1
|
Pagès-Vilà N, Gamba I, Clémancey M, Latour JM, Company A, Costas M. Proton-triggered chemoselective halogenation of aliphatic C-H bonds with nonheme Fe IV-oxo complexes. J Inorg Biochem 2024; 259:112643. [PMID: 38924872 DOI: 10.1016/j.jinorgbio.2024.112643] [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: 04/26/2024] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Halogenation of aliphatic C-H bonds is a chemical transformation performed in nature by mononuclear nonheme iron dependent halogenases. The mechanism involves the formation of an iron(IV)-oxo-chloride species that abstracts the hydrogen atom from the reactive C-H bond to form a carbon-centered radical that selectively reacts with the bound chloride ligand, a process commonly referred to as halide rebound. The factors that determine the halide rebound, as opposed to the reaction with the incipient hydroxide ligand, are not clearly understood and examples of well-defined iron(IV)-oxo-halide compounds competent in C-H halogenation are scarce. In this work we have studied the reactivity of three well-defined iron(IV)-oxo complexes containing variants of the tetradentate 1-(2-pyridylmethyl)-1,4,7-triazacyclononane ligand (Pytacn). Interestingly, these compounds exhibit a change in their chemoselectivity towards the functionalization of C-H bonds under certain conditions: their reaction towards C-H bonds in the presence of a halide anionleads to exclusive oxygenation, while the addition of a superacid results in halogenation. Almost quantitative halogenation of ethylbenzene is observed when using the two systems with more sterically congested ligands and even the chlorination of strong C-H bonds such as those of cyclohexane is performed when a methyl group is present in the sixth position of the pyridine ring of the ligand. Mechanistic studies suggest that both reactions, oxygenation and halogenation, proceed through a common rate determining hydrogen atom transfer step and the presence of the acid dictates the fate of the resulting alkyl radical towards preferential halogenation over oxygenation.
Collapse
Affiliation(s)
- Neus Pagès-Vilà
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Ilaria Gamba
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain; Departamento de Química, Facultad de Ciencias, Universidad de La Laguna, Av. Astrofísico Sánchez s/n, 38200 La Laguna, Spain.
| | - Martin Clémancey
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Anna Company
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.
| |
Collapse
|
2
|
Molla M, Saha A, Barman SK, Mandal S. Monomeric Fe(III)-Hydroxo and Fe(III)-Aqua Complexes Display Oxidative Asynchronous Hydrogen Atom Abstraction Reactivity. Chemistry 2024; 30:e202401163. [PMID: 38953593 DOI: 10.1002/chem.202401163] [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: 03/22/2024] [Revised: 06/16/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
This paper presents the synthesis and characterization of a series of novel monomeric aqua-ligated iron(III) complexes, [FeIII(L5R)(OH2)]2+ (R=OMe, H, Cl, NO2), supported by an amide-containing pentadentate N5 donor ligand, L5R [HL5R=2-(((1-methyl-1H-imidazol-2-yl)methyl)(pyridin-2-yl-methyl)amino)-N-(5-R-quinolin-8-yl)acetamide]. The complexes were characterized by various spectroscopic and analytical techniques, including electrochemistry and magnetic measurements. The Fe(III)-hydroxo complexes, [FeIII(L5R)(OH)]1+, were generated in situ by deprotonating the corresponding aqua complexes in a pH ~7 aqueous medium. In another way, adding one equivalent of a base to a methanolic solution of the Fe(III)-aqua complexes also produced the Fe(III)-hydroxo complexes. The study uses linoleic fatty acid as a substrate to explore the hydrogen atom abstraction (HAA) reactivity of both hydroxo and aqua complexes. The investigation highlights the substitution effect of the L5R ligand on reactivity, revealing a higher rate when an electron-withdrawing group is present. Hammett analyses and(or) determination of the asynchronicity factor (η) suggest an oxidative asynchronous concerted proton-electron transfer (CPET) pathway for the HAA reactions. Aqua complexes exhibited a higher asynchronicity in CPET, resulting in higher reaction rates than their hydroxo analogs. Overall, the work provides insights into the beneficial role of a higher imbalance in electron-transfer-proton-transfer (ET-PT) contributions in HAA reactivity.
Collapse
Affiliation(s)
- Mofijul Molla
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Anannya Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Manauli, 140306, India
| | - Suman K Barman
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Manauli, 140306, India
| | - Sukanta Mandal
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| |
Collapse
|
3
|
Wenger ES, Martinie RJ, Ushimaru R, Pollock CJ, Sil D, Li A, Hoang N, Palowitch GM, Graham BP, Schaperdoth I, Burke EJ, Maggiolo AO, Chang WC, Allen BD, Krebs C, Silakov A, Boal AK, Bollinger JM. Optimized Substrate Positioning Enables Switches in the C-H Cleavage Site and Reaction Outcome in the Hydroxylation-Epoxidation Sequence Catalyzed by Hyoscyamine 6β-Hydroxylase. J Am Chem Soc 2024; 146:24271-24287. [PMID: 39172701 PMCID: PMC11374477 DOI: 10.1021/jacs.4c04406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Hyoscyamine 6β-hydroxylase (H6H) is an iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase that produces the prolifically administered antinausea drug, scopolamine. After its namesake hydroxylation reaction, H6H then couples the newly installed C6 oxygen to C7 to produce the drug's epoxide functionality. Oxoiron(IV) (ferryl) intermediates initiate both reactions by cleaving C-H bonds, but it remains unclear how the enzyme switches the target site and promotes (C6)O-C7 coupling in preference to C7 hydroxylation in the second step. In one possible epoxidation mechanism, the C6 oxygen would─analogously to mechanisms proposed for the Fe/2OG halogenases and, in our more recent study, N-acetylnorloline synthase (LolO)─coordinate as alkoxide to the C7-H-cleaving ferryl intermediate to enable alkoxyl coupling to the ensuing C7 radical. Here, we provide structural and kinetic evidence that H6H does not employ substrate coordination or repositioning for the epoxidation step but instead exploits the distinct spatial dependencies of competitive C-H cleavage (C6 vs C7) and C-O-coupling (oxygen rebound vs cyclization) steps to promote the two-step sequence. Structural comparisons of ferryl-mimicking vanadyl complexes of wild-type H6H and a variant that preferentially 7-hydroxylates instead of epoxidizing 6β-hydroxyhyoscyamine suggest that a modest (∼10°) shift in the Fe-O-H(C7) approach angle is sufficient to change the outcome. The 7-hydroxylation:epoxidation partition ratios of both proteins increase more than 5-fold in 2H2O, reflecting an epoxidation-specific requirement for cleavage of the alcohol O-H bond, which, unlike in the LolO oxacyclization, is not accomplished by iron coordination in advance of C-H cleavage.
