Strategies for Substrate-Regulated P450 Catalysis: From Substrate Engineering to Co-catalysis

Cytochrome P450 enzymes (P450s) catalyze the monooxygenation of various organic substrates. These enzymes are fascinating and promising biocatalysts for synthetic applications. Despite the impressive abilities of P450s in the oxidation of C−H bonds, their practical applications are restricted by intrinsic drawbacks, such as poor stability, low turnover rates, the need for expensive cofactors (e.g., NAD(P)H), and the narrow scope of useful non-native substrates. These issues may be overcome through the general strategy of protein engineering, which focuses on the improvement of the catalysts themselves. Alternatively, several emerging strategies have been developed that regulate the P450 catalytic process from the viewpoint of the substrate. These strategies include substrate engineering, decoy molecule, and dual-functional small-molecule co-catalysis. Substrate engineering focuses on improving the substrate acceptance and reaction selectivity by means of an anchoring group. The latter two strategies utilize co-substrate-like small molecules that either are proposed to reform the active site, thereby switching the substrate specificity, or directly participate in the catalytic process, thereby creating new catalytic peroxygenation capabilities towards non-native substrates. For at least 10 years, these approaches have played unique roles in solving the problems highlighted above, either alone or in conjunction with protein engineering. Herein, we review three strategies for substrate regulation in the P450-catalyzed oxidation of non-native substrates. Furthermore, we address remaining challenges and potential solutions associated with these approaches.     

Selective Enzymatic Oxidation of Silanes to Silanols

Compared to the biological world's rich chemistry for functionalizing carbon, enzymatic transformations of the heavier homologue silicon are rare. We report that a wild-type cytochrome P450 monooxygenase (P450_BM3 from Bacillus megaterium, CYP102A1) has promiscuous activity for oxidation of hydrosilanes to give silanols. Directed evolution was applied to enhance this non-native activity and create a highly efficient catalyst for selective silane oxidation under mild conditions with oxygen as the terminal oxidant. The evolved enzyme leaves C−H bonds present in the silane substrates untouched, and this biotransformation does not lead to disiloxane formation, a common problem in silanol syntheses. Computational studies reveal that catalysis proceeds through hydrogen atom abstraction followed by radical rebound, as observed in the native C−H hydroxylation mechanism of the P450 enzyme. This enzymatic silane oxidation extends nature's impressive catalytic repertoire.     

Site-Selective Alkoxylation of Benzylic C−H Bonds by Photoredox Catalysis

Methods that enable the direct C−H alkoxylation of complex organic molecules are significantly underdeveloped, particularly in comparison to analogous strategies for C−N and C−C bond formation. In particular, almost all methods for the incorporation of alcohols by C−H oxidation require the use of the alcohol component as a solvent or co-solvent. This condition limits the practical scope of these reactions to simple, inexpensive alcohols. Reported here is a photocatalytic protocol for the functionalization of benzylic C−H bonds with a wide range of oxygen nucleophiles. This strategy merges the photoredox activation of arenes with copper(II)-mediated oxidation of the resulting benzylic radicals, which enables the introduction of benzylic C−O bonds with high site selectivity, chemoselectivity, and functional-group tolerance using only two equivalents of the alcohol coupling partner. This method enables the late-stage introduction of complex alkoxy groups into bioactive molecules, providing a practical new tool with potential applications in synthesis and medicinal chemistry.     

Kinetic and Product Study of the S-oxidation vs HAT Chemoselectivity in Reactions Promoted by Nonheme Iron(IV)-oxo Complex/NHPI Mediator System

