MD simulations and QM/MM calculations reveal the key mechanistic elements which are responsible for the efficient C-H amination reaction performed by a bioengineered P450 enzyme

Origin of Enantioselectivity in Engineered Cytochrome c-Catalyzed Carbon-Radical FePP Hydrolysis Revealed Using QM/MM (ABEEM Polarizable Force Field) and MD Simulations

The origin of highly efficient asymmetric aminohydroxylation of styrene catalyzed by engineered cytochrome c is investigated by the developed Atom-Bond Electronegativity Equalization Method polarizable force field (ABEEM PFF), which is a combined outcome of electronic and steric effects. Model molecules were used to establish the charge parameters of the ABEEM PFF, for which the bond-stretching and angle-bending parameters were obtained by using a combination of modified Seminario and scan methods. The interactions between carbon-radical Fe-porphyrin (FePP) and waters are simulated by molecular dynamics, which shows a clear preference for the pre-R over the pre-S. This preference is attributed to the hydrogen-bond between the mutated 100S and 101P residues as well as van der Waals interactions, enforcing a specific conformation of the carbon-radical FePP complex within the binding pocket. Meanwhile, the hydrogen-bond between water and the nitrogen atom in the active intermediate dictates the stereochemical outcome. Quantum mechanics/molecular mechanics (QM/MM (ABEEM PFF)) and free-energy perturbation calculations elucidate that the 3RTS is characterized by sandwich-like structure among adjacent amino acid residues, which exhibits greater stability than crowed arrangement in 3STS and enables the R enantiomer to form more favorably. Thus, this study provides mechanistic insight into the catalytic reaction of hemoproteins.

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.

Stereoselective Construction of β-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation

Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Methods for the asymmetric synthesis of these molecules are therefore highly desirable, particularly through the selective functionalization of unreactive aliphatic C-H bonds. Here we show the development of a strategy for the asymmetric synthesis of β-, γ-, and δ-lactams via hemoprotein-catalysed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation yielding the desired lactam products in high yields, high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Additionally, an alkaloid natural product and a drug molecule were synthesized chemoenzymatically in much fewer steps (7-8 vs. 11-12) than previously reported, further demonstrating the power of biosynthetic strategy for the preparation of complex bioactive molecules.

Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases

Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.

How Axial Coordination Regulates the Electronic Structure and C-H Amination Reactivity of Fe-Porphyrin-Nitrene?

Detailed electronic structure and its correlation with the intramolecular C-H amination reactivity of Fe-porphyrin-nitrene intermediates bearing different "axial" coordination have been investigated using multiconfigurational complete active space self-consistent field (CASSCF), N-electron valence perturbation theory (NEVPT2), and hybrid density functional theory (DFT-B3LYP) calculations. Three types of "axial" coordination, -OMe/-O(H)Me (1-Sul/2-Sul), -SMe/-S(H)Me (3-Sul/4-Sul), and -NMeIm (MeIm = 3-methyl-imidazole) (5-Sul) mimicking serine, cysteine, and histidine, respectively, along with no axial coordination (6-Sul) have been considered to decipher how the "axial" coordination of different strengths regulates the electronic integrity of the Fe-N core and nitrene-transfer reactivity of Fe-porphyrin-nitrene intermediates. CASSCF-based natural orbitals reveal two distinct classes of electronic structures: Fe-nitrenes (1-Sul and 3-Sul) with relatively stronger axial coordination (-OMe and -SMe) display "imidyl" nature and those (2-Sul, 4-Sul, and 6-Sul) with weaker axial coordination (-O(H)Me, -S(H)Me and no axial coordination) exhibit "imido-like" character. A borderline between the two classes is also observed with NMeIm axial coordination (5-Sul). Axial coordination of different strengths not only regulates the electronic structure but also modulates the Fe-3d orbital energies, as revealed through the d-d transition energies obtained by CASSCF/NEVPT2 calculations. The relatively lower energy of Fe-3dz2 orbital allows easy access to low-lying high-spin quintet states in the cases of weaker "axial" coordination (2-Sul, 4-Sul, and 6-Sul), and the associated hydrogen atom transfer (HAT) reactivity appears to involve two-state triplet-quintet reactivity through minimum energy crossing point (3,5MECP) between the spin states. In stark contrast, Fe-nitrenes with relatively stronger "axial" coordination (1-Sul and 3-Sul) undergo triplet-only HAT reactivity. Overall, this in-depth electronic structure investigation and HAT reactivity evaluation reveal that the weaker axial coordination in Fe-porphyrin-nitrene complexes (2-Sul, 4-Sul, and 6-Sul) can promote more efficient C-H oxidation through the quintet spin state.

