1
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He W, Huang Z, Nian C, Huang L, Kong M, Liao M, Zhang Q, Li W, Hu Y, Wu J. Discovery and evaluation of novel spiroheterocyclic protective agents via a SIRT1 upregulation mechanism in cisplatin-induced premature ovarian failure. Bioorg Med Chem 2024; 110:117834. [PMID: 39029436 DOI: 10.1016/j.bmc.2024.117834] [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: 05/08/2024] [Revised: 07/02/2024] [Accepted: 07/08/2024] [Indexed: 07/21/2024]
Abstract
Currently, no effective treatment exists for premature ovarian failure (POF). To obtain compounds with protective effects against POF, we aimed to design and synthesize a series of spiroheterocyclic protective agents with a focus on minimizing toxicity while enhancing their protective effect against cisplatin-induced POF. This was achieved through systematic modifications of Michael receptors and linkers within the molecular structure of 1,5-diphenylpenta-1,4-dien-3-one analogs. To assess the cytotoxicity and activity of these compounds, we constructed quantitative conformational relationship models using an artificial intelligence random forest algorithm, resulting in R2 values exceeding 0.87. Among these compounds, j2 exhibited optimal protective activity. It significantly increased the survival of cisplatin-injured ovarian granulosa KGN cells, improved post-injury cell morphology, reduced apoptosis, and enhanced cellular estradiol (E2) levels. Subsequent investigations revealed that j2 may exert its protective effect via a novel mechanism involving the activation of the SIRT1/AKT signal pathway. Furthermore, in cisplatin-injured POF in rats, j2 was effective in increasing body, ovarian, and uterine weights, elevating the number of follicles at all levels in the ovary, improving ovarian and uterine structures, and increasing serum E2 levels in rats with cisplatin-injured POF. In conclusion, this study introduces a promising compound j2 and a novel target SIRT1 with substantial protective activity against cisplatin-induced POF.
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Affiliation(s)
- Wenfei He
- The Second Affiliated Hospital and Yuying Children's Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Oujiang Laboratory Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325000, China; School of Pharmaceutical Sciences, Wenzhou Medical Universtiy, Wenzhou, Zhejiang 325035, China.
| | - Zhicheng Huang
- School of Pharmaceutical Sciences, Wenzhou Medical Universtiy, Wenzhou, Zhejiang 325035, China; Department of Pharmacy, Ezhou Central Hospital, Ezhou, Hubei 436000, China
| | - Chunhui Nian
- School of Pharmaceutical Sciences, Wenzhou Medical Universtiy, Wenzhou, Zhejiang 325035, China
| | - Luoqi Huang
- The Second Affiliated Hospital and Yuying Children's Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Miaomiao Kong
- The 1th Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Mengqin Liao
- School of Pharmaceutical Sciences, Wenzhou Medical Universtiy, Wenzhou, Zhejiang 325035, China
| | - Qiong Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Wulan Li
- The 1th Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yue Hu
- The Second Affiliated Hospital and Yuying Children's Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
| | - Jianzhang Wu
- The Second Affiliated Hospital and Yuying Children's Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Oujiang Laboratory Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325000, China; The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University; Wenzhou 325027, China.
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2
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Papadopoulou A, Meyer F, Buller RM. Engineering Fe(II)/α-Ketoglutarate-Dependent Halogenases and Desaturases. Biochemistry 2023; 62:229-240. [PMID: 35446547 DOI: 10.1021/acs.biochem.2c00115] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fe(II)/α-ketoglutarate-dependent dioxygenases (α-KGDs) are widespread enzymes in aerobic biology and serve a remarkable array of biological functions, including roles in collagen biosynthesis, plant and animal development, transcriptional regulation, nucleic acid modification, and secondary metabolite biosynthesis. This functional diversity is reflected in the enzymes' catalytic flexibility as α-KGDs can catalyze an intriguing set of synthetically valuable reactions, such as hydroxylations, halogenations, and desaturations, capturing the interest of scientists across disciplines. Mechanistically, all α-KGDs are understood to follow a similar activation pathway to generate a substrate radical, yet how individual members of the enzyme family direct this key intermediate toward the different reaction outcomes remains elusive, triggering structural, computational, spectroscopic, kinetic, and enzyme engineering studies. In this Perspective, we will highlight how first enzyme and substrate engineering examples suggest that the chemical reaction pathway within α-KGDs can be intentionally tailored using rational design principles. We will delineate the structural and mechanistic investigations of the reprogrammed enzymes and how they begin to inform about the enzymes' structure-function relationships that determine chemoselectivity. Application of this knowledge in future enzyme and substrate engineering campaigns will lead to the development of powerful C-H activation catalysts for chemical synthesis.
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Affiliation(s)
- Athena Papadopoulou
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Fabian Meyer
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rebecca M Buller
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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3
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Tu S, Qi Z, Li W, Zhang S, Zhang Z, Wei J, Yang L, Wei S, Du X, Yi D. Chemodivergent photocatalytic access to 1-pyrrolines and 1-tetralones involving switchable C(sp3)–H functionalization. Front Chem 2022; 10:1058596. [PMID: 36385998 PMCID: PMC9641198 DOI: 10.3389/fchem.2022.1058596] [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: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
A chemodivergent photocatalytic approach to 1-pyrrolines and 1-tetralones from alkyl bromides and vinyl azides has been developed through chemoselectively controllable intermolecular [3 + 2] and [4 + 2] cyclization. This photoredox-neutral two-component protocol involves intermolecular radical addition and switchable distal C(sp3)–H functionalization enabled by iminyl radical-mediated 1,5-hydrogen atom transfer. Meanwhile, chemoselectivity between C(sp3)–N bond formation and C(sp3)–C(sp2) bond formation is precisely switched by photocatalysts (Ru(bpy)3(PF6)2 vs. fac-Ir(ppy)3) and additives (base vs. acid).
