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Fu Y, Yu J, Fan F, Wang B, Cao Z. Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations. J Phys Chem B 2024; 128:5567-5575. [PMID: 38814729 DOI: 10.1021/acs.jpcb.4c00970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Methyl-parathion hydrolase (MPH), which evolved from dihydrocoumarin hydrolase, offers one of the most efficient enzymes for the hydrolysis of methyl-parathion. Interestingly, the substrate preference of MPH shifts from the methyl-parathion to the lactone dihydrocoumarin (DHC) after its mutation of five specific residues (R72L, L273F, L258H, T271I, and S193Δ, m5-MPH). Here, extensive QM/MM calculations and MM MD simulations have been used to delve into the structure-function relationship of MPH enzymes and plausible mechanisms for the chemical and nonchemical steps, including the transportation and binding of the substrate DHC to the active site, the hydrolysis reaction, and the product release. The results reveal that the five mutations remodel the active pocket and reposition DHC within the active site, leading to stronger enzyme-substrate interactions. The MM/GBSA-estimated binding free energies are about -20.7 kcal/mol for m5-MPH and -17.1 kcal/mol for wild-type MPH. Furthermore, this conformational adjustment of the protein may facilitate the chemical step of DHC hydrolysis and the product release, although there is a certain influence on the substrate transport. The hydrolytic reaction begins with the nucleophilic attack of the bridging OH- with the energy barriers of 22.0 and 18.0 kcal/mol for the wild-type and m5-MPH enzymes, respectively, which is rate-determining for the entire process. Unraveling these mechanistic intricacies may help in the understanding of the natural evolution of enzymes for diverse substrates and establish the enzyme structure-function relationship.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jun Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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2
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Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- PpoI. Phys Chem Chem Phys 2024; 26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
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Harariya MS, Gogoi R, Goswami A, Sharma AK, Jindal G. Is Enol Always the Culprit? The Curious Case of High Enantioselectivity in a Chiral Rh(II) Complex Catalyzed Carbene Insertion Reaction. Chemistry 2023; 29:e202301910. [PMID: 37665257 DOI: 10.1002/chem.202301910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/05/2023]
Abstract
The mechanism of Rh2 (S-NTTL)4 catalyzed carbene insertion into C(3)-H of indole is investigated using DFT methods. Since the commonly accepted enol mechanism cannot account for enantioinduction, a concerted oxocarbenium pathway was proposed in an earlier work using a model catalyst. However, after considering the full catalytic system, this study finds that akin to other reactions, here, too, the enol pathway is of lower energy, which now naturally raises a conundrum regarding the mode of chiral induction. Herein, a new water promoted mechanistic pathway involving a metal-associated enol intermediate hydrogen bonding and stereochemical model are proposed to solve this puzzle. It is shown how the catalyst bowl-shaped structure along with substrate-catalyst binding is crucial for achieving high levels of enantioselectivity. A stereodetermining water-assisted proton transfer is proposed and confirmed through deuterium-labeling experiments. The water molecules are held together by H-bonding interactions with the carboxylate ligands that is reminiscent of enzyme catalysis. Although several previous studies have aimed at understanding the mechanism of metal catalyzed carbene insertion reactions, the origin of high stereoinduction especially with chiral metal complexes remains unclear, and till date there is no transition state model that can explain the high enantioselectivity with such chiral Rh complexes. The metal-associated enol pathway is currently underrepresented in catalytic cycles and may play a crucial role in catalyst design. Since the enol pathway is commonly adopted in other metal-catalyzed X-H insertion reactions involving a diazoester, the presented results are not specific to the current reaction. Therefore, this study could provide the direction for achieving high levels of enantioselectivity which is otherwise difficult to achieve with a single metal catalyst.