Collapse
Affiliation(s)
- Eliott S Wenger
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Pan J, Wenger ES, Lin CY, Zhang B, Sil D, Schaperdoth I, Saryazdi S, Grossman RB, Krebs C, Bollinger JM. An Unusual Ferryl Intermediate and Its Implications for the Mechanism of Oxacyclization by the Loline-Producing Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, LolO. Biochemistry 2024; 63:1674-1683. [PMID: 38898603 PMCID: PMC11219260 DOI: 10.1021/acs.biochem.4c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
N-Acetylnorloline synthase (LolO) is one of several iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases that catalyze sequential reactions of different types in the biosynthesis of valuable natural products. LolO hydroxylates C2 of 1-exo-acetamidopyrrolizidine before coupling the C2-bonded oxygen to C7 to form the tricyclic loline core. Each reaction requires cleavage of a C-H bond by an oxoiron(IV) (ferryl) intermediate; however, different carbons are targeted, and the carbon radicals have different fates. Prior studies indicated that the substrate-cofactor disposition (SCD) controls the site of H· abstraction and can affect the reaction outcome. These indications led us to determine whether a change in SCD from the first to the second LolO reaction might contribute to the observed reactivity switch. Whereas the single ferryl complex in the C2 hydroxylation reaction was previously shown to have typical Mössbauer parameters, one of two ferryl complexes to accumulate during the oxacyclization reaction has the highest isomer shift seen to date for such a complex and abstracts H· from C7 ∼ 20 times faster than does the first ferryl complex in its previously reported off-pathway hydroxylation of C7. The detectable hydroxylation of C7 in competition with cyclization by the second ferryl complex is not enhanced in 2H2O solvent, suggesting that the C2 hydroxyl is deprotonated prior to C7-H cleavage. These observations are consistent with the coordination of the C2 oxygen to the ferryl complex, which may reorient its oxo ligand, the substrate, or both to positions more favorable for C7-H cleavage and oxacyclization.
Collapse
Affiliation(s)
- Juan Pan
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Eliott S. Wenger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | - Irene Schaperdoth
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Setareh Saryazdi
- Department of Chemistry, The University of Kentucky, Lexington, Kentucky 40506, United States
- Present address: College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Robert B. Grossman
- Department of Chemistry, The University of Kentucky, Lexington, Kentucky 40506, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
5
|
Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
Collapse
Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
6
|
Del Rio Flores A, Zhai R, Zhang W. Isonitrile biosynthesis by non-heme iron(II)-dependent oxidases/decarboxylases. Methods Enzymol 2024; 704:143-172. [PMID: 39300646 PMCID: PMC11424024 DOI: 10.1016/bs.mie.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The isonitrile group is a compact, electron-rich moiety coveted for its commonplace as a building block and bioorthogonal functionality in synthetic chemistry and chemical biology. Hundreds of natural products containing an isonitrile group with intriguing bioactive properties have been isolated from diverse organisms. Our recent discovery of a conserved biosynthetic gene cluster in some Actinobacteria species highlighted a novel enzymatic pathway to isonitrile formation involving a non-heme iron(II) and α-ketoglutarate-dependent dioxygenase. Here, we focus this chapter on recent advances in understanding and probing the biosynthetic machinery for isonitrile synthesis by non-heme iron(II) and α-ketoglutarate-dependent dioxygenases. We will begin by describing how to harness isonitrile enzymatic machinery through heterologous expression, purification, synthetic strategies, and in vitro biochemical/kinetic characterization. We will then describe a generalizable strategy to probe the mechanism for isonitrile formation by combining various spectroscopic methods. The chapter will also cover strategies to study other enzyme homologs by implementing coupled assays using biosynthetic pathway enzymes. We will conclude this chapter by addressing current challenges and future directions in understanding and engineering isonitrile synthesis.
Collapse
Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States.
| |
Collapse
|
7
|
Tian T, Ogura Y, Ise Y, Takikawa H, Okada S, Matsunaga S, Tang GL. Absolute Configuration of 4-Chloroisoleucine in Cyclolithistide A: An Antifungal Peptide Lactone Discovered in Marine Lithistid Sponges. J Org Chem 2024; 89:9135-9138. [PMID: 38860861 DOI: 10.1021/acs.joc.4c00913] [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: 06/12/2024]
Abstract
Cyclolithistide A is a peptide lactone isolated from marine lithistid sponges. Its entire structure, including absolute configurations, has been reported except the relative and absolute configurations of its characteristic residue, 4-chloroisoleucine (4-CIle). We synthesized four isomers of 4-CIle from furfural-derived N-Boc imine and propionaldehyde. Analysis of the acid hydrolysate of cyclolithistide A and the synthetic samples of 4-CIle after derivatization with l- and d-FDAA permitted us to propose the absolute configuration of the 4-chloroisoleucine residue in cyclolithistide A as 2S,3R,4R.
Collapse
Affiliation(s)
- Tian Tian
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yusuke Ogura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yuji Ise
- The Kuroshio Biological Research Institute, Kochi 788-0333, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Gong-Li Tang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute for Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
8
|
Solomon EI, Gipson RR. Spectroscopic definition of ferrous active sites in non-heme iron enzymes. Methods Enzymol 2024; 703:29-49. [PMID: 39261000 PMCID: PMC11391101 DOI: 10.1016/bs.mie.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Non-heme iron enzymes play key roles in antibiotic, neurotransmitter, and natural product biosynthesis, DNA repair, hypoxia regulation, and disease states. These enzymes had been refractory to traditional bioinorganic spectroscopic methods. Thus, we developed variable-temperature variable-field magnetic circular dichroism (VTVH MCD) spectroscopy to experimentally define the excited and ground ligand field states of non-heme ferrous enzymes (Solomon et al., 1995). This method provides detailed geometric and electronic structure insight and thus enables a molecular level understanding of catalytic mechanisms. Application of this method across the five classes of non-heme ferrous enzymes has defined that a general mechanistic strategy is utilized where O2 activation is controlled to occur only in the presence of all cosubstrates.
Collapse
Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Acceleration Laboratory, Stanford University, Menlo Park, CA, United States.
| | - Robert R Gipson
- Department of Chemistry, Stanford University, Stanford, CA, United States
| |
Collapse
|
9
|
Paris JC, Hei Cheung Y, Zhang T, Chang WC, Liu P, Guo Y. New Frontiers in Nonheme Enzymatic Oxyferryl Species. Chembiochem 2024:e202400307. [PMID: 38900645 DOI: 10.1002/cbic.202400307] [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: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024]
Abstract
Non-heme mononuclear iron dependent (NHM-Fe) enzymes exhibit exceedingly diverse catalytic reactivities. Despite their catalytic versatilities, the mononuclear iron centers in these enzymes show a relatively simple architecture, in which an iron atom is ligated with 2-4 amino acid residues, including histidine, aspartic or glutamic acid. In the past two decades, a common high-valent reactive iron intermediate, the S=2 oxyferryl (Fe(IV)-oxo or Fe(IV)=O) species, has been repeatedly discovered in NHM-Fe enzymes containing a 2-His-Fe or 2-His-1-carboxylate-Fe center. However, for 3-His/4-His-Fe enzymes, no common reactive intermediate has been identified. Recently, we have spectroscopically characterized the first S=1 Fe(IV) intermediate in a 3-His-Fe containing enzyme, OvoA, which catalyzes a novel oxidative carbon-sulfur bond formation. In this review, we summarize the broad reactivities demonstrated by S=2 Fe(IV)-oxo intermediates, the discovery of the first S=1 Fe(IV) intermediate in OvoA and the mechanistic implication of such a discovery, and the intrinsic reactivity differences of the S=2 and the S=1 Fe(IV)-oxo species. Finally, we postulate the possible reasons to utilize an S=1 Fe(IV) species in OvoA and their implications to other 3-His/4-His-Fe enzymes.