The chemoselectivity between S-oxidation and hydrogen atom transfer (HAT) from C−H bonds has been investigated in the oxidations of a series of aryl sulfides, alkyl aromatic compounds and benzylic alcohols promoted by the iron(IV)-oxo complex [(N4Py)Fe^IV(O)]²⁺ (N4Py: N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)-methylamine) either alone or in the presence of the N-hydroxyphthalimide (NHPI) mediator via kinetic and product studies. Kinetic analyses indicate a generally higher reactivity of [(N4Py)Fe^IV(O)]²⁺ for S-oxidation process while HAT is favored in the reactions promoted by phthalimide-N-oxyl radical (PINO) deriving from NHPI oxidation. Product analysis in intermolecular competitive oxidations confirms the kinetic results with sulfoxides obtained as major products in the oxidation promoted by [(N4Py)Fe^IV(O)]²⁺. Conversely, when NHPI is employed as a mediator, significant differences in terms of chemoselectivity are observed, and HAT-derived products are obtained in higher yields which translate into an inversion of selectivity in the case of the substrates containing activated C−H bonds like diphenylmethane, triphenylmethane and benzylic alcohols. A similar change of chemoselectivity is also observed in the oxidation of aromatic substrates containing both a sulfur atom and α to OH benzylic C−H bonds, with the sulfoxide product more abundant in the absence of NHPI and carbonyl products prevailing with the [(N4Py)Fe^IV(O)]²⁺/NHPI system.     

Kinetic isotope effects implicate the iron-oxene as the sole oxidant in P450-catalyzed N-dealkylation

Multiple oxidants have been implicated as playing a role in cytochrome P450-mediated oxidations. Herein, we report results on N-dealkylation, one of the most facile reactions mediated by P450 enzymes. We have employed the N-oxides of a series of para-substituted 13C2H2-labeled N,N-dimethylanilines to function as both substrates and surrogate oxygen atom donors for P450cam and P4502E1. Kinetic isotope effect profiles obtained using the N-oxide system were found to closely match the profiles produced using the complete NAD(P)H/NAD(P)-P450 reductase/O2 system. The results are consistent with oxidation occurring solely through an iron-oxene species.     

Enzymatic C−H Oxidation–Amidation Cascade in the Production of Natural and Unnatural Thiotetronate Antibiotics with Potentiated Bioactivity

The selective activation of unreactive hydrocarbons by biosynthetic enzymes has inspired new synthetic methods in C−H bond activation. Herein, we report the unprecedented two‐step biosynthetic conversion of thiotetromycin to thiotetroamide C involving the tandem oxidation and amidation of an unreactive ethyl group. We detail the genetic and biochemical basis for the terminal amidation in thiotetroamide C biosynthesis, which involves a uniquely adapted cytochrome P450–amidotransferase enzyme pair and highlights the first oxidation–amidation enzymatic cascade reaction leading to the selective formation of a primary amide group from a chemically inert alkyl group. Motivated by the ten‐fold increase in antibiotic potency of thiotetroamide C ascribed to the acetamide group and the unusual enzymology involved, we enzymatically interrogated diverse thiolactomycin analogues and prepared an unnatural thiotetroamide C analogue with potentiated bioactivity compared to the parent molecule.     

P450 fingerprinting method for rapid discovery of terpene hydroxylating P450 catalysts with diversified regioselectivity

Engineered P450 enzymes constitute attractive catalysts for the selective oxidation of unactivated C-H bonds in complex molecules. A current bottleneck in the use of P450 catalysis for chemical synthesis is the time and effort required to identify the P450 variant(s) with the desired level of activity and selectivity. In this report, we describe a method to map the active site configuration of engineered P450 variants in high throughput using a set of semisynthetic chromogenic probes. Through analysis of the resulting 'fingerprints', reliable predictions can be made regarding the reactivity of these enzymes toward complex substrates structurally related to the fingerprint probes. In addition, fingerprint analysis offers a convenient and time-effective means to assess the regioselectivity properties of the fingerprinted P450s. The described approach can represent a valuable tool to expedite the discovery of P450 oxidation catalysts for the functionalization of relevant natural products such as members of the terpene family.     