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Affiliation(s)
- Shijing Tu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Zhongyu Qi
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Weicai Li
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Shiqi Zhang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan, China
- *Correspondence: Shiqi Zhang, ; Xi Du, ; Dong Yi,
| | - Zhijie Zhang
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jun Wei
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Lin Yang
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Siping Wei
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xi Du
- Department of Chemistry, School of Basic Medical Science, Southwest Medical University, Luzhou, China
- *Correspondence: Shiqi Zhang, ; Xi Du, ; Dong Yi,
| | - Dong Yi
- Central Nervous System Drug Key Laboratory of Sichuan Province, Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Shiqi Zhang, ; Xi Du, ; Dong Yi,
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4
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Sinner EK, Li R, Marous DR, Townsend CA. ThnL, a B12-dependent radical S-adenosylmethionine enzyme, catalyzes thioether bond formation in carbapenem biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2206494119. [PMID: 35969793 PMCID: PMC9407657 DOI: 10.1073/pnas.2206494119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Complex carbapenems are important clinical antibiotics used to treat recalcitrant infections. Their biosynthetic gene clusters contain three essential B12-dependent radical S-adenosylmethionine (rSAM) enzymes. The majority of characterized enzymes in this subfamily catalyze methyl transfer, but only one is required to sequentially install all methionine-derived carbons in complex carbapenems. Therefore, it is probable that the other two rSAM enzymes have noncanonical functions. Through a series of fermentation and in vitro experiments, we show that ThnL uses radical SAM chemistry to catalyze thioether bond formation between C2 of a carbapenam precursor and pantetheine, uniting initial bicycle assembly common to all carbapenems with later tailoring events unique to complex carbapenems. ThnL also catalyzes reversible thiol/disulfide redox on pantetheine. Neither of these functions has been observed previously in a B12-dependent radical SAM enzyme. ThnL expands the known activity of this subclass of enzymes beyond carbon-carbon bond formation or rearrangement. It is also the only radical SAM enzyme currently known to catalyze carbon-sulfur bond formation with only an rSAM Fe-S cluster and no additional auxiliary clusters.
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Affiliation(s)
- Erica K. Sinner
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Daniel R. Marous
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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5
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McBride MJ, Nair MA, Sil D, Slater JW, Neugebauer M, Chang MCY, Boal AK, Krebs C, Bollinger JM. Substrate-Triggered μ-Peroxodiiron(III) Intermediate in the 4-Chloro-l-Lysine-Fragmenting Heme-Oxygenase-like Diiron Oxidase (HDO) BesC: Substrate Dissociation from, and C4 Targeting by, the Intermediate. Biochemistry 2022; 61:689-702. [PMID: 35380785 PMCID: PMC9047515 DOI: 10.1021/acs.biochem.1c00774] [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: 11/29/2022]
Abstract
The enzyme BesC from the β-ethynyl-l-serine biosynthetic pathway in Streptomyces cattleya fragments 4-chloro-l-lysine (produced from l-Lysine by BesD) to ammonia, formaldehyde, and 4-chloro-l-allylglycine and can analogously fragment l-Lys itself. BesC belongs to the emerging family of O2-activating non-heme-diiron enzymes with the "heme-oxygenase-like" protein fold (HDOs). Here, we show that the binding of l-Lys or an analogue triggers capture of O2 by the protein's diiron(II) cofactor to form a blue μ-peroxodiiron(III) intermediate analogous to those previously characterized in two other HDOs, the olefin-installing fatty acid decarboxylase, UndA, and the guanidino-N-oxygenase domain of SznF. The ∼5- and ∼30-fold faster decay of the intermediate in reactions with 4-thia-l-Lys and (4RS)-chloro-dl-lysine than in the reaction with l-Lys itself and the primary deuterium kinetic isotope effects (D-KIEs) on decay of the intermediate and production of l-allylglycine in the reaction with 4,4,5,5-[2H4]-l-Lys suggest that the peroxide intermediate or a reversibly connected successor complex abstracts a hydrogen atom from C4 to enable olefin formation. Surprisingly, the sluggish substrate l-Lys can dissociate after triggering intermediate formation, thereby allowing one of the better substrates to bind and react. The structure of apo BesC and the demonstrated linkage between Fe(II) and substrate binding suggest that the triggering event involves an induced ordering of ligand-providing helix 3 (α3) of the conditionally stable HDO core. As previously suggested for SznF, the dynamic α3 also likely initiates the spontaneous degradation of the diiron(III) product cluster after decay of the peroxide intermediate, a trait emerging as characteristic of the nascent HDO family.
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Affiliation(s)
- Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mrutyunjay A. Nair
- 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
| | - Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Monica 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
| | - 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
| | - 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
| | - 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
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6
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Das A, Chatani N. Rh(I)-catalysed imine-directed C-H functionalization via the oxidative [3 + 2] cycloaddition of benzylamine derivatives with maleimides. Chem Commun (Camb) 2022; 58:1123-1126. [PMID: 34981093 DOI: 10.1039/d1cc06622f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Rh(I)-catalysed imine-directed oxidative [3 + 2] cycloaddition of benzylamines with maleimides is reported. A wide range of both benzylamines and maleimides is applicable to the reaction. A one-pot three component strategy using benzylamines, 2-pyridinecarboxaldehyde, and maleimides is successfully achieved. Mechanistic studies including deuterium labelling experiments suggest that a zwitterionic intermediate is formed and is a key intermediate through the Rh-catalysed activation of a benzylic C(sp3)-H bond of the imine.