Collapse
Affiliation(s)
- Jared C Paris
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| | - Yuk Hei Cheung
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Tao Zhang
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, MA, 02215, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA, 15213, USA
| |
Collapse
|
10
|
Smithwick ER, Bhagi-Damodaran A, Damodaran AR. Equilibrium dialysis with HPLC detection to measure substrate binding affinity of a non-heme iron halogenase. Methods Enzymol 2024; 703:51-63. [PMID: 39261003 DOI: 10.1016/bs.mie.2024.05.004] [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] [Indexed: 09/13/2024]
Abstract
Determination of substrate binding affinity (Kd) is critical to understanding enzyme function. An extensive number of methods have been developed and employed to study ligand/substrate binding, but the best approach depends greatly on the substrate and the enzyme in question. Below we describe how to measure the Kd of BesD, a non-heme iron halogenase, for its native substrate lysine using equilibrium dialysis coupled with High Performance Liquid Chromatography (HPLC) for subsequent detection. This method can be performed in anaerobic glove bag settings. It requires readily available HPLC instrumentation for ligand quantitation and is adaptable to meet the needs of a variety of substrate affinity measurements.
Collapse
Affiliation(s)
- Elizabeth R Smithwick
- Department of Chemistry, University of Minnesota - Twin Cities, Minneapolis, MN, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota - Twin Cities, Minneapolis, MN, United States.
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota - Twin Cities, Minneapolis, MN, United States.
| |
Collapse
|
11
|
Hunter Wilson R, Damodaran AR, Bhagi-Damodaran A. Machine learning guided rational design of a non-heme iron-based lysine dioxygenase improves its total turnover number. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597480. [PMID: 38895203 PMCID: PMC11185610 DOI: 10.1101/2024.06.04.597480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Highly selective C-H functionalization remains an ongoing challenge in organic synthetic methodologies. Biocatalysts are robust tools for achieving these difficult chemical transformations. Biocatalyst engineering has often required directed evolution or structure-based rational design campaigns to improve their activities. In recent years, machine learning has been integrated into these workflows to improve the discovery of beneficial enzyme variants. In this work, we combine a structure-based machine-learning algorithm with classical molecular dynamics simulations to down select mutations for rational design of a non-heme iron-dependent lysine dioxygenase, LDO. This approach consistently resulted in functional LDO mutants and circumvents the need for extensive study of mutational activity before-hand. Our rationally designed single mutants purified with up to 2-fold higher yields than WT and displayed higher total turnover numbers (TTN). Combining five such single mutations into a pentamutant variant, LPNYI LDO, leads to a 40% improvement in the TTN (218±3) as compared to WT LDO (TTN = 160±2). Overall, this work offers a low-barrier approach for those seeking to synergize machine learning algorithms with pre-existing protein engineering strategies.
Collapse
Affiliation(s)
- R Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, 55455
| | - Anoop R Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, 55455
| | | |
Collapse
|
12
|
Smithwick ER, Bhagi-Damodaran A, Damodaran AR. Equilibrium dialysis with HPLC detection to measure substrate binding affinity of a non-heme iron halogenase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588023. [PMID: 38617253 PMCID: PMC11014511 DOI: 10.1101/2024.04.03.588023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Determination of substrate binding affinity (Kd) is critical to understanding enzyme function. An extensive number of methods have been developed and employed to study ligand/substrate binding, but the best approach depends greatly on the substrate and the enzyme in question. Below we describe how to measure the Kd of BesD, a non-heme iron halogenase, for its native substrate lysine using equilibrium dialysis with subsequent detection with High Performance Liquid Chromatography (HPLC). This method can be performed in anaerobic glove bag settings, requires readily available HPLC instrumentation for subsequent detection, and is adaptable to meet the needs of a variety of substrate affinity measurements.
Collapse
Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| |
Collapse
|
13
|
Vennelakanti V, Jeon M, Kulik HJ. How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases? Inorg Chem 2024; 63:4997-5011. [PMID: 38428015 DOI: 10.1021/acs.inorgchem.3c04421] [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: 03/03/2024]
Abstract
We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.
Collapse
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mugyeom Jeon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
14
|
Krishnan A, Waheed SO, Varghese A, Cherilakkudy FH, Schofield CJ, Karabencheva-Christova TG. Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH. Chem Sci 2024; 15:3466-3484. [PMID: 38455014 PMCID: PMC10915816 DOI: 10.1039/d3sc05974j] [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: 11/07/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.
Collapse
Affiliation(s)
- Anandhu Krishnan
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University Houghton MI 49931 USA
| | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford OX1 3TA Oxford UK
| | | |
Collapse
|
15
|
Monkcom EC, Gómez L, Lutz M, Ye S, Bill E, Costas M, Klein Gebbink RJM. Synthesis, Structure and Reactivity of a Mononuclear N,N,O-Bound Fe(II) α-Keto-Acid Complex. Chemistry 2024; 30:e202302710. [PMID: 37882223 DOI: 10.1002/chem.202302710] [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: 08/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
A bulky, tridentate phenolate ligand (ImPh2 NNOtBu ) was used to synthesise the first example of a mononuclear, facial, N,N,O-bound iron(II) benzoylformate complex, [Fe(ImPh2 NNOtBu )(BF)] (2). The X-ray crystal structure of 2 reveals that the iron centre is pentacoordinate (τ=0.5), with a vacant site located cis to the bidentate BF ligand. The Mössbauer parameters of 2 are consistent with high-spin iron(II), and are very close to those reported for α-ketoglutarate-bound non-heme iron enzyme active sites. According to NMR and UV-vis spectroscopies, the structural integrity of 2 is retained in both coordinating and non-coordinating solvents. Cyclic voltammetry studies show that the iron centre has a very low oxidation potential and is more prone to electrochemical oxidation than the redox-active phenolate ligand. Complex 2 reacts with NO to form a S=3 /2 {FeNO}7 adduct in which NO binds directly to the iron centre, according to EPR, UV-vis, IR spectroscopies and DFT analysis. Upon O2 exposure, 2 undergoes oxidative decarboxylation to form a diiron(III) benzoate complex, [Fe2 (ImPh2 NNOtBu )2 (μ2 -OBz)(μ2 -OH)2 ]+ (3). A small amount of hydroxylated ligand was also observed by ESI-MS, hinting at the formation of a high-valent iron(IV)-oxo intermediate. Initial reactivity studies show that 2 is capable of oxygen atom transfer reactivity with O2 , converting methyl(p-tolyl)sulfide to sulfoxide.