Preparation, characterization, and substrate metabolism of gold-immobilized cytochrome P450 2C9

The cytochrome P450 enzymes represent an important class of heme-containing enzymes. There is considerable interest in immobilizing these enzymes on a surface so that interactions between a single enzyme and other species can be studied with respect to electron transfer, homodimer or heterodimer interactions, or for construction of biological-based chips for standardizing cytochrome P450 metabolism or for high-throughput screening of pharmaceutical agents. Previous studies have generally immobilized P450 enzymes in a matrix or on a surface. Here, we have attached CYP2C9 to gold substrates such that the resulting construct maintains the ability to bind and metabolize substrates in the presence of NADPH and cytochrome P450 reductase. The activity of these chips is directly dependent upon the linkers used to attach CYP2C9 and to the presence of key molecules in the active site during enzyme attachment. A novel method to detect substrate-enzyme binding, namely, superconducting quantum interference device (SQUID) magnetometry, was used to monitor the binding of substrates. Most significantly, conditions that allow measurable CYP2C9 metabolism to occur have been developed.     

Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C−H Bonds**

Fe^II- and α-ketoglutarate-dependent halogenases and oxygenases can catalyze site-selective functionalization of C−H bonds via a variety of C−X bond forming reactions, but achieving high chemoselectivity for functionalization using non-native functional groups remains rare. The current study shows that directed evolution can be used to engineer variants of the dioxygenase SadX that address this challenge. Site-selective azidation of succinylated amino acids and a succinylated amine was achieved as a result of mutations throughout the SadX structure. The installed azide group was reduced to a primary amine, and the succinyl group required for azidation was enzymatically cleaved to provide the corresponding amine. These results provide a promising starting point for evolving additional SadX variants with activity on structurally distinct substrates and for enabling enzymatic C−H functionalization with other non-native functional groups.     

Mechanistic Insights into the Regio- and Stereoselectivities of Testosterone and Dihydrotestosterone Hydroxylation Catalyzed by CYP3A4 and CYP19A1

The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio- and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi-scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio- and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s.     

Divergent Coupling of Benzocyclobutenones with Indoles via C−H and C−C Activations

Highly selective divergent coupling reactions of benzocyclobutenones and indoles, in which the chemoselectivity is controlled by catalysts, are reported herein. The substrates undergo C2(indole)–C8(benzocyclobutenone) coupling to produce benzylated indoles and benzo[b]carbazoles in the Ni- and Ru-catalyzed reactions. A completely different selectivity pattern C2(indole)–C2(benzocyclobutenone) coupling to form arylated indoles is observed in the Rh-catalyzed reaction. Preliminary mechanistic studies suggest C−H and C−C activations in the reaction pathway. Synthetic utility of this protocol is demonstrated by the selective synthesis of three different types of carbazoles from the representative products.     

Metal-catalyzed alkyne oxidation/C?H functionalization: Effects of oxidant,temperature, and metal catalyst on chemoselectivity

Gold-catalyzed intermolecular alkyne oxidation has attracted much synthetic attention, but mostly suffering undesired over-oxidation. Recent experiments demonstrated that over-oxidation could be dramatically suppressed in zinc(II)-catalyzed intermolecular alkyne oxidation/C H functionalization. By means of first-principle density functional theory calculations, we explored the mechanism of the M-catalyzed intermolecular alkyne oxidations (M = Zn(OTf)₂ and Au⁺PR₃) as well as the effects of oxidants, temperature, and metal catalysts on chemoselectivity, in an effort to disclose the origin of the extraordinary chemoselectivity pertaining to zinc catalysis. Our calculations indicate that the Zn-catalyzed intermolecular alkyne oxidation/C H functionalization proceeds by a Friedel–Crafts alkylation mechanism rather than metal carbene insertion mechanism. The chemoselectivity of C H functionalization against over-oxidation in Zn catalysis, in comparison with gold catalysis, can be jointly controlled by four factors: (1) the use of less nucleophilic N-oxide, (2) the enhanced electrophilicity and carbocationic nature of the carbenic site in the α-oxo metal carbenoid intermediate, (3) enhanced steric repulsion to incoming oxidant exerted by bulky ancillary ligand in the close nearby of the carbenic site to disfavor intermolecular over-oxidation and (4) the large negative value of activation entropy in the intermolecular over-oxidation pathway, that jointly give rise to lower activation free energy for the intramolecular cyclization/C H functionalization pathway than for the intermolecular over-oxidation pathway. © 2018 Wiley Periodicals, Inc.     

