Biosynthesis of Biscognienyne B Involving a Cytochrome P450-Dependent Alkynylation

The alkyne is a biologically significant moiety found in many natural products and a versatile functional group widely used in modern chemistry. Recent studies have revealed the biosynthesis of acetylenic bonds in fatty acids and amino acids. However, the molecular basis for the alkynyl moiety in acetylenic prenyl chains occurring in a number of meroterpenoids remains obscure. Here, we identify the biosynthetic gene cluster and characterize the biosynthetic pathway of an acetylenic meroterpenoid biscognienyne B based on heterologous expression, feeding experiments, and in vitro assay. This work shows that the alkyne moiety is constructed by an unprecedented cytochrome P450 enzyme BisI, which shows promiscuous activity towards C5 and C15 prenyl chains. This finding provides an opportunity for discovery of new compounds, featuring acetylenic prenyl chains, through genome mining, and it also expands the enzyme inventory for de novo biosynthesis of alkynes.     

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants

Previously, stereoselective hydroxylation of α-ionone by Cytochrome P450 BM3 mutants M01 A82W and M11 L437N was observed. While both mutants hydroxylate α-ionone in a regioselective manner at the C3 position, M01 A82W catalyzes formation of trans-3-OH-α-ionone products whereas M11 L437N exhibits opposite stereoselectivity, producing trans-(3S,6S)-OH-α-ionone and cis-(3S,6R)-OH-α-ionone. Here, we explore the stereoselective C3 hydroxylation of α-ionone by Cytochrome P450 BM3 mutants M01 A82W and M11 L437N using molecular dynamics-based free energy calculations to study the interaction between the enzyme and both the substrates and the products. The one-step perturbation approach is applied using an optimized reference state for substrates and products. While the free energy differences between the substrates free in solution amount to ～0 kJ mol(-1), the differences in mutant M01 A82W agree with the experimentally obtained dissociation constants K(d). Moreover, a correlation with experimentally observed trends in product formation is found in both mutants. The trans isomers show the most favorable relative binding free energy in the range of all four possible hydroxylated diastereomers for mutant M01 A82W, while the trans product from (6S)-α-ionone and the cis product from (6R)-α-ionone show highest affinity for mutant M11 L437N. Marcus theory is subsequently used to relate the thermodynamic stability to transition state energies and rates of formation.     

Regio- and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants

Steroidal C7β alcohols and their respective esters have shown significant promise as neuroprotective and anti-inflammatory agents to treat chronic neuronal damage like stroke, brain trauma, and cerebral ischemia. Since C7 is spatially far away from any functional groups that could direct C−H activation, these transformations are not readily accessible using modern synthetic organic techniques. Reported here are P450-BM3 mutants that catalyze the oxidative hydroxylation of six different steroids with pronounced C7 regioselectivities and β stereoselectivities, as well as high activities. These challenging transformations were achieved by a focused mutagenesis strategy and application of a novel technology for protein library construction based on DNA assembly and USER (Uracil-Specific Excision Reagent) cloning. Upscaling reactions enabled the purification of the respective steroidal alcohols in moderate to excellent yields. The high-resolution X-ray structure and molecular dynamics simulations of the best mutant unveil the origin of regio- and stereoselectivity.     

Insights into the Activation Mode of α-Carbonyl Sulfoxonium Ylides in Rhodium-Catalyzed C−H Activation: A Theoretical Study

A computational study has been performed to investigate the mechanism of Rh^III-catalyzed C−H bond activation using sulfoxonium ylides as a carbene precursor. The stepwise and concerted activation modes for sulfoxonium ylides were investigated. Detailed theoretical results showed that the favored stepwise pathway involves C−H bond activation, carbonization, carbene insertion, and protonation. The free energy profiles for dialkylation of 2-phenylpyridine were also calculated to account for the low yield of this reaction. Furthermore, the substituent effect was elucidated by comparing the energy barriers for the protonation of meta- and para-substituted sulfoxonium ylides calculated by density functional theory.     

Catalytic Mechanism of Cytochrome P450 2D6 for 4-Hydroxylation of Aripiprazole： A QM/MM Study

Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 （CYP2D6） is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports.     