Collapse
Affiliation(s)
- Emily C Monkcom
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Laura Gómez
- Serveis Tècnics de Recerca, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Martin Lutz
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, 45470, Mülheim an der Ruhr, Germany
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Pic de Peguera 15, Parc Cientific, 17003, Girona, Spain
| | - Robertus J M Klein Gebbink
- Organic Chemistry and Catalysis, Institute for Sustainable and Circular Chemistry, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| |
Collapse
|
16
|
Vennelakanti V, Li GL, Kulik HJ. Why Nonheme Iron Halogenases Do Not Fluorinate C-H Bonds: A Computational Investigation. Inorg Chem 2023; 62:19758-19770. [PMID: 37972340 DOI: 10.1021/acs.inorgchem.3c03215] [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: 11/19/2023]
Abstract
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
Collapse
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Grace L Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
17
|
Slater JW, Lin CY, Neugebauer ME, McBride MJ, Sil D, Nair M, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. Biochemistry 2023; 62:2480-2491. [PMID: 37542461 PMCID: PMC10829012 DOI: 10.1021/acs.biochem.3c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl- or Br-), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three nongaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O2. Halide, 2OG, and (lastly) O2 all coordinate directly to the cofactor to initiate its conversion to a cis-halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l-lysine 4-chlorinase, BesD. After addition of 2OG, subsequent coordination of the halide to the cofactor and binding of cationic l-Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon the addition of O2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l-Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate•l-Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l-Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply (i) that BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l-Lys binding and chloride coordination following the loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
Collapse
Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Present address: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Alliance Pharma, New York, NY 10065, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Department of Chemistry, Indian Institute of Science Education & Research (IISER)-Pune, Pune-411008, India
| | - Mrutyunjay Nair
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Tri-Institutional MD-PhD Program, Weill Cornell Medical College and Cornell University, New York, NY 10065, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| |
Collapse
|
18
|
Smithwick ER, Wilson RH, Chatterjee S, Pu Y, Dalluge JJ, Damodaran AR, Bhagi-Damodaran A. Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542349. [PMID: 37292651 PMCID: PMC10245910 DOI: 10.1101/2023.05.25.542349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.
Collapse
Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Yu Pu
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN 55455, USA
| |
Collapse
|
19
|
Slater JW, Neugebauer ME, McBride MJ, Sil D, Lin CY, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of the l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539147. [PMID: 37205437 PMCID: PMC10187165 DOI: 10.1101/2023.05.02.539147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl - or Br - ), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three non-gaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O 2 . Halide, 2OG, and (lastly) O 2 all coordinate directly to the cofactor to initiate its conversion to a cis -halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l -lysine 4-chlorinase, BesD. After 2OG adds, subsequent coordination of the halide to the cofactor and binding of cationic l -Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon addition of O 2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l -Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate• l -Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l -Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply that (i) BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l -Lys binding and chloride coordination following loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
Collapse
Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Present address: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
20
|
Gomez CA, Mondal D, Du Q, Chan N, Lewis JC. Directed Evolution of an Iron(II)- and α-Ketoglutarate-Dependent Dioxygenase for Site-Selective Azidation of Unactivated Aliphatic C-H Bonds. Angew Chem Int Ed Engl 2023; 62:e202301370. [PMID: 36757808 PMCID: PMC10050089 DOI: 10.1002/anie.202301370] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/10/2023]
Abstract
FeII - 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.
Collapse
Affiliation(s)
- Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
- Kalsec Inc., 3713W. Main St., Kalamazoo, MI 49006, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Natalie Chan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
21
|
Hausinger RP. Five decades of metalloenzymology. Enzymes 2023; 54:71-105. [PMID: 37945178 DOI: 10.1016/bs.enz.2023.03.001] [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] [Indexed: 11/12/2023]
Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
Collapse
Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
| |
Collapse
|
22
|
Fraley AE, Dell M, Schmalhofer M, Meoded RA, Bergande C, Groll M, Piel J. Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation. Structure 2023; 31:565-572.e4. [PMID: 36917986 DOI: 10.1016/j.str.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/14/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
Abstract
Bacterial modular polyketide synthases (PKSs) generate diverse, complex and bioactive natural products that are constructed mainly based on principles of fatty acid biosynthesis. The cytotoxic oocydin-type polyketides contain a vinyl chloride moiety introduced during polyketide chain elongation. Required for modular polyketide backbone halogenation are a non-heme iron and ɑ-ketoglutarate-dependent halogenase OocP and OocQ lacking characterized homologs. This work provides structural insights into these unusual PKS components and their interactions via a high-resolution X-ray crystallography structure of the heterocomplex. By mapping the protein-protein interactions and comparison with structures of similar halogenases, we illustrate the potential of this heterodimer complex as a replacement for the conserved homodimeric structure of homologous enzymes. The OocPQ protein pair has thus evolved as a means of stabilizing the halogenase and facilitating chemical transformations with great synthetic utility.
Collapse
Affiliation(s)
- Amy E Fraley
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maria Dell
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maximilian Schmalhofer
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Cedric Bergande
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
| |
Collapse
|
23
|
Walsh CT. Tailoring enzyme strategies and functional groups in biosynthetic pathways. Nat Prod Rep 2023; 40:326-386. [PMID: 36268810 DOI: 10.1039/d2np00048b] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2000 to 2022Secondary metabolites are assembled by drawing off and committing some of the flux of primary metabolic building blocks to sets of enzymes that tailor the maturing scaffold to increase architectural and framework complexity, often balancing hydrophilic and hydrophobic surfaces. In this review we examine the small number of chemical strategies that tailoring enzymes employ in maturation of scaffolds. These strategies depend both on the organic functional groups present at each metabolic stage and one of two tailoring enzyme strategies. Nonoxidative tailoring enzymes typically transfer electrophilic fragments, acyl, alkyl and glycosyl groups, from a small set of thermodynamically activated but kinetically stable core metabolites. Oxidative tailoring enzymes can be oxygen-independent or oxygen-dependent. The oxygen independent oxidoreductases are often reversible nicotinamide-utilizing redox catalysts, flipping the nucleophilicity and electrophilicity of functional groups in pathway intermediates. O2-dependent oxygenases, both mono- and dioxygenases, act by orthogonal, one electron strategies, generating carbon radical species. At sp3 substrate carbons, product alcohols may then behave as nucleophiles for subsequent waves of enzymatic tailoring. At sp2 carbons in olefins, electrophilic epoxides have opposite reactivity and often function as "disappearing groups", opened by intramolecular nucleophiles during metabolite maturation. "Thwarted" oxygenases generate radical intermediates that rearrange internally and are not captured oxygenatively.
Collapse
|
24
|
Zhou A, Li XX, Sun D, Cao X, Wu Z, Chen H, Zhao Y, Nam W, Wang Y. Theoretical investigation on the elusive structure-activity relationship of bioinspired high-valence nickel-halogen complexes in oxidative fluorination reactions. Dalton Trans 2023; 52:1977-1988. [PMID: 36691931 DOI: 10.1039/d2dt03212k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Very recently, bioinspired high-valence metal-halogen complexes have been proven to be competent oxidants in the C-H bond activation and heteroatom dihalogenation reactions. However, the structure-activity relationship of such active species and the reaction mechanisms of oxidations mediated by these oxidants are still elusive. In this study, density functional theory (DFT) calculations were performed to systematically study the oxidizing ability of the high-valence NiIII-X (X = F and Cl) complexes Et4N[NiIII(Cl/F)(L)], (1Cl/F, Et = ethyl, L = N,N'-(2,6-dimethylphenyl)-2,6-pyridinedicarboxamide), such as the reaction mechanism of fluorination of 1,4-cyclohexadiene (CHD) by 1F in the presence of AgF and the reaction mechanism of difluorination of triphenyl phosphine (PPh3) by 1F. All calculated results fit well with the experiments and present new mechanistic findings. The C-H bond activation by the high-valence nickel(III)-halogen complexes was found to proceed via a hydrogen-atom transfer (HAT) mechanism by analysis of the molecular orbitals of the transition states. C-H bond activation by 1F takes a Ni-F-H angle of ca. 180°, whereas that by 1Cl takes an angle of ca. 120° on the transition states. These results indicate that the exchange-enhanced reactivity is responsible for the dramatic oxidative difference between these two oxidants. The role of AgF in C-H fluorination of CHD by 1F is proposed to act as a Lewis acid adduct, AgF-binding Ni(III)-fluorine complex 1F-Ag-F, which acts both as an oxidant in C-H bond activation and as a fluorine donor in the fluorination step. A cooperative oxidation mechanism involving two 1F oxidants was proposed for the difluorination of PPh3 by 1F. These theoretical findings will enrich the knowledge of high-valence metal-halogen chemistry and play a positive role in the rational design of new catalysts.
