponins, etc., which have great development value in the medical field. In the biosynthetic pathways of these natural products, cytochrome P450 enzymes often play an important role. They can serve as rate-limiting enzymes in the biosynthetic pathways or as modifying enzymes for the structural diversity of compounds. So, a deeper understanding of cytochrome P450 enzymes in the natural product synthesis pathway will enhance the development of natural products and advance the study of their synthetic biology. This review offers an overview of the biosynthesis of key medicinal natural products, with a particular focus on the critical role of cytochrome P450 enzymes in key catalytic steps. It also highlights recent advancements in the research of natural product biosynthesis and synthetic biology.

Understanding the Scope of Cytochrome P450-Catalyzed Radical Dimerization of Diketopiperazines

DtpC was isolated from the ditryptophenaline biosynthetic pathway found in filamentous fungi as a cytochrome P450 (P450) that catalyzes the dimerization of diketopiperazines. More recently, several similar P450s were discovered. While a vast majority of such P450s generate asymmetric diketopiperazine dimers, DtpC and other fungal P450s predominantly catalyze the formation of symmetric dimer products. Dimeric compounds can have interesting biological activities, and the mode of dimerization can substantially affect their bioactivities substantially. Here, we set out to examine the mechanism and scope of diketopiperazine dimerization catalyzed by DtpC using both chemically modified substrate molecules and DtpC mutants that were selected by the screening of randomly mutated recombinant variants. Use of N1- and N10-methylated diketopiperazine substrates supports the proposal that the initial radical formation occurs by extraction of the N1 indole nitrogen for this fungal P450 dimerase. Further in vitro studies revealed that DtpC was capable of accepting a range of structurally variable substrates, including N-demethylated diketopiperazines, and forming symmetric homo- and heterodimeric products. Moreover, the introduction of single mutations identified through the screening of random mutants at and around the substrate-binding pocket led to the conversion of DtpC into a catalyst that predominantly generated asymmetric dimers of various diketopiperazines. The versatility of DtpC can serve as a good starting point for directed evolution of P450s that can serve as versatile catalysts for generation of various dimers of not only diketopiperazines derived from standard and nonstandard amino acids but also possibly structurally more divergent analogs of diketopiperazines.

Secondary Sphere Lewis Acid Activated Heme Superoxo Adducts Mimic Crucial Non-Covalent Interactions in IDO/TDO Heme Dioxygenases

Heme enzymes play a central role in a medley of reactivities within a wide variety of crucial biological systems. Their active sites are highly decorated with pivotal evolutionarily optimized non-covalent interactions that precisely choreograph their biological functionalities with specific regio-, stereo-, and chemo-selectivities. Gaining a clear comprehension of how such weak interactions within the active sites control reactivity offers powerful information to be implemented into the design of future therapeutic agents that target these heme enzymes. To shed light on such critical details pertaining to tryptophan dioxygenating heme enzymes, this study investigates the indole dioxygenation reactivities of Lewis acid-activated heme superoxo model systems, wherein an unprecedented kinetic behavior is revealed. In that, the activated heme superoxo adduct is observed to undergo indole dioxygenation with the intermediacy of a non-covalently organized precursor complex, which forms prior to the rate-limiting step of the overall reaction landscape. Spectroscopic and theoretical characterization of this precursor complex draws close parallels to the ternary complex of heme dioxygenases, which has been postulated to be of crucial importance for successful 2,3-dioxygenative cleavage of indole moieties.

A Cytochrome P450 TxtE Model System with Mechanistic and Theoretical Evidence for a Heme Peroxynitrite Active Species

The cytochrome P450 homolog, TxtE, efficiently catalyzes the direct and regioselective aromatic nitration of the indolyl moiety of L-tryptophan to 4-nitro-L-tryptophan, using nitric oxide (NO) and dioxygen (O2) as co-substrates. Pathways for such direct and selective nitration of heteroaromatic motifs present platforms for engineering new nitration biocatalysts for pharmacologically beneficial targets, among a medley of other pivotal industrial applications. Precise mechanistic details concerning this pathway are only weakly understood, albeit a heme iron(III)-peroxynitrite active species has been postulated. To shed light on this unique reaction landscape, we investigated the indole nitration pathway of a series of biomimetic ferric heme superoxide mimics, [(Por)FeIII(O2 -⋅)], in the presence of NO. Therein, our model systems gave rise to three distinct nitroindole products, including 4-nitroindole, the product analogous to that obtained with TxtE. Moreover, 15N and 18O isotope labeling studies, along with meticulously designed control experiments lend credence to a heme peroxynitrite active nitrating agent, drawing close similarities to the tryptophan nitration mechanism of TxtE. All organic and inorganic reaction components have been fully characterized using spectroscopic methods. Theoretical investigation into several mechanistic possibilities deem a unique indolyl radical based reaction pathway as the most energetically favorable, products of which, are in excellent agreement with experimental findings.

