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Brol A, Olszewski TK. Deamination of 1-Aminoalkylphosphonic Acids: Reaction Intermediates and Selectivity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248849. [PMID: 36557979 PMCID: PMC9783495 DOI: 10.3390/molecules27248849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Deamination of 1-aminoalkylphosphonic acids in the reaction with HNO2 (generated "in situ" from NaNO2) yields a mixture of substitution products (1-hydroxyalkylphosphonic acids), elimination products (vinylphosphonic acid derivatives), rearrangement and substitution products (2-hydroxylkylphosphonic acids) as well as H3PO4. The variety of formed reaction products suggests that 1-phosphonoalkylium ions may be intermediates in such deamination reactions.
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2
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Lyagin I, Efremenko E. Enzymes, Reacting with Organophosphorus Compounds as Detoxifiers: Diversity and Functions. Int J Mol Sci 2021; 22:1761. [PMID: 33578824 PMCID: PMC7916636 DOI: 10.3390/ijms22041761] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/05/2023] Open
Abstract
Organophosphorus compounds (OPCs) are able to interact with various biological targets in living organisms, including enzymes. The binding of OPCs to enzymes does not always lead to negative consequences for the body itself, since there are a lot of natural biocatalysts that can catalyze the chemical transformations of the OPCs via hydrolysis or oxidation/reduction and thereby provide their detoxification. Some of these enzymes, their structural differences and identity, mechanisms, and specificity of catalytic action are discussed in this work, including results of computational modeling. Phylogenetic analysis of these diverse enzymes was specially realized for this review to emphasize a great area for future development(s) and applications.
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Affiliation(s)
| | - Elena Efremenko
- Faculty of Chemistry, Lomonosov Moscow State University, Lenin Hills 1/3, 119991 Moscow, Russia;
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3
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Lu J, Wang B, Shaik S, Lai W. QM/MM Calculations Reveal the Important Role of α-Heteroatom Substituents in Controlling Selectivity of Mononuclear Nonheme HppE-Catalyzed Reactions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiarui Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - Sason Shaik
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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4
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Zhou C, Luo X, Chen N, Zhang L, Gao J. C-P Natural Products as Next-Generation Herbicides: Chemistry and Biology of Glufosinate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3344-3353. [PMID: 32125843 DOI: 10.1021/acs.jafc.0c00052] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In modern agriculture and weed management practices, herbicides have been widely used to control weeds effectively and represent more than 50% of commercial pesticides applied in the world. Herbicides with unique mechanisms of actions (MOA) have historically been discovered and commercialized every two or three years from the 1950s to the 1980s. However, this trend lowered dramatically as no herbicide with a novel MOA has been marketed for more than 30 years. The fast-growing resistance to commercial herbicides has reignited the agricultural chemical industry interest in new structural scaffolds targeting novel sites in plants. Carbon-phosphorus bonds (C-P) containing natural products (NPs) have played an essential role in herbicide discovery as the chemical diversity, and the promising bioactivity of natural C-P phytotoxins can provide exciting opportunities for the discovery of both natural and semisynthetic herbicides with novel targets. Among commercial herbicides, glyphosate (Roundup), a famous C-P containing herbicide, is by far the most universally used herbicide worldwide. Furthermore, glufosinate is one of the most widely used natural herbicides in the world. Therefore, C-P NPs are a treasure for discovering new herbicides with novel mechanisms of actions (MOAs). Here, we present an overview of the chemistry and biology of glufosinate including isolation and characterization, mode of action, herbicidal use, biosynthesis, and chemical synthesis since its discovery in order to not only help scientists reassess the role of this famous herbicide in the field of agrichemical chemistry but also build a new stage for discovering novel C-P herbicides with new MOAs.