What factors influence the ratio of C-H hydroxylation versus C=C epoxidation by a nonheme cytochrome P450 biomimetic?

Density functional calculations on a nonheme biomimetic (Fe=O(TMCS+) have been performed and its catalytic properties versus propene investigated. Our studies show that this catalyst is able to chemoselectively hydroxylate C=H bonds even in the presence of C=C double bonds. This phenomenon has been analyzed and found to occur due to Pauli repusions between protons on the TMCS ligand with protons attached to the approaching substrate. The geometries of the rate determining transition states indicate that the steric hindrance is larger in the epoxidation transition states than in the hydroxylation ones with much shorter distances; hence the hydroxylation pathway is favored over the epoxidation. Although, the reactant experiences close lying triplet and quintet spin states, the dominant reaction mechanism takes place on the quintet spin state surface; i.e., Fe=O(TMCS)+ reacts via single-state reactivity. Our calculations show that this spin state selectivity is the result of geometric orientation of the transition state structures, whereby the triplet ones are destabilized by electrostatic repulsions between the substrate and the ligand while the quintet spin transition states are aligned along the ideal axis. The reactivity patterns and geometries are compared with oxoiron species of dioxygenase and monoxygenase enzymes. Thus, Fe=O(TMCS)+ shows some similarities with P450 enzyme reactivity: it chemoselectively hydroxylates C=H bonds even in the presence of a C=C double bond and therefore is an acceptable P450 biomimetic. However, the absolute barriers of substrate oxidation by Fe=O(TMCS)+ are higher than the ones obtained with heme enzymes, but the chemoselectivity is lesser affected by external perturbations such as hydrogen bonding of a methanol molecule toward the thiolate sulfur or a dielectric constant. This is the first oxoiron complex whereby we calculated a chemoselective hydroxylation over epoxidation in the gas phase.     

One-Pot Synthesis of Primary and Secondary Aliphatic Amines via Mild and Selective sp3 C−H Imination

The direct replacement of sp³ C−H bonds with simple amine units (−NH₂) remains synthetically challenging, although primary aliphatic amines are ubiquitous in medicinal chemistry and natural product synthesis. We report a mild and selective protocol for preparing primary and secondary aliphatic amines in a single pot, based on intermolecular sp³ C−H imination. The first C−H imination of diverse alkanes, this method shows useful site-selectivity within substrates bearing multiple sp³ C−H bonds. Furthermore, this reaction tolerates polar functional groups relevant for complex molecule synthesis, highlighted in the synthesis of amine pharmaceuticals and amination of natural products. We characterize a unique C−H imination mechanism based on radical rebound to an iminyl radical, supported by kinetic isotope effects, stereoablation, resubmission, and computational modeling. This work constitutes a selective method for complex amine synthesis and a new mechanistic platform for C−H amination.     

Selective Enzymatic Oxidation of Silanes to Silanols

Compared to the biological world's rich chemistry for functionalizing carbon, enzymatic transformations of the heavier homologue silicon are rare. We report that a wild‐type cytochrome P450 monooxygenase (P450_BM3 from Bacillus megaterium, CYP102A1) has promiscuous activity for oxidation of hydrosilanes to give silanols. Directed evolution was applied to enhance this non‐native activity and create a highly efficient catalyst for selective silane oxidation under mild conditions with oxygen as the terminal oxidant. The evolved enzyme leaves C?H bonds present in the silane substrates untouched, and this biotransformation does not lead to disiloxane formation, a common problem in silanol syntheses. Computational studies reveal that catalysis proceeds through hydrogen atom abstraction followed by radical rebound, as observed in the native C?H hydroxylation mechanism of the P450 enzyme. This enzymatic silane oxidation extends nature's impressive catalytic repertoire.     