Mechanism of CO2 Reduction to Methanol with H2 on an Iron(II)-scorpionate Catalyst

CO2 utilization is an important process in the chemical industry with great environmental power. In this work we show how CO2 and H2 can be reacted to form methanol on an iron(II) center and highlight the bottlenecks for the reaction and what structural features of the catalyst are essential for efficient turnover. The calculations predict the reactions to proceed through three successive reaction cycles that start with heterolytic cleavage of H2 followed by sequential hydride and proton transfer processes. The H2 splitting process is an endergonic process and hence high pressures will be needed to overcome this step and trigger the hydrogenation reaction. Moreover, H2 cleavage into a hydride and proton requires a metal to bind hydride and a nearby source to bind the proton, such as an amide or pyrazolyl group, which the scorpionate ligand used here facilitates. As such the computations highlight the non-innocence of the ligand scaffold through proton shuttle from H2 to substrate as an important step in the reaction mechanism.

Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations

Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen dilemma faced by cytochrome P450s and exhibit greater stability than the latter. As such, they hold great potential for industrial applications. A thorough understanding of their catalysis is needed to improve their catalytic performance. However, it remains elusive how UPOs effectively convert peroxide to Compound I (CpdI), the principal oxidizing intermediate in the catalytic cycle. Previous computational studies of this process primarily focused on heme peroxidases and P450s, which have significant differences in the active site from UPOs. Additionally, the roles of peroxide unbinding in the kinetics of CpdI formation, which is essential for interpreting existing experiments, have been understudied. Moreover, there has been a lack of free energy characterizations with explicit sampling of protein and hydration dynamics, which is critical for understanding the thermodynamics of the proton transport (PT) events involved in CpdI formation. To bridge these gaps, we employed multiscale simulations to comprehensively characterize the CpdI formation in wild-type UPO from Agrocybe aegerita (AaeUPO). Extensive free energy and potential energy calculations were performed in a quantum mechanics/molecular mechanics setting. Our results indicate that substrate-binding dehydrates the active site, impeding the PT from H2O2 to a nearby catalytic base (Glu196). Furthermore, the PT is coupled with considerable hydrogen bond network rearrangements near the active site, facilitating subsequent O-O bond cleavage. Finally, large unbinding free energy barriers kinetically stabilize H2O2 at the active site. These findings reveal a delicate balance among PT, hydration dynamics, hydrogen bond rearrangement, and cosubstrate unbinding, which collectively enable efficient CpdI formation. Our simulation results are consistent with kinetic measurements and offer new insights into the CpdI formation mechanism at atomic-level details, which can potentially aid the design of next-generation biocatalysts for sustainable chemical transformations of feedstocks.

Investigating the role of Sterol C24-Methyl transferase mutation on drug resistance in leishmaniasis and identifying potential inhibitors

Leishmaniasis is a fatal disease caused by the leishmania parasite. For the survival of the leishmania parasite, Sterol C24-Methyl Transferase (SMT) is essential which is an enzyme of the ergosterol pathway. SMT protein mutation is responsible for Amphotericin-B drug resistance in Leishmania, which is the main treatment for visceral leishmaniasis. Amphotericin-B resistance is caused by three mutated residues V131I, V321I and F72C. The underlying mechanisms and structural changes in SMT enzymes responsible for resistance due to mutation are still not well understood. In the current study, the potential mechanism of resistance due to these mutations and the structure variation of wild and mutant SMT proteins were investigated through molecular dynamics simulations and molecular docking analysis. The results showed that AmB established strong bonding interaction with wild SMT as compare to mutants SMT. The binding energy calculation showed that binding energy of AmB with mutants SMT increases as compare to the wild SMT. Further structural based virtual screening was carried out to design potential inhibitors for the mutant SMT. On the basis of structural-based virtual screening four inhibitors (SANC01057, SANC00882, SANC00414, SANC01047) were computationally identified as potential mutant SMT (F72C) inhibitors. This work provides valuable information for improved management of drug resistant Leishmaniasis.Communicated by Ramaswamy H. Sarma.

Computational Mechanistic Investigations of Biocatalytic Nitrenoid C-H Functionalizations via Engineered Heme Proteins

Engineered heme proteins were developed to possess numerous excellent biocatalytic nitrenoid C-H functionalizations. Computational approaches such as density functional theory (DFT), hybrid quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics (MD) calculations were employed to help understand some important mechanistic aspects of these heme nitrene transfer reactions. This review summarizes advances of computational reaction pathway results of these biocatalytic intramolecular and intermolecular C-H aminations/amidations, focusing on mechanistic origins of reactivity, regioselectivity, enantioselectivity, diastereoselectivity as well as effects of substrate substituent, axial ligand, metal center, and protein environment. Some important common and distinctive mechanistic features of these reactions were also described with brief outlook of future development.