Palladium-Catalyzed C8-Arylation of Naphthalenes through C−H Activation: A Combined Experimental and Computational Study

Herein, a direct C8-arylation reaction of 1-amidonaphthalenes is described. By using diaryliodonium salts as arylating agents, the palladium-catalyzed C−H activation reaction showed perfect C8 regioselectivity and a wide functional group tolerance. In most cases, the desired polyaromatic compounds were isolated in good to excellent yields. To explain the observed regioselectivity, DFT calculations were performed and highlighted the crucial role of the amide directing group. Finally, the utility of this method is showcased by the synthesis of benzanthrone derivatives.     

The Alkylidenphthalan–1-Alkylisobenzofuran Equilibrium: A Computational Study

Semiempirical (AM1, PM3) and density functional theoretical studies (B3LYP/6-31G*) are reported for the tautomerism of 2-methylidene-2,5-dihydrofurans (3a–e) and the corresponding 2-methylfurans (4a–e) and of benzannulated derivatives (5a–e, 6a–e, 7–14).     

Drug Metabolism by Cytochrome P450 Enzymes: What Distinguishes the Pathways Leading to Substrate Hydroxylation Over Desaturation?

Cytochrome P450 enzymes are highly versatile biological catalysts in our body that react with a broad range of substrates. Key functions in the liver include the metabolism of drugs and xenobiotics. One particular metabolic pathway that is poorly understood relates to the P450 activation of aliphatic groups leading to either hydroxylation or desaturation pathways. A DFT and QM/MM study has been carried out on the factors that determine the regioselectivity of aliphatic hydroxylation over desaturation of compounds by P450 isozymes. The calculations establish multistate reactivity patterns, whereby the product distributions differ on each of the spin‐state surfaces; hence spin‐selective product formation was found. The electronic and thermochemical factors that determine the bifurcation pathways were analysed and a model that predicts the regioselectivity of aliphatic hydroxylation over desaturation pathways was established from valence bond and molecular orbital theories. Thus, the difference in energy of the O?H versus the O?C bond formed and the π‐conjugation energy determines the degree of desaturation products. In addition, environmental effects of the substrate binding pocket that affect the regioselectivities were identified. These studies imply that bioengineering P450 isozymes for desaturation reactions will have to include modifications in the substrate binding pocket to restrict the hydroxylation rebound reaction.     

Cytochrome P450 119 Compounds I Formed by Chemical Oxidation and Photooxidation Are the Same Species

Compound I from cytochrome P450 119 prepared by the photooxidation method involving peroxynitrite oxidation of the resting enzyme to Compound II followed by photooxidation to Compound I was compared to Compound I generated by m-chloroperoxybenzoic acid (MCPBA) oxidation of the resting enzyme. The two methods gave the same UV/Visible spectra, the same products from oxidations of lauric acid and palmitic acid and their (ω-2,ω-2,ω-3,ω-3)-tetradeuterated analogues, and the same kinetics for oxidations of lauric acid and caprylic acid. The experimental identities between the transients produced by the two methods leave no doubt that the same Compound I species is formed by the two methods.     

Enzymatic Formation of Indolactam Scaffold by C−N Bond-Forming Cytochrome P450 Oxidases in Teleocidin Biosynthesis

Teleocidins are potent protein kinase C activators, and possess a unique indole-fused nine-membered lactam structure. Teleocidin biosynthesis starts from the formation of a dipeptide by non-ribosomal peptide synthetase (NRPS), followed by oxidative C−N bond formation by a cytochrome P450 oxidase, reverse-prenylation by a prenyltransferase, and methylation-initiated terpene cyclization by a C-methyltransferase. This minireview focuses on recent research progress toward the elucidation of the molecular basis for the remarkable P450-catalyzed intramolecular C−N bond-forming reaction, which is challenging in synthetic chemistry, to generate the indolactam scaffold. In addition, precursor-directed biosynthesis with the promiscuous P450 enzymes led to the formation of a series of unnatural and novel molecular scaffolds, including a sulfur-substituted indolactam with a different conformation from that of indolactam V.     