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Affiliation(s)
- Amrita Das
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Naoto Chatani
- Department of Applied Chemistry, Faculty of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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7
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Kim S, Kim D, Hong SY, Chang S. Tuning Orbital Symmetry of Iridium Nitrenoid Enables Catalytic Diastereo- and Enantioselective Alkene Difunctionalizations. J Am Chem Soc 2021; 143:3993-4004. [DOI: 10.1021/jacs.1c00652] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Suhyeon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Dongwook Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Seung Youn Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Sukbok Chang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 34141, Korea
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8
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Li X, Liang H, Yang YO, Wang X, Zhang J, Wang D, Sun F, Du Y. Synthesis of Spiro[benzofuran‐2,2'‐benzo[
b
]thiophene]‐3,3'‐diones via PIDA/CuBr‐Mediated Spirocyclization. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xuemin Li
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
| | - Huiyuan Liang
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
| | - Yaxin O Yang
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
| | - Xi Wang
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
| | - Jingran Zhang
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
| | - Donghua Wang
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
| | - Fengxia Sun
- College of Chemical and Pharmaceutical Engineering Hebei Research Center of Pharmaceutical and Chemical Engineering Hebei University of Science and Technology 050018 Shijiazhuang China
| | - Yunfei Du
- School of Pharmaceutical Science and Technology Tianjin University 300072 Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin China
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9
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Maldonado-Domínguez M, Srnec M. Understanding and Predicting Post H-Atom Abstraction Selectivity through Reactive Mode Composition Factor Analysis. J Am Chem Soc 2020; 142:3947-3958. [PMID: 32000494 DOI: 10.1021/jacs.9b12800] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The selective functionalization of C-H bonds is one of the Grails of synthetic chemistry. In this work, we demonstrate that the selectivity toward fast hydroxylation or radical diffusion (known as the OH-rebound and dissociation mechanisms) following H-atom abstraction (HAA) from a substrate C-H bond by high-valent iron-oxo oxidants is already encoded in the HAA step when the post-HAA barriers are much lower than the preceding one. By applying the reactive mode composition factor (RMCF) analysis, which quantifies the kinetic energy distribution (KED) at the reactive mode (RM) of transition states, we show that reactions following the OH-rebound coordinate concentrate the RM kinetic energy on the motion of the reacting oxygen atom and the nascent substrate radical, whereas reactions following the dissociation channel localize most of their kinetic energy in H-atom motion. These motion signatures serve to predict the post-HAA selectivity, and since KED is affected by the free energy of reaction and asynchronicity (factor η) of HAA, we show that bimolecular HAA reactions in solution that are electron transfer-driven and highly exergonic have the lowest fraction of KED on the transferred H-atom and the highest chance to follow rebound hydroxylation. Finally, the RMCF analysis predicts that the H/D primary kinetic isotope effect can serve as a probe for these mechanisms, as confirmed in virtually all reported examples in the literature.
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Affiliation(s)
- Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3 , Prague 8 18223 , Czech Republic
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10
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Pan J, Wenger ES, Matthews ML, Pollock CJ, Bhardwaj M, Kim AJ, Allen BD, Grossman RB, Krebs C, Bollinger JM. Evidence for Modulation of Oxygen Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases. J Am Chem Soc 2019; 141:15153-15165. [PMID: 31475820 DOI: 10.1021/jacs.9b06689] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases generate iron(IV)-oxo (ferryl) intermediates that can abstract hydrogen from aliphatic carbons (R-H). Hydroxylation proceeds by coupling of the resultant substrate radical (R•) and oxygen of the Fe(III)-OH complex ("oxygen rebound"). Nonhydroxylation outcomes result from different fates of the Fe(III)-OH/R• state; for example, halogenation results from R• coupling to a halogen ligand cis to the hydroxide. We previously suggested that halogenases control substrate-cofactor disposition to disfavor oxygen rebound and permit halogen coupling to prevail. Here, we explored the general implication that, when a ferryl intermediate can ambiguously target two substrate carbons for different outcomes, rebound to the site capable of the alternative outcome should be slower than to the adjacent, solely hydroxylated site. We evaluated this prediction for (i) the halogenase SyrB2, which exclusively hydroxylates C5 of norvaline appended to its carrier protein but can either chlorinate or hydroxylate C4 and (ii) two bifunctional enzymes that normally hydroxylate one carbon before coupling that oxygen to a second carbon (producing an oxacycle) but can, upon encountering deuterium at the first site, hydroxylate the second site instead. In all three cases, substrate hydroxylation incorporates a greater fraction of solvent-derived oxygen at the site that can also undergo the alternative outcome than at the other site, most likely reflecting an increased exchange of the initially O2-derived oxygen ligand in the longer-lived Fe(III)-OH/R• states. Suppression of rebound may thus be generally important for nonhydroxylation outcomes by these enzymes.
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Affiliation(s)
| | | | | | | | - Minakshi Bhardwaj
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40546-0312 , United States
| | | | | | - Robert B Grossman
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40546-0312 , United States
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11
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Abstract
C–H functionalization is a chemically challenging but highly desirable transformation. 2-oxoglutarate-dependent oxygenases (2OGXs) are remarkably versatile biocatalysts for the activation of C–H bonds. In nature, they have been shown to accept both small and large molecules carrying out a plethora of reactions, including hydroxylations, demethylations, ring formations, rearrangements, desaturations, and halogenations, making them promising candidates for industrial manufacture. In this review, we describe the current status of 2OGX use in biocatalytic applications concentrating on 2OGX-catalyzed oxyfunctionalization of amino acids and synthesis of antibiotics. Looking forward, continued bioinformatic sourcing will help identify additional, practical useful members of this intriguing enzyme family, while enzyme engineering will pave the way to enhance 2OGX reactivity for non-native substrates.
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12
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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13
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Kato S, Suzuki Y, Suzuki K, Haraguchi R, Fukuzawa SI. Silver-Catalyzed Diastereo- and Enantioselective Michael Addition and 1,3-Dipolar Cycloaddition Reactions of Imino Esters to 3-Methyl-4-nitro-5-styrylisoxazoles. J Org Chem 2018; 83:13965-13972. [DOI: 10.1021/acs.joc.8b02309] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shuma Kato
- Department of Applied Chemistry, Institute of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Yuko Suzuki
- Department of Applied Chemistry, Institute of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Kota Suzuki
- Department of Applied Chemistry, Institute of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Ryosuke Haraguchi
- Department of Applied Chemistry, Institute of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Shin-ichi Fukuzawa
- Department of Applied Chemistry, Institute of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
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14
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Rabe P, Kamps JJAG, Schofield CJ, Lohans CT. Roles of 2-oxoglutarate oxygenases and isopenicillin N synthase in β-lactam biosynthesis. Nat Prod Rep 2018; 35:735-756. [PMID: 29808887 PMCID: PMC6097109 DOI: 10.1039/c8np00002f] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/01/2023]
Abstract
Covering: up to 2017 2-Oxoglutarate (2OG) dependent oxygenases and the homologous oxidase isopenicillin N synthase (IPNS) play crucial roles in the biosynthesis of β-lactam ring containing natural products. IPNS catalyses formation of the bicyclic penicillin nucleus from a tripeptide. 2OG oxygenases catalyse reactions that diversify the chemistry of β-lactams formed by both IPNS and non-oxidative enzymes. Reactions catalysed by the 2OG oxygenases of β-lactam biosynthesis not only involve their typical hydroxylation reactions, but also desaturation, epimerisation, rearrangement, and ring-forming reactions. Some of the enzymes involved in β-lactam biosynthesis exhibit remarkable substrate and product selectivities. We review the roles of 2OG oxygenases and IPNS in β-lactam biosynthesis, highlighting opportunities for application of knowledge of their roles, structures, and mechanisms.