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Affiliation(s)
- Mahesh S Harariya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Romin Gogoi
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Anubhav Goswami
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Akhilesh K Sharma
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 1643007, Tarragona, 560012, Spain
| | - Garima Jindal
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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4
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Zhang Y, Chu JM. Computational Mechanistic Investigations of Biocatalytic Nitrenoid C-H Functionalizations via Engineered Heme Proteins. Chembiochem 2023; 24:e202300260. [PMID: 37134298 DOI: 10.1002/cbic.202300260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
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.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| | - Jia-Min Chu
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
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5
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Chatterjee R, Jindal G. Role of mutations in a chemoenzymatic enantiodivergent C(sp 3)-H insertion: exploring the mechanism and origin of stereoselectivity. Chem Sci 2023; 14:8810-8822. [PMID: 37621422 PMCID: PMC10445471 DOI: 10.1039/d3sc02788k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/23/2023] [Indexed: 08/26/2023] Open
Abstract
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.
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Affiliation(s)
- Ritwika Chatterjee
- Department of Organic Chemistry, Chemical Sciences Division, Indian Institute of Science Bangalore 560012 India
| | - Garima Jindal
- Department of Organic Chemistry, Chemical Sciences Division, Indian Institute of Science Bangalore 560012 India
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6
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Ma Y, Zhang X, Zhu L, Feng X, Kowah JAH, Jiang J, Wang L, Jiang L, Liu X. Machine Learning and Quantum Calculation for Predicting Yield in Cu-Catalyzed P-H Reactions. Molecules 2023; 28:5995. [PMID: 37630247 PMCID: PMC10458182 DOI: 10.3390/molecules28165995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
The paper discussed the use of machine learning (ML) and quantum chemistry calculations to predict the transition state and yield of copper-catalyzed P-H insertion reactions. By analyzing a dataset of 120 experimental data points, the transition state was determined using density functional theory (DFT). ML algorithms were then applied to analyze 16 descriptors derived from the quantum chemical transition state to predict the product yield. Among the algorithms studied, the Support Vector Machine (SVM) achieved the highest prediction accuracy of 97%, with over 80% correlation in Leave-One-Out Cross-Validation (LOOCV). Sensitivity analysis was performed on each descriptor, and a comprehensive investigation of the reaction mechanism was conducted to better understand the transition state characteristics. Finally, the ML model was used to predict reaction plans for experimental design, demonstrating strong predictive performance in subsequent experimental validation.
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Affiliation(s)
- Youfu Ma
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
| | - Xianwei Zhang
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
| | - Lin Zhu
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
| | - Xiaowei Feng
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Jamal A. H. Kowah
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Jun Jiang
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
| | - Lisheng Wang
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
| | - Lihe Jiang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Xu Liu
- Medical College, Guangxi University, Nanning 530004, China; (Y.M.); (L.Z.); (X.F.); (J.A.H.K.); (J.J.)
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
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7
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Kaur R, Nikkel DJ, Aboelnga MM, Wetmore SD. The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1. J Phys Chem B 2022; 126:10672-10683. [PMID: 36485014 DOI: 10.1021/acs.jpcb.2c06756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.,Chemistry Department, Faculty of Science, Damietta University, New Damietta 34517, Egypt