Discovery of a Dual Function Cytochrome P450 that Catalyzes Enyne Formation in Cyclohexanoid Terpenoid Biosynthesis

The 1,3-enyne moiety is commonly found in cyclohexanoid natural products produced by endophytic and plant pathogenic fungi. Asperpentyn ( 1 ) is a 1,3-enyne-containing cyclohexanoid terpenoid isolated from Aspergillus and Pestalotiopsis. The genetic basis and biochemical mechanism of 1,3-enyne biosynthesis in 1 , and other natural products containing this motif, has remained enigmatic despite their potential ecological roles. Identified here is the biosynthetic gene cluster and characterization of two crucial enzymes in the biosynthesis of 1 . A P450 monooxygenase that has a dual function, to first catalyze dehydrogenation of the prenyl chain to generate a cis-diene intermediate and then serve as an acetylenase to yield an alkyne moiety, and thus the 1,3-enyne, was discovered. A UbiA prenyltransferase was also characterized and it is unusual in that it favors transferring a five-carbon prenyl chain, rather than a polyprenyl chain, to a p-hydroxybenzoic acid acceptor.     

Origin of the Regioselective Fatty‐Acid Hydroxylation versus Decarboxylation by a Cytochrome P450 Peroxygenase: What Drives the Reaction to Biofuel Production?

The cytochromes P450 are heme‐based mono‐oxygenases or peroxygenases involved in vital reaction processes for human health. A recently described P450 per‐oxygenase, OleT_JE, converts long‐chain fatty acids to terminal olefins and as such may have biotechnological relevance in biodiesel production. However, the reaction produces significant amounts of α‐ and β‐hydroxylation by‐products, and their origin are poorly understood. Herein, we elucidate through a QM/MM study on the bifurcation pathways how the three possible products are generated and show how the enzyme can be further engineered for optimum desaturase activity. The studies showed that the polarity and the solvent accessibility of the substrate in the binding pocket destabilize the OH‐rebound pathways and kinetically enable a thermodynamically otherwise unfavorable decarboxylation reaction. The origins of the bifurcation pathways are analyzed with valence‐bond models that highlight the differences in reaction mechanism.     

Exploiting a C–N Bond Forming Cytochrome P450 Monooxygenase for C–S Bond Formation

C–S bond formation reactions are widely distributed in the biosynthesis of biologically active molecules, and thus have received much attention over the past decades. Herein, we report intramolecular C–S bond formation by a P450 monooxygenase, TleB, which normally catalyzes a C−N bond formation in teleocidin biosynthesis. Based on the proposed reaction mechanism of TleB, a thiol-substituted substrate analogue was synthesized and tested in the enzyme reaction, which afforded the unprecedented sulfur-containing thio-indolactam V, in addition to an unusual indole-fused 6/5/8-tricyclic product whose structure was determined by the crystalline sponge method. Interestingly, conformational analysis revealed that the SOFA conformation is stable in thio-indolactam V, in sharp contrast to the major TWIST form in indolactam V, resulting in differences in their biological activities.     

Cytochrome P450 Catalyzed Oxidative Hydroxylation of Achiral Organic Compounds with Simultaneous Creation of Two Chirality Centers in a Single C?H Activation Step

Regio‐ and stereoselective oxidative hydroxylation of achiral or chiral organic compounds mediated by synthetic reagents, catalysts, or enzymes generally leads to the formation of one new chiral center that appears in the respective enantiomeric or diastereomeric alcohols. By contrast, when subjecting appropriate achiral compounds to this type of C H activation, the simultaneous creation of two chiral centers with a defined relative and absolute configuration may result, provided that control of the regio‐, diastereo‐, and enantioselectivity is ensured. The present study demonstrates that such control is possible by using wild type or mutant forms of the monooxygenase cytochrome P450 BM3 as catalysts in the oxidative hydroxylation of methylcyclohexane and seven other monosubstituted cyclohexane derivatives.     

Separation and Concentration of Rare Earths by Recycling Liquid–Liquid Chromatography with Multiple Sample Injection: A Computational Study

Our computational studies into the separation of two- and three-component mixtures of rareearth salts by recycling liquid–liquid chromatography (RLC) with multiple sample injection show that this method considerably enhances metal separation efficiency and makes it possible to concentrate one of the components of mixture.