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Affiliation(s)
- Patrick Rabe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Jos J A G Kamps
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher T Lohans
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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15
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Wen W, Chen L, Luo MJ, Zhang Y, Chen YC, Ouyang Q, Guo QX. Chiral Aldehyde Catalysis for the Catalytic Asymmetric Activation of Glycine Esters. J Am Chem Soc 2018; 140:9774-9780. [PMID: 29995401 DOI: 10.1021/jacs.8b06676] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chiral aldehyde catalysis is uniquely suitable for the direct asymmetric α-functionalization of N-unprotected amino acids, because aldehydes can reversibly form imines. However, there have been few successful reports of these transformations. In fact, only chiral aldehyde catalyzed aldol reactions of amino acids and alkylation of 2-amino malonates have been reported with good chiral induction. Here, we report a novel type of chiral aldehyde catalyst based on face control of the enolate intermediates. The resulting chiral aldehyde is the first efficient nonpyridoxal-dependent catalyst that can promote the direct asymmetric α-functionalization of N-unprotected glycine esters. Possible transition states and the proton transfer process were investigated by density functional theory calculations.
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Affiliation(s)
- Wei Wen
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Lei Chen
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Ming-Jing Luo
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Yan Zhang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
| | - Ying-Chun Chen
- College of Pharmacy , Third Military Medical University , Chongqing 400038 , China
| | - Qin Ouyang
- College of Pharmacy , Third Military Medical University , Chongqing 400038 , China
| | - Qi-Xiang Guo
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , China
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16
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Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli. Nat Chem Biol 2018; 14:794-800. [DOI: 10.1038/s41589-018-0084-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/27/2018] [Indexed: 12/14/2022]
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17
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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18
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Huang Z, Zhan M, Zhang S, Luo Q, Zhang WX, Xi Z. Synthesis of dibromo- and tetrabromo-bipyrrolines and their corresponding 2,6-diazasemibullvalene derivatives. Org Chem Front 2017. [DOI: 10.1039/c7qo00287d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Treatment of Δ1-dipyrrolines with NBS afforded α,α′-dibromo-Δ1-bipyrrolines and α,α,α′,α′-tetrabromo-Δ1-bipyrrolines, which were efficiently transformed into 2,6-diazasemibullvalene derivatives via reduction with lithium.
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Affiliation(s)
- Zhe Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871
| | - Ming Zhan
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871
| | - Shaoguang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871
| | - Qian Luo
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871
| | - Wen-Xiong Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871
| | - Zhenfeng Xi
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- College of Chemistry
- Peking University
- Beijing 100871
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19
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Townsend CA. Convergent biosynthetic pathways to β-lactam antibiotics. Curr Opin Chem Biol 2016; 35:97-108. [PMID: 27693891 DOI: 10.1016/j.cbpa.2016.09.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 02/05/2023]
Abstract
Five naturally-occurring families of β-lactams have inspired a class of drugs that constitute >60% of the antimicrobials used in human medicine. Their biosynthetic pathways reveal highly individualized synthetic strategies that yet converge on a common azetidinone ring assembled in structural contexts that confer selective binding and inhibition of d,d-transpeptidases that play essential roles in bacterial cell wall (peptidoglycan) biosynthesis. These enzymes belong to a single 'clan' of evolutionarily distinct serine hydrolases whose active site geometry and mechanism of action is specifically matched by these antibiotics for inactivation that is kinetically competitive with their native function. Unusual enzyme-mediated reactions and catalytic multitasking in these pathways are discussed with particular attention to the diverse ways the β-lactam itself is generated, and more broadly how the intrinsic reactivity of this core structural element is modulated in natural systems through the introduction of ring strain and electronic effects.
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Affiliation(s)
- Craig A Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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20
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Bai XF, Li L, Xu Z, Zheng ZJ, Xia CG, Cui YM, Xu LW. Asymmetric Michael Addition of Aldimino Esters with Chalcones Catalyzed by Silver/Xing-Phos: Mechanism-Oriented Divergent Synthesis of Chiral Pyrrolines. Chemistry 2016; 22:10399-404. [DOI: 10.1002/chem.201601945] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Xing-Feng Bai
- State Key Laboratory for Oxo Synthesis and Selective Oxidation; Lanzhou Institute of Chemical Physics (CAS) and; University of the Chinese Academy of Sciences; P. R. China
| | - Li Li
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education; Hangzhou Normal University; P. R. China
| | - Zheng Xu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education; Hangzhou Normal University; P. R. China
| | - Zhan-Jiang Zheng
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education; Hangzhou Normal University; P. R. China
| | - Chun-Gu Xia
- State Key Laboratory for Oxo Synthesis and Selective Oxidation; Lanzhou Institute of Chemical Physics (CAS) and; University of the Chinese Academy of Sciences; P. R. China
| | - Yu-Ming Cui
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education; Hangzhou Normal University; P. R. China
| | - Li-Wen Xu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation; Lanzhou Institute of Chemical Physics (CAS) and; University of the Chinese Academy of Sciences; P. R. China
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education; Hangzhou Normal University; P. R. China
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21
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Wu LF, Meng S, Tang GL. Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:453-70. [DOI: 10.1016/j.bbapap.2016.01.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 01/29/2023]
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22
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Ma G, Zhu W, Su H, Cheng N, Liu Y. Uncoupled Epimerization and Desaturation by Carbapenem Synthase: Mechanistic Insights from QM/MM Studies. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01275] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guangcai Ma
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Hao Su
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Na Cheng
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Laboratory
of Colloid
and Interface Chemistry, Ministry of Education, School of Chemistry
and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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23
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Abstract
Mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases comprise a large family of enzymes that utilize an Fe(IV)-oxo intermediate to initiate diverse oxidative transformations with important biological roles. Here, four of the major types of Fe(II)/2OG-dependent reactions are detailed: hydroxylation, halogenation, ring formation, and desaturation. In addition, an atypical epimerization reaction is described. Studies identifying several key intermediates in catalysis are concisely summarized, and the proposed mechanisms are explained. In addition, a variety of other transformations catalyzed by selected family members are briefly described to further highlight the chemical versatility of these enzymes.