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis

Natural products and their derivatives are widely used across various industries, particularly pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing and meeting the growing need for diverse natural products. Natural enzymes, on the other hand, often exhibit unsatisfactory catalytic characteristics and necessitate further enzyme engineering modifications. QM/MM, as a powerful and extensively used computational tool in the field of enzyme catalysis, has been increasingly applied in rational enzyme engineering over the past decade. In this review, we summarize recent advances in QM/MM computational investigation on enzyme catalysis and enzyme engineering for natural product biosynthesis. The challenges and perspectives for future QM/MM applications aided enzyme engineering in natural product biosynthesis will also be discussed.

Role of mutations in a chemoenzymatic enantiodivergent C(sp3)-H insertion: exploring the mechanism and origin of stereoselectivity

New-to-nature enzymes have emerged as powerful catalysts in recent years for streamlining various stereoselective organic transformations. While synthetic strategies employing engineered enzymes have witnessed proliferating success, there is limited clarity on the mechanistic front and more so when considering molecular-level insights into the role of selected mutations, dramatically escalating catalytic competency and selectivity. We have investigated the mechanism and correlation between mutations and exquisite stereoselectivity of a lactone carbene insertion into the C(sp3)-H bond of substituted aniline, catalyzed by two mutants of a cytochrome P450 variant, "P411" (engineered through directed evolution) in which the axial cysteine has been mutated to serine, utilizing various computational tools. The pivotal role of S264 and L/R328 mutations in the active site has been delineated computationally using two cluster models, thus rationalizing the enantiodivergence. This report provides much-needed insights into the origin of enantiodivergence, furnishing a mechanistic framework for understanding the anchoring effects of H-bond donor residues with the lactone ring. This study is expected to have important implications in the rational design of stereodivergent enzymes and toward successful in silico enzyme designing.

Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Mechanistic Insights into Photochemical CO2 Reduction to CH4 by a Molecular Iron-Porphyrin Catalyst

Iron tetraphenylporphyrin complex modified with four trimethylammonium groups (Fe-p-TMA) is found to be capable of catalyzing the eight-electron eight-proton reduction of CO₂ to CH₄ photochemically in acetonitrile. In the present work, density functional theory (DFT) calculations have been performed to investigate the reaction mechanism and to rationalize the product selectivity. Our results revealed that the initial catalyst Fe-p-TMA ([Cl-Fe(III)-LR₄]⁴⁺, where L = tetraphenylporphyrin ligand with a total charge of -2, and R₄ = four trimethylammonium groups with a total charge of +4) undergoes three reduction steps, accompanied by the dissociation of the chloride ion to form [Fe(II)-L^••2-R₄]²⁺. [Fe(II)-L^••2-R₄]²⁺, bearing a Fe(II) center ferromagnetically coupled with a tetraphenylporphyrin diradical, performs a nucleophilic attack on CO₂ to produce the ¹η-CO₂ adduct [CO₂^•--Fe(II)-L^•-R₄]²⁺. Two intermolecular proton transfer steps then take place at the CO₂ moiety of [CO₂^•--Fe(II)-L^•-R₄]²⁺, resulting in the cleavage of the C-O bond and the formation of the critical intermediate [Fe(II)-CO]⁴⁺ after releasing a water molecule. Subsequently, [Fe(II)-CO]⁴⁺ accepts three electrons and one proton to generate [CHO-Fe(II)-L^•-R₄]²⁺, which finally undergoes a successive four-electron-five-proton reduction to produce methane without forming formaldehyde, methanol, or formate. Notably, the redox non-innocent tetraphenylporphyrin ligand was found to play an important role in CO₂ reduction since it could accept and transfer electron(s) during catalysis, thus keeping the ferrous ion at a relatively high oxidation state. Hydrogen evolution reaction via the formation of Fe-hydride ([Fe(II)-H]³⁺) turns out to endure a higher total barrier than the CO₂ reduction reaction, therefore providing a reasonable explanation for the origin of the product selectivity.