Collapse
Affiliation(s)
- Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Xiao-Xi Li
- Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Xuanyu Cao
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Zhimin Wu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| |
Collapse
|
25
|
Del Rio Flores A, Narayanamoorthy M, Cai W, Zhai R, Yang S, Shen Y, Seshadri K, De Matias K, Xue Z, Zhang W. Biosynthesis of Isonitrile Lipopeptide Metallophores from Pathogenic Mycobacteria. Biochemistry 2023; 62:824-834. [PMID: 36638317 PMCID: PMC9905339 DOI: 10.1021/acs.biochem.2c00611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Isonitrile lipopeptides (INLPs) are known to be related to the virulence of pathogenic mycobacteria by mediating metal transport, but their biosynthesis remains obscure. In this work, we use in vitro biochemical assays, site-directed mutagenesis, chemical synthesis, and spectroscopy techniques to scrutinize the activity of core enzymes required for INLP biosynthesis in mycobacteria. Compared to environmental Streptomyces, pathogenic Mycobacterium employ a similar chemical logic and enzymatic machinery in INLP biosynthesis, differing mainly in the fatty-acyl chain length, which is controlled by multiple enzymes in the pathway. Our in-depth study on the non-heme iron(II) and α-ketoglutarate-dependent dioxygenase for isonitrile generation, including Rv0097 from Mycobacterium tuberculosis (Mtb), demonstrates that it recognizes a free-standing small molecule substrate, different from the recent hypothesis that a carrier protein is required for Rv0097 in Mtb. A key residue in Rv0097 is further identified to dictate the varied fatty-acyl chain length specificity between Streptomyces and Mycobacterium.
Collapse
Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Maanasa Narayanamoorthy
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Siyue Yang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Kyle De Matias
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Zhaoqiang Xue
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
26
|
Kastner DW, Nandy A, Mehmood R, Kulik HJ. Mechanistic Insights into Substrate Positioning That Distinguish Non-heme Fe(II)/α-Ketoglutarate-Dependent Halogenases and Hydroxylases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- David W. Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
27
|
Zhai G, Gong R, Lin Y, Zhang M, Li J, Deng Z, Sun J, Chen W, Zhang Z. Structural Insight into the Catalytic Mechanism of Non-Heme Iron Halogenase AdaV in 2′-Chloropentostatin Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guoqing Zhai
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Rong Gong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yaxin Lin
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Meng Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiahui Li
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zixin Deng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jiazhong Sun
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Wenqing Chen
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Abichem Biotech Joint Center for Pharmaceutical Innovation, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhengyu Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| |
Collapse
|
28
|
Shen C, Dagnaw WM, Fong CW, Lau KC, Chow CF. Selective functionalization of C(sp 3)-H bonds: catalytic chlorination and bromination by Iron III-acacen-halide under ambient condition. Chem Commun (Camb) 2022; 58:10627-10630. [PMID: 36069398 DOI: 10.1039/d2cc02924c] [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
The oxidative catalytic halogenations of the C(sp3)-H bond of alkanes promoted by FeIII(acacen)Cl (1III-Cl) and FeIII(acacen)Br (1III-Br) in the presence of trifluoroacetic acid (TFA) were investigated. Four major steps were involved: (i) formation of [FeV(acacen)(oxo)X] species (X = Cl or Br), (ii) hydrogen-atom transfer, (iii) halogen atom rebound, and (iv) regeneration of 1III-Cl or 1III-Br. TFA played a significant role in (i) forming the high-valent iron-oxo intermediate and (ii) generating the reaction selectivity.
Collapse
Affiliation(s)
- Chang Shen
- Department of Science and Environmental Studies, The Education University of Hong Kong, 10 Lo Ping Road, Tai Po, Hong Kong SAR, China.
| | - Wasihun Menberu Dagnaw
- Department of Chemistry, The City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, SAR, China.
| | - Ching Wai Fong
- Department of Science and Environmental Studies, The Education University of Hong Kong, 10 Lo Ping Road, Tai Po, Hong Kong SAR, China.
| | - Kai Chung Lau
- Department of Chemistry, The City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, SAR, China.
| | - Cheuk-Fai Chow
- Department of Science and Environmental Studies, The Education University of Hong Kong, 10 Lo Ping Road, Tai Po, Hong Kong SAR, China.
| |
Collapse
|
29
|
Hsiao YH, Huang SJ, Lin EC, Hsiao PY, Toh SI, Chen IH, Xu Z, Lin YP, Liu HJ, Chang CY. Crystal structure of the α-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer. Front Chem 2022; 10:1001311. [PMID: 36176888 PMCID: PMC9513391 DOI: 10.3389/fchem.2022.1001311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
CmnC is an α-ketoglutarate (α-KG)-dependent non-heme iron oxygenase involved in the formation of the l-capreomycidine (l-Cap) moiety in capreomycin (CMN) biosynthesis. CmnC and its homologues, VioC in viomycin (VIO) biosynthesis and OrfP in streptothricin (STT) biosynthesis, catalyze hydroxylation of l-Arg to form β-hydroxy l-Arg (CmnC and VioC) or β,γ-dihydroxy l-Arg (OrfP). In this study, a combination of biochemical characterization and structural determination was performed to understand the substrate binding environment and substrate specificity of CmnC. Interestingly, despite having a high conservation of the substrate binding environment among CmnC, VioC, and OrfP, only OrfP can hydroxylate the substrate enantiomer d-Arg. Superposition of the structures of CmnC, VioC, and OrfP revealed a similar folds and overall structures. The active site residues of CmnC, VioC, and OrfP are almost conserved; however Leu136, Ser138, and Asp249 around the substrate binding pocket in CmnC are replaced by Gln, Gly, and Tyr in OrfP, respectively. These residues may play important roles for the substrate binding. The mutagenesis analysis revealed that the triple mutant CmnCL136Q,S138G,D249Y switches the substrate stereoselectivity from l-Arg to d-Arg with ∼6% relative activity. The crystal structure of CmnCL136Q,S138G,D249Y in complex with d-Arg revealed that the substrate loses partial interactions and adopts a different orientation in the binding site. This study provides insights into the enzyme engineering to α-KG non-heme iron oxygenases for adjustment to the substrate stereoselectivity and development of biocatalysts.