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Affiliation(s)
- Salette Martinez
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Robert P Hausinger
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824; Departments of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
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24
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Mel’nik OY, Chornous VA, Vovk MV. Polyfunctional imidazoles: IX. Synthesis of 1-aryl-5-(2-aryl-3,4-dihydro-2H-pyrrol-4-yl)-4-chloro-1H-imidazoles. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2015. [DOI: 10.1134/s1070428015020189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Zhan M, Zhang S, Huang Z, Xi Z. Efficient synthesis of aza-triquinacene derivatives via cycloaddition of 2,6-diazasemibullvalenes with nitroso compounds. Chem Asian J 2014; 10:862-4. [PMID: 25393100 DOI: 10.1002/asia.201403030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/20/2014] [Indexed: 11/07/2022]
Abstract
The reaction between 2,6-diazasemibullvalenes and nitroso compounds was investigated. Aza-triquinacene derivatives of interesting structural and synthetic chemistry were generated highly selectively in good to excellent isolated yields. This reaction, which was rarely found between common aziridine derivatives and nitroso compounds, could be attributed to the rigid polycyclic ring system and the substitution patterns of 2,6-diazasemibullvalenes. Δ(1) -Bipyrroline derivatives were formed in excellent yields when these aza-triquinacene derivatives were treated with SmI2 .
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Affiliation(s)
- Ming Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871 (China), Fax: (+86) 10-6275-1708
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26
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Chang WC, Guo Y, Wang C, Butch SE, Rosenzweig AC, Boal AK, Krebs C, Bollinger JM. Mechanism of the C5 stereoinversion reaction in the biosynthesis of carbapenem antibiotics. Science 2014; 343:1140-4. [PMID: 24604200 PMCID: PMC4160820 DOI: 10.1126/science.1248000] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The bicyclic β-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by β-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H•) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H• to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H•-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.
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Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yisong Guo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susan E. Butch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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27
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Li R, Lloyd EP, Moshos KA, Townsend CA. Identification and characterization of the carbapenem MM 4550 and its gene cluster in Streptomyces argenteolus ATCC 11009. Chembiochem 2014; 15:320-31. [PMID: 24420617 PMCID: PMC3972073 DOI: 10.1002/cbic.201300319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 10/25/2013] [Indexed: 11/11/2022]
Abstract
Nearly 50 naturally occurring carbapenem β-lactam antibiotics, most produced by Streptomyces, have been identified. The structural diversity of these compounds is limited to variance of the C-2 and C-6 side chains as well as the stereochemistry at C-5/C-6. These structural motifs are of interest both for their antibiotic effects and their biosynthesis. Although the thienamycin gene cluster is the only active gene cluster publically available in this group, more comparative information is needed to understand the genetic basis of these structural differences. We report here the identification of MM 4550, a member of the olivanic acids, as the major carbapenem produced by Streptomyces argenteolus ATCC 11009. Its gene cluster was also identified by degenerate PCR and targeted gene inactivation. Sequence analysis revealed that the genes encoding the biosynthesis of the bicyclic core and the C-6 and C-2 side chains are well conserved in the MM 4550 and thienamycin gene clusters. Three new genes, cmmSu, cmm17 and cmmPah were found in the new cluster, and their putative functions in the sulfonation and epimerization of MM 4550 are proposed. Gene inactivation showed that, in addition to cmmI, two new genes, cmm22 and -23, encode a two-component response system thought to regulate the production of MM 4550. Overexpression of cmmI, cmm22 and cmm23 promoted MM 4550 production in an engineered strain. Finally, the involvement and putative roles of all genes in the MM 4550 cluster are proposed based on the results of bioinformatics analysis, gene inactivation, and analysis of disruption mutants. Overall, the differences between the thienamycin and MM 4550 gene clusters are reflected in characteristic structural elements and provide new insights into the biosynthesis of the complex carbapenems.
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Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 (USA)
| | - Evan P. Lloyd
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 (USA)
| | | | - Craig. A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 (USA)
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28
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Phelan RM, Townsend CA. Mechanistic insights into the bifunctional non-heme iron oxygenase carbapenem synthase by active site saturation mutagenesis. J Am Chem Soc 2013; 135:7496-502. [PMID: 23611403 PMCID: PMC3683866 DOI: 10.1021/ja311078s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The carbapenem class of β-lactam antibiotics is known for its remarkable potency, antibacterial spectrum, and resistance to β-lactamase-mediated inactivation. While the biosynthesis of structurally "complex" carbapenems, such as thienamycin, share initial biochemical steps with carbapenem-3-carboxylate ("simple" carbapenem), the requisite inversion at C5 and formation of the characteristic α,β-unsaturated carboxylate are different in origin between the two groups. Here, we consider carbapenem synthase, a mechanistically distinct bifunctional non-heme iron α-ketoglutarate-dependent enzyme responsible for the terminal reactions, C5 epimerization and desaturation, in simple carbapenem production. Interestingly, this enzyme accepts two stereoisomeric substrates and transforms each to a common active antibiotic. Owing both to enzyme and product instability, resorting to saturation mutagenesis of active site and selected second-sphere residues gave clearly differing profiles of CarC tolerance to structural modification. Guided by a crystal structure and the mutational data, in silico docking was used to suggest the positioning of each disastereomeric substrate in the active site. The two orientations relative to the reactive iron-oxo center are manifest in the two distinct reactions, C5-epimerization and C2/3-desaturation. These observations favor a two-step reaction scheme involving two complete oxidative cycles as opposed to a single catalytic cycle in which an active site tyrosine, Tyr67, after hydrogen donation to achieve bicyclic ring inversion, is further hypothesized to serve as a radical carrier.