Origin of the Distinctive Electronic Structure of Co- and Fe-Porphyrin-Nitrene and Its Effect on Their Nitrene Transfer Reactivity

Metal-bound nitrene species are the crucial intermediate in catalytic nitrene transfer reactions exhibited by engineered enzymes and molecular catalysts. The electronic structure of such species and its correlation with nitrene transfer reactivity have not been fully understood yet. This work presents an in-depth electronic structure analysis and nitrene transfer reactivity of two prototypical metal-nitrene species derived from Co^II(TPP) and Fe^II(TPP) (TPP = meso-tetraphenylporphyrin) complexes and tosyl azide nitrene precursor. Parallel to the well-known "cobalt(III)-imidyl" electronic structure of the Co-porphyrin-nitrene species, the formation mechanism and electronic structure of the elusive Fe-porphyrin-nitrene have been established using density functional theory (DFT) and multiconfigurational complete active-space self-consistent field (CASSCF) calculations. Electronic structure evolution analysis for the metal-nitrene formation step and CASSCF-derived natural orbitals advocates that the electronic nature of the metal-nitrene (M-N) core of Fe(TPP) is strikingly different from that of the Co(TPP). Specifically, the "imidyl" nature of the Co-porphyrin-nitrene [(TPP)Co^III-^•NTos] (Tos = tosyl) (I1_Co) is contrasted by the "imido-like" character of the Fe-porphyrin-nitrene [(TPP)Fe^IV[Formula: see text]NTos] (I1_Fe). This difference between Co- and Fe-nitrene has been attributed to the additional interactions between Fe-d_π and N-p_π orbitals in Fe-nitrene, which is further complemented by the shortened Fe-N bond length of 1.71 Å. This stronger M-N bond in Fe-nitrene compared to the Co-nitrene is also reflected in the higher exothermicity (ΔΔH = 16 kcal/mol) of the Fe-nitrene formation step. The "imido-like" character renders a relatively lower spin population on the nitrene nitrogen (+0.42) in the Fe-nitrene complex I1_Fe, which undergoes the nitrene transfer to the C═C bond of styrene with a considerably higher enthalpy barrier (ΔH^‡ = 10.0 kcal/mol) compared to the Co congener I1_Co (ΔH^‡ = 5.6 kcal/mol) possessing a higher nitrogen spin population (+0.88) and a relatively weaker M-N bond (Co-N = 1.80 Å).

How the Conformational Movement of the Substrate Drives the Regioselective C-N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations

P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol into indolactam V through selective intramolecular C-H bond amination at the indole C4 position. Understanding its catalytic mechanism is instrumental for the engineering or design of P450-catalyzed C-H amination reactions. Using multiscale computational methods, we show that the reaction proceeds through a diradical pathway, involving a hydrogen atom transfer (HAT) from N1-H to Cpd I, a conformational transformation of the substrate radical species, and a second HAT from N13-H to Cpd II. Intriguingly, the conformational transformation is found to be the key to enabling efficient and selective C-N coupling between N13 and C4 in the subsequent diradical coupling reaction. The underlined conformational transformation is triggered by the first HAT, which proceeds with an energy-demanding indole ring flip and is followed by the facile approach of the N13-H group to Cpd II. Detailed analysis shows that the internal electric field (IEF) from the protein environment plays key roles in the transformation process, which not only provides the driving force but also stabilizes the flipped conformation of the indole radical. Our simulations provide a clear picture of how the P450 enzyme can smartly modulate the selective C-N coupling reaction. The present findings are in line with all available experimental data, highlighting the crucial role of substrate dynamics in controlling this highly valuable reaction.

Stereoselective Construction of β-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation

Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Given their widespread presence in bioactive molecules, methods for the asymmetric synthesis of these molecules, in particular through the selective functionalization of ubiquitous yet unreactive aliphatic C-H bonds, are highly desirable. In this study, we report the development of a novel strategy for the asymmetric synthesis of 4-, 5-, and 6-membered lactams via an unprecedented hemoprotein-catalyzed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation producing an array of β-, γ-, and δ-lactam molecules in high yields, with high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps in these reactions and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Using this system, it was possible to accomplish the chemoenzymatic total synthesis of an alkaloid natural product and a drug molecule in much fewer steps (7-8 vs. 11-12) than previously possible, which showcases the power of this biosynthetic strategy toward enabling the preparation of complex bioactive molecules.