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Affiliation(s)
- Chengzeng Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxia Luo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Science, Tarim University, Alar 843300, China
| | - Nengyi Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Science, Tarim University, Alar 843300, China
| | - Jiangtao Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Cao Y, Peng Q, Li S, Deng Z, Gao J. The intriguing biology and chemistry of fosfomycin: the only marketed phosphonate antibiotic. RSC Adv 2019; 9:42204-42218. [PMID: 35548698 PMCID: PMC9088020 DOI: 10.1039/c9ra08299a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/27/2019] [Indexed: 11/29/2022] Open
Abstract
Recently infectious diseases caused by the increased emergence and rapid spread of drug-resistant bacterial isolates have been one of the main threats to global public health because of a marked surge in both morbidity and mortality. The only phosphonate antibiotic in the clinic, fosfomycin, is a small broad-spectrum molecule that effectively inhibits the initial step in peptidoglycan biosynthesis by blocking the enzyme, MurA in both Gram-positive and Gram-negative bacteria. As fosfomycin has a novel mechanism of action, low toxicity, a broad spectrum of antibacterial activity, excellent pharmacodynamic/pharmacokinetic properties, and good bioavailability, it has been approved for clinical use in the treatment of urinary tract bacterial infections in many countries for several decades. Furthermore, its potential use for difficult-to-treat bacterial infections has become promising, and fosfomycin has become an ideal candidate for the effective treatment of bacterial infections caused by multidrug-resistant isolates, especially in combination with other therapeutic drugs. Here we aim to present an overview of the biology and chemistry of fosfomycin including isolation and characterization, pharmacology, biosynthesis and chemical synthesis since its discovery in order to not only help scientists reassess the role of this exciting drug in fighting antibiotic resistance but also build the stage for discovering more novel phosphonate antibiotics in the future.
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Affiliation(s)
- Yingying Cao
- College of Life Sciences, Fujian Agriculture and Forestry University Fuzhou 350002 China
| | - Qingyao Peng
- College of Life Sciences, Fujian Agriculture and Forestry University Fuzhou 350002 China
| | - Shanni Li
- College of Life Sciences, Fujian Agriculture and Forestry University Fuzhou 350002 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Jiangtao Gao
- College of Life Sciences, Fujian Agriculture and Forestry University Fuzhou 350002 China
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6
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Zhou S, Pan J, Davis KM, Schaperdoth I, Wang B, Boal AK, Krebs C, Bollinger JM. Steric Enforcement of cis-Epoxide Formation in the Radical C-O-Coupling Reaction by Which ( S)-2-Hydroxypropylphosphonate Epoxidase (HppE) Produces Fosfomycin. J Am Chem Soc 2019; 141:20397-20406. [PMID: 31769979 DOI: 10.1021/jacs.9b10974] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
(S)-2-Hydroxypropylphosphonate [(S)-2-HPP, 1] epoxidase (HppE) reduces H2O2 at its nonheme-iron cofactor to install the oxirane "warhead" of the antibiotic fosfomycin. The net replacement of the C1 pro-R hydrogen of 1 by its C2 oxygen, with inversion of configuration at C1, yields the cis-epoxide of the drug [(1R,2S)-epoxypropylphosphonic acid (cis-Fos, 2)]. Here we show that HppE achieves ∼95% selectivity for C1 inversion and cis-epoxide formation via steric guidance of a radical-coupling mechanism. Published structures of the HppE·FeII·1 and HppE·ZnII·2 complexes reveal distinct pockets for C3 of the substrate and product and identify four hydrophobic residues-Leu120, Leu144, Phe182, and Leu193-close to C3 in one of the complexes. Replacement of Leu193 in the substrate C3 pocket with the bulkier Phe enhances stereoselectivity (cis:trans ∼99:1), whereas the Leu120Phe substitution in the product C3 pocket diminishes it (∼82:18). Retention of C1 configuration and trans-epoxide formation become predominant with the bulk-reducing Phe182Ala substitution in the substrate C3 pocket (∼13:87), trifluorination of C3 (∼23:77), or both (∼1:99). The effect of C3 trifluorination is counteracted by the more constrained substrate C3 pockets in the Leu193Phe (∼56:44) and Leu144Phe/Leu193Phe (∼90:10) variants. The ability of HppE to epoxidize substrate analogues bearing halogens at C3, C1, or both is inconsistent with a published hypothesis of polar cyclization via a C1 carbocation. Rather, specific enzyme-substrate contacts drive inversion of the C1 radical-as proposed in a recent computational study-to direct formation of the more potently antibacterial cis-epoxide by radicaloid C-O coupling.
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Affiliation(s)
- Shengbin Zhou
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Juan Pan
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Katherine M Davis
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Irene Schaperdoth
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Bo Wang
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Amie K Boal
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry & Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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Ulrich EC, Kamat SS, Hove-Jensen B, Zechel DL. Methylphosphonic Acid Biosynthesis and Catabolism in Pelagic Archaea and Bacteria. Methods Enzymol 2018; 605:351-426. [DOI: 10.1016/bs.mie.2018.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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9
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Kal S, Que L. Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants. J Biol Inorg Chem 2017; 22:339-365. [PMID: 28074299 DOI: 10.1007/s00775-016-1431-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/13/2016] [Indexed: 11/24/2022]
Abstract
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O2 activation and the key roles played by iron-based oxidants.
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Affiliation(s)
- Subhasree Kal
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lawrence Que
- Department of Chemistry, Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN, 55455, USA.