Collapse
Affiliation(s)
- Yu-Hsuan Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Szu-Jo Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - En-Chi Lin
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Po-Yun Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Shu-Ing Toh
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - I-Hsuan Chen
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing, China
| | - Yu-Pei Lin
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Hsueh-Ju Liu
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- *Correspondence: Chin-Yuan Chang,
| |
Collapse
|
30
|
Chan NH, Gomez CA, Vennelakanti V, Du Q, Kulik HJ, Lewis JC. Non-Native Anionic Ligand Binding and Reactivity in Engineered Variants of the Fe(II)- and α-Ketoglutarate-Dependent Oxygenase, SadA. Inorg Chem 2022; 61:14477-14485. [PMID: 36044713 PMCID: PMC9789792 DOI: 10.1021/acs.inorgchem.2c02872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mononuclear non-heme Fe(II)- and α-ketoglutarate-dependent oxygenases (FeDOs) catalyze a site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to an FeDO facial triad variant, SadX, and the effects of that binding on HO• vs X• rebound. We establish not only that chloride and bromide enable non-native halogenation reactions but also that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand leads us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of the FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving these ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.
Collapse
Affiliation(s)
- Natalie H. Chan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Christian A. Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Qian Du
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jared C. Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| |
Collapse
|
31
|
Kumar R, Awasthi A, Gupta S, Eerlapally R, Draksharapu A. Spectroscopic characterization of a Ru(III)-OCl intermediate: a structural mimic of haloperoxidase enzymes. Dalton Trans 2022; 51:12848-12854. [PMID: 35968730 DOI: 10.1039/d2dt01947g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Haloperoxidase enzymes utilize metal hypohalite species to halogenate aliphatic and aromatic C-H bonds to C-X (X = Cl, Br, I) in nature. In this work, we report the synthesis and spectroscopic characterization of a unique RuIII-OCl species as a structural mimic of haloperoxidase enzymes. The reaction of [(BnTPEN)RuII(NCCH3)]2+ (BnTPEN = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) with hypochlorite in the presence of an acid in CH3CN : H2O mixtures generated a novel [(BnTPEN)RuIII-OCl]2+ species that persists for 4.5 h at room temperature. This new species was characterized by UV-vis absorption, EPR, and resonance Raman spectroscopic techniques, and ESI-MS. The RuIII-OCl species is capable of performing oxygen atom transfer and hydrogen atom abstraction to various organic substrates.
Collapse
Affiliation(s)
- Rakesh Kumar
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Ayushi Awasthi
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Sikha Gupta
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Raju Eerlapally
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| | - Apparao Draksharapu
- Southern Laboratories-208A, Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India.
| |
Collapse
|
32
|
Wilson RH, Chatterjee S, Smithwick ER, Dalluge JJ, Bhagi-Damodaran A. Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-heme Iron Enzymes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- R. Hunter Wilson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Sourav Chatterjee
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Joseph J. Dalluge
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
33
|
Li RN, Chen SL. Mechanism for the Halogenation and Azidation of Lysine Catalyzed by Non-heme Iron BesD Enzyme. Chem Asian J 2022; 17:e202200438. [PMID: 35763338 DOI: 10.1002/asia.202200438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Selective halogenation is important in synthetic chemistry. BesD, a new member of the non-heme Fe(II)/α-ketoglutarate (αKG)-dependent halogenase family, can activate the sp3 C-H bond and halogenate lysine, in particular without a carrier protein. Using the density functional calculations, a chlorination mechanism in BesD has been proposed, mainly including the formation of Cl-Fe(IV)=O through the αKG decarboxylation, the isomerization of Cl-Fe(IV)=O, the substrate hydrogen abstraction by Fe(IV)=O, and the rebound of chloro to the substrate carbon radical. The hydrogen abstraction is rate-limiting. The isomerization of Cl-Fe(IV)=O is essential for the hydrogen abstraction and the chiral selectivity. The BesD-catalyzed bromination and azidation of lysine adopt the same mechanism as the chlorination. The hardly-changed overall barriers indicate that the introduced ligands (X) do not affect the reaction rate significantly, implying that the X-introduced reactions catalyzed by BesD may be extended to other X anions.
Collapse
Affiliation(s)
- Rui-Ning Li
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 100081, Beijing, CHINA
| | - Shi-Lu Chen
- Beijing Institute of Technology, School of Chemistry and Chemical Engineering, 5th, ZhongGuanCun South Street, 100081, Beijing, CHINA
| |
Collapse
|
34
|
Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
Collapse
Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| |
Collapse
|
35
|
Gérard EF, Yadav V, Goldberg DP, de Visser SP. What Drives Radical Halogenation versus Hydroxylation in Mononuclear Nonheme Iron Complexes? A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:10752-10767. [PMID: 35537044 PMCID: PMC9228086 DOI: 10.1021/jacs.2c01375] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Nonheme iron halogenases
are unique enzymes in nature that selectively
activate an aliphatic C–H bond of a substrate to convert it
into C–X (X = Cl/Br, but not F/I). It is proposed that they
generate an FeIII(OH)(X) intermediate in their catalytic
cycle. The analogous FeIII(OH) intermediate in nonheme
iron hydroxylases transfers OH• to give alcohol
product, whereas the halogenases transfer X• to
the carbon radical substrate. There remains significant debate regarding
what factors control their remarkable selectivity of the halogenases.
The reactivity of the complexes FeIII(BNPAPh2O)(OH)(X) (X = Cl, Br) with a secondary carbon radical (R•) is described. It is found that X• transfer occurs
with a secondary carbon radical, as opposed to OH• transfer with tertiary radicals. Comprehensive computational studies
involving density functional theory were carried out to examine the
possible origins of this selectivity. The calculations reproduce the
experimental findings, which indicate that halogen transfer is not
observed for the tertiary radicals because of a nonproductive equilibrium
that results from the endergonic nature of these reactions, despite
a potentially lower reaction barrier for the halogenation pathway.
In contrast, halogen transfer is favored for secondary carbon radicals,
for which the halogenated product complex is thermodynamically more
stable than the reactant complex. These results are rationalized by
considering the relative strengths of the C–X bonds that are
formed for tertiary versus secondary carbon centers. The computational
analysis also shows that the reaction barrier for halogen transfer
is significantly dependent on secondary coordination sphere effects,
including steric and H-bonding interactions.