Computations reveal a crucial role of an aromatic dyad in the catalytic function of plant cytochrome P450 mint superfamily

Enzymes are highly specific for their native functions, however with advances in bioengineering tools such as directed evolution, several enzymes are being repurposed for the secondary function of contemporary significance(Khersonsky and Tawfik, 2010 [1]⁾. Due to the functional versatility, the Cytochrome P450 (CYP450) superfamily has become the ideal scaffold for such bioengineering. In the current study, using MD (molecular dynamics) simulations and hybrid QM/MM (Quantum mechanics/molecular mechanics) calculations, we have studied the mechanism of spontaneous emergence of a secondary function due to a single site mutation in two plant CYP450 enzymes from the mint family. The MD simulations of WT (wild type) CYP71D18 and CYP71D13 enzymes and their variants show a crucial gating mechanism by aromatic dyad formed by Phe121 and Phe363 which regulates the substrate recognition. The QM/MM calculations reveal that the hydroxylation reactions at C3 and C6 positions in WT CYP71D18 and CYP71D13 enzymes as well as their variants follow a hydrogen atom transfer (HAT) followed by a single electron transfer (SET) mechanism, which is different from the typical rebound mechanism shown by most of the CYP450 enzymes.

Biocatalytic Intramolecular C-H aminations via Engineered Heme Proteins: Full Reaction Pathways and Axial Ligand Effects

Engineered heme protein biocatalysts provide an efficient and sustainable approach to develop amine-containing compounds through C-H amination. A quantum chemical study to reveal the complete heme catalyzed intramolecular C-H amination pathway and protein axial ligand effect was reported, using reactions of an experimentally used arylsulfonylazide with hemes containing L=none, SH- , MeO- , and MeOH to simulate no axial ligand, negatively charged Cys and Ser ligands, and a neutral ligand for comparison. Nitrene formation was found as the overall rate-determining step (RDS) and the catalyst with Ser ligand has the best reactivity, consistent with experimental reports. Both RDS and non-RDS (nitrene transfer) transition states follow the barrier trend of MeO- Collapse

Key Words

• amination
• biocatalysis
• density functional calculations
• heme proteins
• reaction mechanism

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MESH Headings

• Hemeproteins
• Ligands
• Amination
• Heme/chemistry
• Amines

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Grants

• CHE-1300912 and CHE-2054897 National Science Foundation
• National Science Foundation

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Affiliation(s)

Yang Wei Department of Chemistry and Chemical BiologyStevens Institute of Technology1 Castle Point on HudsonHobokenNJ 07030USA Department of Chemistry and BiochemistryLoyola University Chicago1032 W Sheridan RdChicagoIL 60660USA
Melissa Conklin Department of Chemistry and Chemical BiologyStevens Institute of Technology1 Castle Point on HudsonHobokenNJ 07030USA
Yong Zhang Department of Chemistry and Chemical BiologyStevens Institute of Technology1 Castle Point on HudsonHobokenNJ 07030USA

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C-N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp3)-H Amination: A Combined Computational and Experimental Investigation

Engineered metalloenzymes represent promising catalysts for stereoselective C-H functionalization reactions. Recently, P450 enzymes have been evolved to allow for new-to-nature intramolecular C(sp3)-H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C-N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C-N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to the spin-state change and ring strain of the cyclization process, thereby allowing stereoablative C-N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism in biocatalytic C(sp3)-H functionalizations involving radical intermediates, opening up new avenues for the development of other challenging asymmetric C(sp3)-H functionalizations.

Local Electric Fields Dictate Function: The Different Product Selectivities Observed for Fatty Acid Oxidation by Two Deceptively Very Similar P450-Peroxygenases OleT and BSβ

Cytochrome P450 peroxygenases use hydrogen peroxide to hydroxylate long-chain fatty acids by bypassing the use of O₂ and a redox partner. Among the peroxygenases, P450_OleT uniquely performs decarboxylation of fatty acids and production of terminal olefins. This route taken by P450_OleT is intriguing, and its importance is augmented by the practical importance of olefin production. As such, this mechanistic choice merits elucidation. To address this puzzle, we use hybrid QM/MM calculations and MD simulations for the OleT enzyme as well as for the structurally analogous enzyme, P450_BSβ. The study of P450_OleT reveals that the protonated His85 in the wild-type P450_OleT plays a crucial role in steering decarboxylation activity by stabilizing the corresponding hydroxoiron(IV) intermediate (Cpd II). In contrast, for P450_BSβ in which Q85 replaces H85, the respective Cpd II species is unstable and it reacts readily with the substrate radical by rebound, producing hydroxylation products. As shown, this single-site difference creates in P450_OleT a local electric field (LEF), which is significantly higher than that in P450_BSβ. In turn, these LEF differences are responsible for the different stabilities of the respective Cpd II/radical intermediates and hence for different functions of the two enzymes. P450_BSβ uses the common rebound mechanism and leads to hydroxylation, whereas P450_OleT proceeds via decarboxylation and generates terminal olefins. Olefin production projects the power of a single residue to alter the LEF and the enzyme's function.