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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Kaur R, Aboelnga MM, Nikkel DJ, Wetmore SD. The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme. Phys Chem Chem Phys 2022; 24:29130-29140. [PMID: 36444615 DOI: 10.1039/d2cp04338f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the one-metal mediated pathway is debated. Furthermore, one-metal mediated nucleases maintain activity in the presence of many different metals, but the underlying reasons for this broad metal specificity are unknown. The human apurinic/apyrimidinic endonuclease (APE1), which plays a key role in DNA repair, transcription regulation, and gene expression, is a prototypical example of a one-metal dependent nuclease. Although Mg2+ is the native metal cofactor, APE1 remains catalytically active in the presence of several metals, with the rate decreasing as Mg2+ > Mn2+ > Ni2+ > Zn2+, while Ca2+ completely abolished the activity. The present work uses quantum mechanics-molecular mechanics techniques to map APE1-facilitated phosphodiester bond hydrolysis in the presence of these metals. The structural differences in stationary points along the reaction pathway shed light on the interplay between several factors that allow APE1 to remain catalytically active for various metals, with the trend in the barrier heights correlating with the experimentally reported APE1 catalytic activity. In contrast, Ca2+ significantly changes the metal coordination and active site geometry, and thus completely inhibits catalysis. Our work thereby provides support for the controversial single-metal mediated phosphodiester bond cleavage and clarifies uncertainties regarding the role of the metal and metal identity in this important reaction. This information is key for future medicinal and biotechnological applications including disease diagnosis and treatment, and protein engineering.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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Sosa Alfaro V, Waheed SO, Palomino H, Knorrscheidt A, Weissenborn M, Christov CZ, Lehnert N. YfeX - A New Platform for Carbene Transferase Development with High Intrinsic Reactivity. Chemistry 2022; 28:e202201474. [PMID: 35948517 PMCID: PMC9691539 DOI: 10.1002/chem.202201474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Indexed: 01/11/2023]
Abstract
Carbene transfer biocatalysis has evolved from basic science to an area with vast potential for the development of new industrial processes. In this study, we show that YfeX, naturally a peroxidase, has great potential for the development of new carbene transferases, due to its high intrinsic reactivity, especially for the N-H insertion reaction of aromatic and aliphatic primary and secondary amines. YfeX shows high stability against organic solvents (methanol and DMSO), greatly improving turnover of hydrophobic substrates. Interestingly, in styrene cyclopropanation, WT YfeX naturally shows high enantioselectivity, generating the trans product with 87 % selectivity for the (R,R) enantiomer. WT YfeX also catalyzes the Si-H insertion efficiently. Steric effects in the active site were further explored using the R232A variant. Quantum Mechanics/Molecular Mechanics (QM/MM) calculations reveal details on the mechanism of Si-H insertion. YfeX, and potentially other peroxidases, are exciting new targets for the development of improved carbene transferases.
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Affiliation(s)
- Victor Sosa Alfaro
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
| | - Sodiq O. Waheed
- Department of ChemistryMichigan Technological UniversityHoughton, Michigan49931United States
| | - Hannah Palomino
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
| | - Anja Knorrscheidt
- Institute of ChemistryMartin-Luther-University Halle-WittenbergKurt-Mothes-Str. 206120HalleGermany
| | - Martin Weissenborn
- Institute of ChemistryMartin-Luther-University Halle-WittenbergKurt-Mothes-Str. 206120HalleGermany
| | - Christo Z. Christov
- Department of ChemistryMichigan Technological UniversityHoughton, Michigan49931United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
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10
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Wei Y, Conklin M, Zhang Y. Biocatalytic Intramolecular C-H aminations via Engineered Heme Proteins: Full Reaction Pathways and Axial Ligand Effects. Chemistry 2022; 28:e202202006. [PMID: 35840505 PMCID: PMC9804930 DOI: 10.1002/chem.202202006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 01/09/2023]
Abstract
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- <SH- <MeOH<None due to the charge donation capability of the axial ligand to influence the key charge transfer process as the electronic driving forces. Results also provide new ideas for future biocatalyst design with enhanced reactivities.