Supramolecular Recognition Allows Remote,Site‐Selective C−H Oxidation of Methylenic Sites in Linear Amines

Site‐selective C−H functionalization of aliphatic alkyl chains is a longstanding challenge in oxidation catalysis, given the comparable relative reactivity of the different methylenes. A supramolecular, bioinspired approach is described to address this challenge. A Mn complex able to catalyze C(sp³)‐H hydroxylation with H₂O₂ is equipped with 18‐benzocrown‐6 ether receptors that bind ammonium substrates via hydrogen bonding. Reversible pre‐association of protonated primary aliphatic amines with the crown ether selectively exposes remote positions (C8 and C9) to the oxidizing unit, resulting in a site‐selective oxidation. Remarkably, such control of selectivity retains its efficiency for a whole series of linear amines, overriding the intrinsic reactivity of C−H bonds, no matter the chain length.     

Supramolecular Recognition Allows Remote,Site‐Selective C−H Oxidation of Methylenic Sites in Linear Amines

Site‐selective C−H functionalization of aliphatic alkyl chains is a longstanding challenge in oxidation catalysis, given the comparable relative reactivity of the different methylenes. A supramolecular, bioinspired approach is described to address this challenge. A Mn complex able to catalyze C(sp³)‐H hydroxylation with H₂O₂ is equipped with 18‐benzocrown‐6 ether receptors that bind ammonium substrates via hydrogen bonding. Reversible pre‐association of protonated primary aliphatic amines with the crown ether selectively exposes remote positions (C8 and C9) to the oxidizing unit, resulting in a site‐selective oxidation. Remarkably, such control of selectivity retains its efficiency for a whole series of linear amines, overriding the intrinsic reactivity of C−H bonds, no matter the chain length.     

Predictable Selectivity in Remote C−H Oxidation of Steroids: Analysis of Substrate Binding Mode

Predictability is a key requirement to encompass late-stage C−H functionalization in synthetic routes. However, prediction (and control) of reaction selectivity is usually challenging, especially for complex substrate structures and elusive transformations such as remote C(sp³)−H oxidation, as it requires distinguishing a specific C−H bond from many others with similar reactivity. Developed here is a strategy for predictable, remote C−H oxidation that entails substrate binding to a supramolecular Mn or Fe catalyst followed by elucidation of the conformation of the host-guest adduct by NMR analysis. These analyses indicate which remote C−H bonds are suitably oriented for the oxidation before carrying out the reaction, enabling prediction of site selectivity. This strategy was applied to late-stage C(sp³)−H oxidation of amino-steroids at C15 (or C16) positions, with a selectivity tunable by modification of catalyst chirality and metal.     

Elucidating the Mechanism and Chemoselectivity in the PBu3-Catalyzed Rauhut-Currier Reaction of Chalcone with Ethyl Acrylate

Disclosing the chemoselectivity and regioselectivity of phosphine-catalyzed Rauhut-Currier (R−C) reaction remains a challenge. Here, a comprehensive study on the possible mechanisms and origins of the chemoselectivity and regioselectivity of PBu₃-catalyzed R−C reactions between ethyl acrylate and chalcone is performed by DFT. Both cross and homo R−C reactions are investigated and compared. The computational results show that the cross R−C reaction is energetically favorable than the homo R−C reaction, with head-to-tail product being generated preferentially. Moreover, the C−C bond formation process is identified to be the regioselectivity- and chemoselectivity-determining step. The CDFT and Parr function analyses are successfully used to predict the origins of chemoselectivity and regioselectivity, respectively. This work would provide a valuable case for exploring the origins of the chemoselectivity and regioselectivity of the phosphine catalyzed reactions, which should be helpful to understand and control the selectivities by rational design.     

Amidinyl Radical Formation through Anodic N−H Bond Cleavage and Its Application in Aromatic C−H Bond Functionalization

We report herein an atom‐economical and sustainable approach to access amidinyl radical intermediates through the anodic cleavage of N−H bonds. The resulting nitrogen‐centered radicals undergo cyclizations with (hetero)arenes, followed by rearomatization, to afford functionalized tetracyclic benzimidazoles in a highly straightforward and efficient manner. This metal‐ and reagent‐free C−H/N−H cross‐coupling reaction exhibits a broad substrate scope and proceeds with high chemoselectivity.