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Huang X, Groves JT. Beyond ferryl-mediated hydroxylation: 40 years of the rebound mechanism and C-H activation. J Biol Inorg Chem 2016; 22:185-207. [PMID: 27909920 PMCID: PMC5350257 DOI: 10.1007/s00775-016-1414-3] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022]
Abstract
Since our initial report in 1976, the oxygen rebound mechanism has become the consensus mechanistic feature for an expanding variety of enzymatic C-H functionalization reactions and small molecule biomimetic catalysts. For both the biotransformations and models, an initial hydrogen atom abstraction from the substrate (R-H) by high-valent iron-oxo species (Fen=O) generates a substrate radical and a reduced iron hydroxide, [Fen-1-OH ·R]. This caged radical pair then evolves on a complicated energy landscape through a number of reaction pathways, such as oxygen rebound to form R-OH, rebound to a non-oxygen atom affording R-X, electron transfer of the incipient radical to yield a carbocation, R+, desaturation to form olefins, and radical cage escape. These various flavors of the rebound process, often in competition with each other, give rise to the wide range of C-H functionalization reactions performed by iron-containing oxygenases. In this review, we first recount the history of radical rebound mechanisms, their general features, and key intermediates involved. We will discuss in detail the factors that affect the behavior of the initial caged radical pair and the lifetimes of the incipient substrate radicals. Several representative examples of enzymatic C-H transformations are selected to illustrate how the behaviors of the radical pair [Fen-1-OH ·R] determine the eventual reaction outcome. Finally, we discuss the powerful potential of "radical rebound" processes as a general paradigm for developing novel C-H functionalization reactions with synthetic, biomimetic catalysts. We envision that new chemistry will continue to arise by bridging enzymatic "radical rebound" with synthetic organic chemistry.
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11
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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12
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Chang WC, Li J, Lee JL, Cronican AA, Guo Y. Mechanistic Investigation of a Non-Heme Iron Enzyme Catalyzed Epoxidation in (-)-4'-Methoxycyclopenin Biosynthesis. J Am Chem Soc 2016; 138:10390-3. [PMID: 27442345 DOI: 10.1021/jacs.6b05400] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mechanisms have been proposed for α-KG-dependent non-heme iron enzyme catalyzed oxygen atom insertion into an olefinic moiety in various natural products, but they have not been examined in detail. Using a combination of methods including transient kinetics, Mössbauer spectroscopy, and mass spectrometry, we demonstrate that AsqJ-catalyzed (-)-4'-methoxycyclopenin formation uses a high-spin Fe(IV)-oxo intermediate to carry out epoxidation. Furthermore, product analysis on (16)O/(18)O isotope incorporation from the reactions using the native substrate, 4'-methoxydehydrocyclopeptin, and a mechanistic probe, dehydrocyclopeptin, reveals evidence supporting oxo↔hydroxo tautomerism of the Fe(IV)-oxo species in the non-heme iron enzyme catalysis.
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Affiliation(s)
- Wei-Chen Chang
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jikun Li
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Justin L Lee
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Andrea A Cronican
- Department of Environmental and Occupational Health, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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Chin JP, McGrath JW, Quinn JP. Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling. Curr Opin Chem Biol 2016; 31:50-7. [DOI: 10.1016/j.cbpa.2016.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
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Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases. Proc Natl Acad Sci U S A 2013; 110:18874-9. [PMID: 24198335 DOI: 10.1073/pnas.1315927110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The founding members of the HD-domain protein superfamily are phosphohydrolases, and newly discovered members are generally annotated as such. However, myo-inositol oxygenase (MIOX) exemplifies a second, very different function that has evolved within the common scaffold of this superfamily. A recently discovered HD protein, PhnZ, catalyzes conversion of 2-amino-1-hydroxyethylphosphonate to glycine and phosphate, culminating a bacterial pathway for the utilization of environmentally abundant 2-aminoethylphosphonate. Using Mössbauer and EPR spectroscopies, X-ray crystallography, and activity measurements, we show here that, like MIOX, PhnZ employs a mixed-valent Fe(II)/Fe(III) cofactor for the O2-dependent oxidative cleavage of its substrate. Phylogenetic analysis suggests that many more HD proteins may catalyze yet-unknown oxygenation reactions using this hitherto exceptional Fe(II)/Fe(III) cofactor. The results demonstrate that the catalytic repertoire of the HD superfamily extends well beyond phosphohydrolysis and suggest that the mechanism used by MIOX and PhnZ may be a common strategy for oxidative C-X bond cleavage.
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