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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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11
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Balhara R, Jindal G. Does an Enol Pathway Preclude High Stereoselectivity in Iron-Catalyzed Indole C-H Functionalization via Carbene Insertion? J Org Chem 2022; 87:7919-7933. [PMID: 35652604 DOI: 10.1021/acs.joc.2c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C-H functionalization of indoles via Fe carbenoids presents an attractive strategy to obtain biologically important structural motifs. However, obtaining good stereoselectivity with Fe has been a significant challenge. It is unclear whether the low selectivity is due to a radical pathway or an ionic mechanism involving metal-free species. We therefore present a density functional theory (DFT) study of indole alkylation with diazoacetates catalyzed by Fe(ClO4)TMEDA/spirobisoxazoline and myoglobin. We explore three mechanistic pathways: nucleophilic, radical, and oxocarbenium routes. The nucleophilic pathway is the most feasible with the formation of an enol species that tautomerizes to furnish the alkylated indole. While this mechanism is routinely proposed, the stereochemical model has been conspicuously absent until now. We show that the conventionally invoked enol pathway is not responsible for the low enantiomeric excess. The enol intermediate can stay coordinated to the catalyst via different binding sites placing the enol in proximity to the chiral environment and affecting the stereoselective proton transfer. Both the binding strength and the chiral environment are crucial for obtaining high selectivity. Our study provides the much needed insights for the modest-low selectivities of Fe systems and could help in expediting the discovery of an efficient catalytic system. These mechanistic underpinnings could also be applicable to other metal (Rh, Pd, Cu, etc.)-catalyzed X-H insertion reactions.
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Affiliation(s)
- Reena Balhara
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Garima Jindal
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
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12
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He Y, Huang Z, Wu K, Ma J, Zhou YG, Yu Z. Recent advances in transition-metal-catalyzed carbene insertion to C-H bonds. Chem Soc Rev 2022; 51:2759-2852. [PMID: 35297455 DOI: 10.1039/d1cs00895a] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
C-H functionalization has been emerging as a powerful method to establish carbon-carbon and carbon-heteroatom bonds. Many efforts have been devoted to transition-metal-catalyzed direct transformations of C-H bonds. Metal carbenes generated in situ from transition-metal compounds and diazo or its equivalents are usually applied as the transient reactive intermediates to furnish a catalytic cycle for new C-C and C-X bond formation. Using this strategy compounds from unactivated simple alkanes to complex molecules can be further functionalized or transformed to multi-functionalized compounds. In this area, transition-metal-catalyzed carbene insertion to C-H bonds has been paid continuous attention. Diverse catalyst design strategies, synthetic methods, and potential applications have been developed. This critical review will summarize the advance in transition-metal-catalyzed carbene insertion to C-H bonds dated up to July 2021, by the categories of C-H bonds from aliphatic C(sp3)-H, aryl (aromatic) C(sp2)-H, heteroaryl (heteroaromatic) C(sp2)-H bonds, alkenyl C(sp2)-H, and alkynyl C(sp)-H, as well as asymmetric carbene insertion to C-H bonds, and more coverage will be given to the recent work. Due to the rapid development of the C-H functionalization area, future directions in this topic are also discussed. This review will give the authors an overview of carbene insertion chemistry in C-H functionalization with focus on the catalytic systems and synthetic applications in C-C bond formation.
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Affiliation(s)
- Yuan He
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zilong Huang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Kaikai Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Juan Ma
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yong-Gui Zhou
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Zhengkun Yu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China. .,State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, P. R. China.,Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, P. R. China
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Mechanism of P-H insertion of α-imino copper carbenes: 1,1-Insertion or 1,3-insertion? Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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14
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Manoj N, Jindal G. DFT study on Ir-quinoid catalyzed C-H functionalization: new radical reactivity or direct carbene transfer? Chem Commun (Camb) 2021; 57:11370-11373. [PMID: 34647118 DOI: 10.1039/d1cc04764g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DFT methods are used to probe the mechanism of a newly developed Ir-quinoid catalyzed C(sp3)-H functionalization of 1,4 dienes. The lowest energy pathway proceeds via an old-school concerted C-H insertion as opposed to a unique hydrogen atom transfer process proposed previously. The concertedness of the reaction shows an intriguing dependence on sterics of the diene leading to either inserted or dehydrogenated products. We use these new insights to tune the axial ligand, and design a more efficient catalyst.
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Affiliation(s)
- Niket Manoj
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka-560012, India.
| | - Garima Jindal
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka-560012, India.
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