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Affiliation(s)
- Ryan M. Phelan
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218
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29
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Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ. The enzymes of β-lactam biosynthesis. Nat Prod Rep 2013; 30:21-107. [DOI: 10.1039/c2np20065a] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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30
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Yu X, Yao Q, Tao H, Yang Y, Li L, Zheng B, Zhu S. A study on the interaction between 3-spiro-piperidones and bovine serum albumin using spectroscopic approaches. LUMINESCENCE 2012; 28:705-12. [DOI: 10.1002/bio.2420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/16/2012] [Accepted: 07/18/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Xianyong Yu
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan Province College Key Laboratory of QSAR/QSPR; School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan; 411201; People's Republic of China
| | - Qing Yao
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan Province College Key Laboratory of QSAR/QSPR; School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan; 411201; People's Republic of China
| | - Hongwen Tao
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan Province College Key Laboratory of QSAR/QSPR; School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan; 411201; People's Republic of China
| | - Ying Yang
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan Province College Key Laboratory of QSAR/QSPR; School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan; 411201; People's Republic of China
| | - Lei Li
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan Province College Key Laboratory of QSAR/QSPR; School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan; 411201; People's Republic of China
| | - Baishu Zheng
- Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education, Hunan Province College Key Laboratory of QSAR/QSPR; School of Chemistry and Chemical Engineering; Hunan University of Science and Technology; Xiangtan; 411201; People's Republic of China
| | - Shizhong Zhu
- Farming Development Services Center; Jinghai; Tianjin; 300016; People's Republic of China
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31
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Phelan RM, DiPardo BJ, Townsend CA. A high-throughput screen for the engineered production of β-lactam antibiotics. ACS Chem Biol 2012; 7:835-40. [PMID: 22428872 DOI: 10.1021/cb200504g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High-throughput screens and selections have had profound impact on our ability to engineer proteins possessing new, desired properties. These methods are especially useful when applied to the modification of existing enzymes to create natural and unnatural products. In an advance upon existing methods we developed a high-throughput, genetically regulated screen for the in vivo production of β-lactam antibiotics using a green fluorescent protein (gfp) reporter. This assay proved reliable and sensitive and presents a dynamic range under which a wide array of β-lactam architectural subclasses can be detected. Moreover, the graded response elicited in this assay can be used to rank mutant activity. The utility of this development was demonstrated in vivo and then applied to the first experimental investigation of a putative catalytic residue in carbapenem synthase (CarC). Information gained about the mutability of this residue defines one parameter for enzymatic activity and sets boundaries for future mechanistic and engineering efforts.
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Affiliation(s)
- Ryan M. Phelan
- Department
of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland
21218, United States
| | - Benjamin J. DiPardo
- Department
of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland
21218, United States
| | - Craig A. Townsend
- Department
of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland
21218, United States
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32
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Padilla S, Adrio J, Carretero JC. Au-Catalyzed Asymmetric Formal [3 + 2] Cycloaddition of Isocyanoacetates with Maleimides. J Org Chem 2012; 77:4161-6. [DOI: 10.1021/jo3003425] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Silvia Padilla
- Departamento
de Química Orgánica, Facultad
de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Javier Adrio
- Departamento
de Química Orgánica, Facultad
de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Juan C. Carretero
- Departamento
de Química Orgánica, Facultad
de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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33
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Hamed RB, Henry L, Gomez-Castellanos JR, Mecinović J, Ducho C, Sorensen JL, Claridge TDW, Schofield CJ. Crotonase Catalysis Enables Flexible Production of Functionalized Prolines and Carbapenams. J Am Chem Soc 2011; 134:471-9. [DOI: 10.1021/ja208318d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Refaat B. Hamed
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Luc Henry
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | | | - Jasmin Mecinović
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christian Ducho
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - John L. Sorensen
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy D. W. Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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Bodner MJ, Li R, Phelan RM, Freeman MF, Moshos KA, Lloyd EP, Townsend CA. Definition of the common and divergent steps in carbapenem β-lactam antibiotic biosynthesis. Chembiochem 2011; 12:2159-65. [PMID: 21913298 PMCID: PMC3281309 DOI: 10.1002/cbic.201100366] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Indexed: 11/11/2022]
Abstract
Approximately 50 naturally occurring carbapenem β-lactam antibiotics are known. All but one of these have been isolated from Streptomyces species and are disubstituted structural variants of a simple core that is synthesized by Pectobacterium carotovorum (Erwinia carotovora), a phylogenetically distant plant pathogen. While the biosynthesis of the simple carbapenem, (5R)-carbapen-2-em-3-carboxylic acid, is impressively efficient requiring only three enzymes, CarA, CarB and CarC, the formation of thienamycin, one of the former group of metabolites from Streptomyces, is markedly more complex. Despite their phylogenetic separation, bioinformatic analysis of the encoding gene clusters suggests that the two pathways could be related. Here we demonstrate with gene swapping, stereochemical and kinetics experiments that CarB and CarA and their S. cattleya orthologues, ThnE and ThnM, respectively, are functionally and stereochemically equivalent, although their catalytic efficiencies differ. The biosynthetic pathways, therefore, to thienamycin, and likely to the other disubstituted carbapenems, and to the simplest carbapenem, (5R)-carbapen-2-em-3-carboxylic acid, are initiated in the same manner, but share only two common steps before diverging.