Collapse
Affiliation(s)
- Emilie F Gérard
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| |
Collapse
|
36
|
Vennelakanti V, Mehmood R, Kulik HJ. Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
37
|
Structural and Functional Insights into a Nonheme Iron- and α-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates. Appl Environ Microbiol 2022; 88:e0249721. [PMID: 35435717 DOI: 10.1128/aem.02497-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nonheme iron- and α-ketoglutarate (αKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C(sp3)-H bonds, exhibit tremendous potential in the challenging asymmetric halogenation. AdeV from Actinomadura sp. ATCC 39365 is the first identified carrier protein-free NHFeHal that catalyzes the chlorination of nucleotide 2'-deoxyadenosine-5'-monophosphate (2'-dAMP) to afford 2'-chloro-2'-deoxyadenosine-5'-monophosphate. Here, we determined the complex crystal structures of AdeV/FeII/Cl and AdeV/FeII/Cl/αKG at resolutions of 1.76 and 1.74 Å, respectively. AdeV possesses a typical β-sandwich topology with H194, H252, αKG, chloride, and one water molecule coordinating FeII in the active site. Molecular docking, mutagenesis, and biochemical analyses reveal that the hydrophobic interactions and hydrogen bond network between the substrate-binding pocket and the adenine, deoxyribose, and phosphate moieties of 2'-dAMP are essential for substrate recognition. Residues H111, R177, and H192 might play important roles in the second-sphere interactions that control reaction partitioning. This study provides valuable insights into the catalytic selectivity of AdeV and will facilitate the rational engineering of AdeV and other NHFeHals for synthesis of halogenated nucleotides. IMPORTANCE Halogenated nucleotides are a group of important antibiotics and are clinically used as antiviral and anticancer drugs. AdeV is the first carrier protein-independent nonheme iron- and α-ketoglutarate (αKG)-dependent halogenase (NHFeHal) that can selectively halogenate nucleotides and exhibits restricted substrate specificity toward several 2'-dAMP analogues. Here, we determined the complex crystal structures of AdeV/FeII/Cl and AdeV/FeII/Cl/αKG. Molecular docking, mutagenesis, and biochemical analyses provide important insights into the catalytic selectivity of AdeV. This study will facilitate the rational engineering of AdeV and other carrier protein-independent NHFeHals for synthesis of halogenated nucleotides.
Collapse
|
38
|
Del Rio Flores A, Kastner DW, Du Y, Narayanamoorthy M, Shen Y, Cai W, Vennelakanti V, Zill NA, Dell LB, Zhai R, Kulik HJ, Zhang W. Probing the Mechanism of Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase. J Am Chem Soc 2022; 144:5893-5901. [PMID: 35254829 PMCID: PMC8986608 DOI: 10.1021/jacs.1c12891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The isonitrile moiety is an electron-rich functionality that decorates various bioactive natural products isolated from diverse kingdoms of life. Isonitrile biosynthesis was restricted for over a decade to isonitrile synthases, a family of enzymes catalyzing a condensation reaction between l-Trp/l-Tyr and ribulose-5-phosphate. The discovery of ScoE, a non-heme iron(II) and α-ketoglutarate-dependent dioxygenase, demonstrated an alternative pathway employed by nature for isonitrile installation. Biochemical, crystallographic, and computational investigations of ScoE have previously been reported, yet the isonitrile formation mechanism remains obscure. In the present work, we employed in vitro biochemistry, chemical synthesis, spectroscopy techniques, and computational simulations that enabled us to propose a plausible molecular mechanism for isonitrile formation. Our findings demonstrate that the ScoE reaction initiates with C5 hydroxylation of (R)-3-((carboxymethyl)amino)butanoic acid to generate 1, which undergoes dehydration, presumably mediated by Tyr96 to synthesize 2 in a trans configuration. (R)-3-isocyanobutanoic acid is finally generated through radical-based decarboxylation of 2, instead of the common hydroxylation pathway employed by this enzyme superfamily.
Collapse
Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - David W. Kastner
- Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Maanasa Narayanamoorthy
- Department of Chemistry, University of California, Berkeley, California, United States 94720
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, United States 94720
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
| | - Nicholas A. Zill
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Luisa B. Dell
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States 02139
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States 94720
- Chan Zuckerberg Biohub, San Francisco, California, United States 94158
| |
Collapse
|
39
|
Wang J, Pang X, Chen C, Gao C, Zhou X, Liu Y, Luo X. Chemistry, Biosynthesis, and Biological Activity of Halogenated Compounds Produced by Marine Microorganisms. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jiamin Wang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaoyan Pang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
| | - Chunmei Chen
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Chenghai Gao
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaowei Luo
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
| |
Collapse
|
40
|
Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
Collapse
Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| |
Collapse
|
41
|
Paik A, Paul S, Bhowmik S, Das R, Naveen T, Rana S. Recent Advances in First Row Transition Metal Mediated C‐H Halogenation of (Hetero)arenes and Alkanes. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aniruddha Paik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabarni Paul
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabyasachi Bhowmik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Rahul Das
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Togati Naveen
- Sardar Vallabhbhai National Institute of Technology Department of Chemistry 395007 Surat INDIA
| | - Sujoy Rana
- University of North Bengal Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India, 734013 734013 Siliguri INDIA
| |
Collapse
|
42
|
Neugebauer ME, Kissman EN, Marchand JA, Pelton JG, Sambold NA, Millar DC, Chang MCY. Reaction pathway engineering converts a radical hydroxylase into a halogenase. Nat Chem Biol 2021; 18:171-179. [PMID: 34937913 DOI: 10.1038/s41589-021-00944-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 10/27/2021] [Indexed: 12/16/2022]
Abstract
FeII/α-ketoglutarate (FeII/αKG)-dependent enzymes offer a promising biocatalytic platform for halogenation chemistry owing to their ability to functionalize unactivated C-H bonds. However, relatively few radical halogenases have been identified to date, limiting their synthetic utility. Here, we report a strategy to expand the palette of enzymatic halogenation by engineering a reaction pathway rather than substrate selectivity. This approach could allow us to tap the broader class of FeII/αKG-dependent hydroxylases as catalysts by their conversion to halogenases. Toward this goal, we discovered active halogenases from a DNA shuffle library generated from a halogenase-hydroxylase pair using a high-throughput in vivo fluorescent screen coupled to an alkyne-producing biosynthetic pathway. Insights from sequencing halogenation-active variants along with the crystal structure of the hydroxylase enabled engineering of a hydroxylase to perform halogenation with comparable activity and higher selectivity than the wild-type halogenase, showcasing the potential of harnessing hydroxylases for biocatalytic halogenation.
Collapse
Affiliation(s)
- Monica E Neugebauer
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Elijah N Kissman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge A Marchand
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jeffrey G Pelton
- QB3 Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas A Sambold
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle C Y Chang
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. .,Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
43
|
Solomon EI, DeWeese DE, Babicz JT. Mechanisms of O 2 Activation by Mononuclear Non-Heme Iron Enzymes. Biochemistry 2021; 60:3497-3506. [PMID: 34266238 PMCID: PMC8768060 DOI: 10.1021/acs.biochem.1c00370] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O2 to form FeIV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the FeIV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.
Collapse
Affiliation(s)
- Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States,SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| |
Collapse
|
44
|
Greve JM, Pinkham AM, Thompson Z, Cowan JA. Active site characterization and activity of the human aspartyl (asparaginyl) β-hydroxylase. Metallomics 2021; 13:6372921. [PMID: 34543426 DOI: 10.1093/mtomcs/mfab056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/06/2021] [Indexed: 01/18/2023]
Abstract
Human aspartyl/asparaginyl beta-hydroxylase (HAAH) is a member of the superfamily of nonheme Fe2+/α-ketoglutarate (αKG) dependent oxygenase enzymes with a noncanonical active site. HAAH hydroxylates epidermal growth factor (EGF) like domains to form the β-hydroxylated product from substrate asparagine or aspartic acid and has been suggested to have a negative impact in a variety of cancers. In addition to iron, HAAH also binds divalent calcium, although the role of the latter is not understood. Herein, the metal binding chemistry and influence on enzyme stability and activity have been evaluated by a combined biochemical and biophysical approach. Metal binding parameters for the HAAH active site were determined by use of isothermal titration calorimetry, demonstrating a high-affinity regulatory binding site for Ca2+ in the catalytic domain in addition to the catalytic Fe2+ cofactor. We have analyzed various active site derivatives, utilizing LC-MS and a new HPLC technique to determine the role of metal binding and the second coordination sphere in enzyme activity, discovering a previously unreported residue as vital for HAAH turnover. This analysis of the in vitro biochemical function of HAAH furthers the understanding of its importance to cellular biochemistry and metabolic pathways.