A nucleobase-driven P450 peroxidase system enables regio- and stereo-specific formation of C─C and C─N bonds

P450 peroxidase activities are valued for their ability to catalyze complex chemical transformations using economical H2O2; however, they have been largely underexplored compared to their monooxygenase and peroxygenase activities. In this study, we identified an unconventional P450 enzyme, PtmB, which catalyzes the dimerization of purine nucleobases and tryptophan-containing diketopiperazines (TDKPs), yielding C3-nucleobase pyrroloindolines and nucleobase-TDKP dimers. Unlike typical TDKP P450 enzymes reliant on NAD(P)H cofactors and electron transfer systems, PtmB, and its analogs exhibit remarkable peroxidase activity in synthesizing adenine and other modified 6-aminopurine nucleobase-TDKP dimers. Structural analysis of the PtmB-substrate complex, mutation assays, and computational investigations reveal adenine's dual role as both substrate and acid-base catalyst in activating H2O2 to generate Compound I (Cpd I). This initiates a specific radical cascade reaction, facilitating the formation of precise C─C and C─N bonds. Biochemical assays and molecular dynamics simulations demonstrate that adenine's 6-NH2 hydrogen-bonding networks induce necessary conformational changes for H2O2 activation, thereby driving peroxidase activity. This study unveils an unusual catalytic mechanism for the P450 peroxidase system and underscores the pivotal role of nucleobases in enzyme-mediated reactions, which offers different prospects for developing P450 peroxidases and nucleobase-based biocatalysts.

Fresh Impetus in the Chemistry of Calcium Peroxides

Redox-inactive metal ions are essential in modulating the reactivity of various oxygen-containing metal complexes and metalloenzymes, including photosystem II (PSII). The heart of this unique membrane-protein complex comprises the Mn4CaO5 cluster, in which the Ca2+ ion acts as a critical cofactor in the splitting of water in PSII. However, there is still a lack of studies involving Ca-based reactive oxygen species (ROS) systems, and the exact nature of the interaction between the Ca2+ center and ROS in PSII still generates intense debate. Here, harnessing a novel Ca-TEMPO complex supported by the β-diketiminate ligand to control the activation of O2, we report the isolation and structural characterization of hitherto elusive Ca peroxides, a homometallic Ca hydroperoxide and a heterometallic Ca/K peroxide. Our studies indicate that the presence of K+ cations is a key factor controlling the outcome of the oxygenation reaction of the model Ca-TEMPO complex. Combining experimental observations with computational investigations, we also propose a mechanistic rationalization for the reaction outcomes. The designed approach demonstrates metal-TEMPO complexes as a versatile platform for O2 activation and advances the understanding of Ca/ROS systems.

Exploring the Diverse Landscape of Fungal Cytochrome P450-Catalyzed Regio- and Stereoselective Dimerization of Diketopiperazines

Dimeric indole-containing diketopiperazines (di-DKPs) are a diverse group of natural products produced through cytochrome P450-catalyzed C-C or C-N coupling reactions. The regio- and stereoselectivity of these reactions plays a significant role in the structural diversity of di-DKPs. Despite their pivotal role, the mechanisms governing the selectivity in fungi are not fully understood. Employing bioinformatics analysis and heterologous expression experiments, five undescribed P450 enzymes (AmiP450, AcrP450, AtP450, AcP450, and AtuP450) responsible for the regio- and stereoselective dimerization of diketopiperazines (DKPs) in fungi are identified. The function of these P450s is consistent with phylogenetic analysis, highlighting their dominant role in controlling the dimerization modes. Combinatorial biosynthesis-based pathway reconstitution of non-native gene clusters expands the chemical space of fungal di-DKPs and reveals that the regioselectivity is influenced by the substrate. Furthermore, multiple sequence alignment and molecular docking of these enzymes demonstrate a C-terminal variable region near the substrate tunnel entrance in AtuP450 that is crucial for its regioselectivity. These findings not only reveal the secret of fungal di-DKPs diversity but also deepen understanding of the mechanisms and catalytic specificity involved in P450-catalyzed dimerization reactions.

Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations

P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.

Enhancing ferryl accumulation in H2O2-dependent cytochrome P450s

A facile strategy is presented to enhance the accumulation of ferryl (iron(IV)-oxo) species in H2O2 dependent cytochrome P450s (CYPs) of the CYP152 family. We report the characterization of a highly chemoselective CYP decarboxylase from Staphylococcus aureus (OleTSA) that is soluble at high concentrations. Examination of OleTSA Compound I (CpdI) accumulation with a variety of fatty acid substrates reveals a dependence on resting spin-state equilibrium. Alteration of this equilibrium through targeted mutagenesis of the proximal pocket favors the high-spin form, and as a result, enhances Cpd-I accumulation to nearly stoichiometric yields.