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Affiliation(s)
- Micah J. Bodner
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Rongfeng Li
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Ryan M. Phelan
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Michael F. Freeman
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Kristos A. Moshos
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Evan P. Lloyd
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University Baltimore, Maryland 21218 (USA)
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Bodner MJ, Phelan RM, Freeman MF, Li R, Townsend CA. Non-heme iron oxygenases generate natural structural diversity in carbapenem antibiotics. J Am Chem Soc 2010; 132:12-3. [PMID: 20017478 PMCID: PMC2821876 DOI: 10.1021/ja907320n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Carbapenems are a clinically important antibiotic family. More than 50 naturally occurring carbapenam/ems are known and are distinguished primarily by their C-2/C-6 side chains where many are only differentiated by the oxidation states of these substituents. With a limited palette of variations the carbapenem family comprises a natural combinatorial library, and C-2/C-6 oxidation is associated with increased efficacy. We demonstrate that ThnG and ThnQ encoded by the thienamycin gene cluster in Streptomyces cattleya oxidize the C-2 and C-6 moieties of carbapenems, respectively. ThnQ stereospecifically hydroxylates PS-5 (5) giving N-acetyl thienamycin (2). ThnG catalyzes sequential desaturation and sulfoxidation of PS-5 (5), giving PS-7 (7) and its sulfoxide (9). The enzymes are relatively substrate selective but are proposed to give rise to the oxidative diversity of carbapenems produced by S. cattleya, and orthologues likely function similarly in allied streptomyces. Elucidating the roles of ThnG and ThnQ will focus further investigations of carbapenem antibiotic biosynthesis.
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Affiliation(s)
- Micah J. Bodner
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Ryan M. Phelan
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Michael F. Freeman
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Rongfeng Li
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St. Baltimore, MD 21218
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López-Pérez A, Adrio J, Carretero JC. The phenylsulfonyl group as a temporal regiochemical controller in the catalytic asymmetric 1,3-dipolar cycloaddition of azomethine ylides. Angew Chem Int Ed Engl 2009; 48:340-3. [PMID: 19065689 DOI: 10.1002/anie.200805063] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ana López-Pérez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Hamed RB, Batchelar ET, Mecinović J, Claridge TDW, Schofield CJ. Evidence that Thienamycin Biosynthesis Proceeds via C-5 Epimerization: ThnE Catalyzes the Formation of (2S,5S)-trans-Carboxymethylproline. Chembiochem 2009; 10:246-50. [DOI: 10.1002/cbic.200800652] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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López-Pérez A, Adrio J, Carretero J. The Phenylsulfonyl Group as a Temporal Regiochemical Controller in the Catalytic Asymmetric 1,3-Dipolar Cycloaddition of Azomethine Ylides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805063] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kristensen TE, Hansen FK, Hansen T. The SelectiveO-Acylation of Hydroxyproline as a Convenient Method for the Large-Scale Preparation of Novel Proline Polymers and Amphiphiles. European J Org Chem 2009. [DOI: 10.1002/ejoc.200800941] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Brandi A, Cicchi S, Cordero FM. Novel Syntheses of Azetidines and Azetidinones. Chem Rev 2008; 108:3988-4035. [DOI: 10.1021/cr800325e] [Citation(s) in RCA: 395] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alberto Brandi
- Dipartimento di Chimica Organica “Ugo Schiff”, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi - HeteroBioLab, Università degli Studi di Firenze, via della Lastruccia 13, 50019 Sesto F.no (FI), Italy
| | - Stefano Cicchi
- Dipartimento di Chimica Organica “Ugo Schiff”, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi - HeteroBioLab, Università degli Studi di Firenze, via della Lastruccia 13, 50019 Sesto F.no (FI), Italy
| | - Franca M. Cordero
- Dipartimento di Chimica Organica “Ugo Schiff”, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi - HeteroBioLab, Università degli Studi di Firenze, via della Lastruccia 13, 50019 Sesto F.no (FI), Italy
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Cabrera S, Reyes E, Alemán J, Milelli A, Kobbelgaard S, Jørgensen KA. Organocatalytic Asymmetric Synthesis of α,α-Disubstituted α-Amino Acids and Derivatives. J Am Chem Soc 2008; 130:12031-7. [DOI: 10.1021/ja804567h] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Silvia Cabrera
- Danish National Research Foundation: Center for Catalysis, Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Efraim Reyes
- Danish National Research Foundation: Center for Catalysis, Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - José Alemán
- Danish National Research Foundation: Center for Catalysis, Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Andrea Milelli
- Danish National Research Foundation: Center for Catalysis, Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sara Kobbelgaard
- Danish National Research Foundation: Center for Catalysis, Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Karl Anker Jørgensen
- Danish National Research Foundation: Center for Catalysis, Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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Yu N, Wang C, Zhao F, Liu L, Zhang WX, Xi Z. Diverse Reactions of 1,4-Dilithio-1,3-dienes with Nitriles: Facile Access to Tricyclic Δ1-Bipyrrolines, Multiply Substituted Pyridines, Siloles, and (Z,Z)-Dienylsilanes by Tuning of Substituents on the Butadienyl Skeleton. Chemistry 2008; 14:5670-9. [DOI: 10.1002/chem.200701742] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Borowski T, Broclawik E, Schofield CJ, Siegbahn PEM. Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study. J Comput Chem 2007; 27:740-8. [PMID: 16521121 DOI: 10.1002/jcc.20384] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases.
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Affiliation(s)
- Tomasz Borowski
- Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S-10691 Stockholm, Sweden.