Collapse
Affiliation(s)
- Jenna M Greve
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Andrew M Pinkham
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Zechariah Thompson
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| |
Collapse
|
45
|
Ren X, Fasan R. Engineered and Artificial Metalloenzymes for Selective C-H Functionalization. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 31:100494. [PMID: 34395950 PMCID: PMC8357270 DOI: 10.1016/j.cogsc.2021.100494] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The direct functionalization of C-H bonds constitutes a powerful strategy to construct and diversify organic molecules. However, controlling the chemo- and site-selectivity of this transformation in particularly complex molecular settings represents a significant challenge. Metalloenzymes are ideal platforms for achieving catalyst-controlled selective C-H bond functionalization as their reactivities can be tuned by protein engineering and/or redesign of their cofactor environment. In this review, we highlight recent progress in the development of engineered and artificial metalloenzymes for C-H functionalization, with a focus on biocatalytic strategies for selective C-H oxyfunctionalization and halogenation as well as C-H amination and C-H carbene insertion via abiological nitrene and carbene transfer chemistries. Engineered heme- and non-heme iron dependent enzymes have emerged as promising scaffolds for executing these transformations with high chemo-, regio- and stereocontrol as well as tunable selectivity. These emerging systems and methodologies have expanded the toolbox of sustainable strategies for organic synthesis and created new opportunities for the generation of chiral building blocks, the late-stage C-H functionalization of complex molecules, and the total synthesis of natural products.
Collapse
Affiliation(s)
- Xinkun Ren
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester NY 14627, USA
| |
Collapse
|
46
|
Mehmood R, Vennelakanti V, Kulik HJ. Spectroscopically Guided Simulations Reveal Distinct Strategies for Positioning Substrates to Achieve Selectivity in Nonheme Fe(II)/α-Ketoglutarate-Dependent Halogenases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03169] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Rimsha Mehmood
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
47
|
Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
Collapse
Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| |
Collapse
|
48
|
Romero E, Jones BS, Hogg BN, Rué Casamajo A, Hayes MA, Flitsch SL, Turner NJ, Schnepel C. Enzymkatalysierte späte Modifizierungen: Besser spät als nie. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:16962-16993. [PMID: 38505660 PMCID: PMC10946893 DOI: 10.1002/ange.202014931] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/15/2021] [Indexed: 03/21/2024]
Abstract
AbstractDie Enzymkatalyse gewinnt zunehmend an Bedeutung in der Synthesechemie. Die durch Bioinformatik und Enzym‐Engineering stetig wachsende Zahl von Biokatalysatoren eröffnet eine große Vielfalt selektiver Reaktionen. Insbesondere für späte Funktionalisierungsreaktionen ist die Biokatalyse ein geeignetes Werkzeug, das oftmals der konventionellen De‐novo‐Synthese überlegen ist. Enzyme haben sich als nützlich erwiesen, um funktionelle Gruppen direkt in komplexe Molekülgerüste einzuführen sowie für die rasche Diversifizierung von Substanzbibliotheken. Biokatalytische Oxyfunktionalisierungen, Halogenierungen, Methylierungen, Reduktionen und Amidierungen sind von besonderem Interesse, da diese Strukturmotive häufig in Pharmazeutika vertreten sind. Dieser Aufsatz gibt einen Überblick über die Stärken und Schwächen der enzymkatalysierten späten Modifizierungen durch native und optimierte Enzyme in der Synthesechemie. Ebenso werden wichtige Beispiele in der Wirkstoffentwicklung hervorgehoben.
Collapse
Affiliation(s)
- Elvira Romero
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGötheborgSchweden
| | - Bethan S. Jones
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Bethany N. Hogg
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Arnau Rué Casamajo
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGötheborgSchweden
| | - Sabine L. Flitsch
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Nicholas J. Turner
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| | - Christian Schnepel
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNVereinigtes Königreich
| |
Collapse
|
49
|
Romero E, Jones BS, Hogg BN, Rué Casamajo A, Hayes MA, Flitsch SL, Turner NJ, Schnepel C. Enzymatic Late-Stage Modifications: Better Late Than Never. Angew Chem Int Ed Engl 2021; 60:16824-16855. [PMID: 33453143 PMCID: PMC8359417 DOI: 10.1002/anie.202014931] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/15/2021] [Indexed: 12/16/2022]
Abstract
Enzyme catalysis is gaining increasing importance in synthetic chemistry. Nowadays, the growing number of biocatalysts accessible by means of bioinformatics and enzyme engineering opens up an immense variety of selective reactions. Biocatalysis especially provides excellent opportunities for late-stage modification often superior to conventional de novo synthesis. Enzymes have proven to be useful for direct introduction of functional groups into complex scaffolds, as well as for rapid diversification of compound libraries. Particularly important and highly topical are enzyme-catalysed oxyfunctionalisations, halogenations, methylations, reductions, and amide bond formations due to the high prevalence of these motifs in pharmaceuticals. This Review gives an overview of the strengths and limitations of enzymatic late-stage modifications using native and engineered enzymes in synthesis while focusing on important examples in drug development.
Collapse
Affiliation(s)
- Elvira Romero
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Bethan S. Jones
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Bethany N. Hogg
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Arnau Rué Casamajo
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Sabine L. Flitsch
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Nicholas J. Turner
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Christian Schnepel
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| |
Collapse
|
50
|
Greve JM, Pinkham AM, Cowan JA. Human Aspartyl (Asparaginyl) Hydroxylase. A Multifaceted Enzyme with Broad Intra- and Extracellular Activity. Metallomics 2021; 13:6324587. [PMID: 34283245 DOI: 10.1093/mtomcs/mfab044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/29/2021] [Indexed: 01/12/2023]
Abstract
Human aspartyl (asparaginyl) β-hydroxylase (HAAH), a unique iron and 2-oxoglutarate dependent oxygenase, has shown increased importance as a suspected oncogenic protein. HAAH and its associated mRNA are upregulated in a wide variety of cancer types, however, the current role of HAAH in the malignant transformation of cells is unknown. HAAH is suspected to play an important role in NOTCH signaling via selective hydroxylation of aspartic acid and asparagine residues of epidermal growth factor (EGF)-like domains. HAAH hydroxylation also potentially mediates calcium signaling and oxygen sensing. In this review we summarize the current state of understanding of the biochemistry and chemical biology of this enzyme, identify key differences from other family members, outline its broader intra- and extracellular roles, and identify the most promising areas for future research efforts.
Collapse
Affiliation(s)
- Jenna M Greve
- Contribution from the Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Andrew M Pinkham
- Contribution from the Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - J A Cowan
- Contribution from the Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| |
Collapse
|