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Abstract
High-valent non-heme iron-oxo intermediates have been proposed for decades as the key intermediates in numerous biological oxidation reactions. In the past three years, the first direct characterization of such intermediates has been provided by studies of several alphaKG-dependent oxygenases that catalyze either hydroxylation or halogenation of their substrates. In each case, the Fe(IV)-oxo intermediate is implicated in cleavage of the aliphatic C-H bond to initiate hydroxylation or halogenation. The observation of non-heme Fe(IV)-oxo intermediates and Fe(II)-containing product(s) complexes with almost identical spectroscopic parameters in the reactions of two distantly related alphaKG-dependent hydroxylases suggests that members of this subfamily follow a conserved mechanism for substrate hydroxylation. In contrast, for the alphaKG-dependent non-heme iron halogenase, CytC3, two distinct Fe(IV) complexes form and decay together, suggesting that they are in rapid equilibrium. The existence of two distinct conformers of the Fe site may be the key factor accounting for the divergence of the halogenase reaction from the more usual hydroxylation pathway after C-H bond cleavage. Distinct transformations catalyzed by other mononuclear non-heme enzymes are likely also to involve initial C-H bond cleavage by Fe(IV)-oxo complexes, followed by diverging reactivities of the resulting Fe(III)-hydroxo/substrate radical intermediates.
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Affiliation(s)
- Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | | | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
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Abstract
Many bacteria use cell-cell communication to monitor their population density, synchronize their behaviour and socially interact. This communication results in a coordinated gene regulation and is generally called quorum sensing. In gram-negative bacteria, the most common quorum signal molecules are acylated homoserine lactones (AHLs), although other low-molecular-mass signalling molecules have been described such as Autoinducer-2 (AI-2). The phenotypes that are regulated in Serratia species by means of AHLs are remarkably diverse and of profound biological and ecological significance, and often interconnected with other global regulators. Furthermore, AHL- and AI-2-mediated systems (less profoundly studied) are continuously being discovered and explored in Serratia spp., many having interesting twists on the basic theme. Therefore, this review will highlight the current known quorum sensing systems in Serratia spp., including the important nosocomial pathogen Serratia marcescens.
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Affiliation(s)
- Rob Van Houdt
- Molecular and Cellular Biology, Institute for Health, Environment and Safety, Belgian Nuclear Research Centre SCK x CEN, Mol, Belgium.
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46
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Hewitson KS, Granatino N, Welford RWD, McDonough MA, Schofield CJ. Oxidation by 2-oxoglutarate oxygenases: non-haem iron systems in catalysis and signalling. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:807-28; discussion 1035-40. [PMID: 15901537 DOI: 10.1098/rsta.2004.1540] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases are a superfamily of enzymes that catalyse a wide range of reactions including hydroxylations, desaturations and oxidative ring closures. Recently, it has been discovered that they act as sensors in the hypoxic response in humans and other animals. Substrate oxidation is coupled to conversion of 2OG to succinate and carbon dioxide. Kinetic, spectroscopic and structural studies are consistent with a consensus mechanism in which ordered binding of (co)substrates enables control of reactive intermediates. Binding of the substrate to the active site triggers the enzyme for ligation of dioxygen to the metal. Oxidative decarboxylation of 2OG then generates the ferryl species thought to mediate substrate oxidation. Structural studies reveal a conserved double-stranded beta-helix core responsible for binding the iron, via a 2His-1carboxylate motif and the 2OG side chain. The rigidity of this core contrasts with the conformational flexibility of surrounding regions that are involved in binding the substrate. Here we discuss the roles of 2OG oxygenases in terms of the generic structural and mechanistic features that render the 2OG oxygenases suited for their functions.
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Affiliation(s)
- K S Hewitson
- The Department of Chemistry and The Oxford Centre for Molecular Sciences, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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47
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Coulthurst SJ, Barnard AML, Salmond GPC. Regulation and biosynthesis of carbapenem antibiotics in bacteria. Nat Rev Microbiol 2005; 3:295-306. [PMID: 15759042 DOI: 10.1038/nrmicro1128] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Carbapenem antibiotics are members of the beta-lactam family of antibiotics, the most important class of antibiotics currently in clinical use. They are active against many important Gram-positive and Gram-negative pathogens. One important feature of carbapenem antibiotics is their resistance to several beta-lactamases. Thienamycin, isolated from Streptomyces cattleya, was the first carbapenem described. Other well-studied carbapenems were isolated from the Gram-negative bacteria Erwinia carotovora subsp. carotovora, Serratia sp. strain ATCC39006 and Photorhabdus luminescens strain TT01. Here, we review the genetics and biochemistry of carbapenem production in these bacteria. Research into carbapenems could uncover a new repertoire of bioactive molecules and biosynthetic enzymes, and exploiting these novel enzymes could lead to development of new classes of antibiotics with useful chemotherapeutic activities.
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Affiliation(s)
- Sarah J Coulthurst
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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48
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Sorensen JL, Sleeman MC, Schofield CJ. Synthesis of deuterium labelledl- andd-glutamate semialdehydes and their evaluation as substrates for carboxymethylproline synthase (CarB)—implications for carbapenem biosynthesis. Chem Commun (Camb) 2005:1155-7. [PMID: 15726176 DOI: 10.1039/b416423g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carboxymethylproline synthase was shown to condense L-glutamate semialdehyde with malonyl-coenzyme A to produce (2S,5S)-carboxymethylproline, while incubation of D-glutamate semialdehyde results only in uncoupled turnover of malonyl-CoA.
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Affiliation(s)
- John L Sorensen
- Chemistry Research Laboratory and Oxford Centre for Molecular Sciences, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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49
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Kershaw NJ, Caines MEC, Sleeman MC, Schofield CJ. The enzymology of clavam and carbapenem biosynthesis. Chem Commun (Camb) 2005:4251-63. [PMID: 16113715 DOI: 10.1039/b505964j] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enzyme-catalysed reactions involved in formation of the bicyclic clavam and carbapenem nuclei, including beta-amino acid and beta-lactam formation, are discussed and compared with those involved in penicillin and cephalosporin biosynthesis. The common role of unusual oxidation reactions in the biosynthetic pathways and the lack of synthetic reagents available to effect them are highlighted.
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Affiliation(s)
- Nadia J Kershaw
- Department of Chemistry and Oxford Centre for Molecular Sciences, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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50
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Alcaide B, Almendros P. Chapter 4 Four-membered ring systems. A CRITICAL REVIEW OF THE 2003 LITERATURE PRECEDED BY TWO CHAPTERS ON CURRENT HETEROCYCLIC TOPICS 2005. [DOI: 10.1016/s0959-6380(05)80046-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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