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Wheadon MJ, Townsend CA. Accurate Substrate-Like Probes for Trapping Late-Stage Intermediates in Nonribosomal Peptide Synthetase Condensation Domains. ACS Chem Biol 2022; 17:2046-2053. [PMID: 35914245 PMCID: PMC10029145 DOI: 10.1021/acschembio.2c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are a family of multidomain enzymes dedicated to the production of peptide natural products. Central to NRPS function are condensation (C) domains, which catalyze peptide bond formation and a number of specialized transformations including dehydroamino acid and β-lactam synthesis. Structures of C domains in catalytically informative states are limited due to a lack of clear strategies for stabilizing C domain interactions with their substrates and client domains. Inspired by a β-lactam forming C domain, we report herein the synthesis and application of 1, which forms irreversible cross-links with engineered thiol nucleophiles in a C domain active site. Deployment of 1 demonstrates the synthetic tractability of trapping late-stage nascent peptides in C domains and provides a readily adaptable tactic for stabilizing C domain interactions in multidomain NRPS fragments.
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Affiliation(s)
- Michael J Wheadon
- Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Johns Hopkins University, 3400 N Charles St., Baltimore, Maryland 21218, United States
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2
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Long DH, Townsend CA. Acyl Donor Stringency and Dehydroaminoacyl Intermediates in β-Lactam Formation by a Non-ribosomal Peptide Synthetase. ACS Chem Biol 2021; 16:806-812. [PMID: 33847484 DOI: 10.1021/acschembio.1c00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensation (C) domains in non-ribosomal peptide synthetases catalyze peptide elongation steps whereby activated amino acid or peptidyl acyl donors are coupled with specific amino acid acceptors. In the biosynthesis of the β-lactam antibiotic nocardicin A, an unusual C domain converts a seryl tetrapeptide into its pentapeptide product containing an integrated β-lactam ring. While indirect evidence for the intermediacy of a dehydroalanyl species has been reported, here we describe observation of the elusive enzyme-bound dehydroamino acyl intermediate generated from the corresponding allo-threonyl tetrapeptide and partitioned into pentapeptide products containing either a dehydrobutyrine residue or an embedded β-lactam. Contrary to trends in the literature where condensation domains have been deemed flexible as to acyl donor structure, this β-lactam synthesizing domain is highly discriminating. The observation of dehydrobutyrine formation links this C domain to related clades associated with natural products containing dehydroamino acid and d-configured residues, suggesting a common mechanistic link.
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Affiliation(s)
- Darcie H. Long
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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3
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Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions. Nat Commun 2019; 10:3868. [PMID: 31455765 PMCID: PMC6711958 DOI: 10.1038/s41467-019-11740-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) underlie the biosynthesis of many natural products that have important medicinal utility. Protection of the NRPS peptide products from proteolysis is critical to these pathways and is often achieved by structural modification, principally the introduction of d-amino acid residues into the elongating peptide. These amino acids are generally formed in situ from their l-stereoisomers by epimerization domains or dual-function condensation/epimerization domains. In singular contrast, the thioesterase domain of nocardicin biosynthesis mediates both the effectively complete l- to d-epimerization of its C-terminal amino acid residue (≥100:1) and hydrolytic product release. We report herein high-resolution crystal structures of the nocardicin thioesterase domain in ligand-free form and reacted with a structurally precise fluorophosphonate substrate mimic that identify the complete peptide binding pocket to accommodate both stereoisomers. These structures combined with additional functional studies provide detailed mechanistic insight into this unique dual-function NRPS domain. NocTE is a nonribosomal peptide synthetase thioesterase that completes the biosynthesis of pro-nocardicin G, the precursor for nocardicin β-lactam antibiotics. Here the authors provide mechanistic insights into NocTE by determining its crystal structures in the ligand-free form and covalently linked to a fluorophosphonate substrate mimic.
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4
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Shimada N, Hirata M, Koshizuka M, Ohse N, Kaito R, Makino K. Diboronic Acid Anhydrides as Effective Catalysts for the Hydroxy-Directed Dehydrative Amidation of Carboxylic Acids. Org Lett 2019; 21:4303-4308. [PMID: 31120259 DOI: 10.1021/acs.orglett.9b01484] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The direct catalytic dehydrative amidation of β-hydroxycarboxylic acids with amines is described. A biphenyl-based diboronic acid anhydride with a B-O-B skeleton is shown to be an exceptionally effective catalyst for the reaction, providing β-hydroxycarboxylic amides in high to excellent yields with a low catalyst loading (minimum of 0.01 mol %, TON up to 7,500). This hydroxy-directed amidation shows excellent chemoselectivity and is applicable to gram-scale drug synthesis.
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Affiliation(s)
- Naoyuki Shimada
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Mai Hirata
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Masayoshi Koshizuka
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Naoki Ohse
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Ryoto Kaito
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Kazuishi Makino
- Laboratory of Organic Chemistry for Drug Development and Medical Research Laboratories, Department of Pharmaceutical Sciences , Kitasato University , Tokyo 108-8641 , Japan
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5
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Late-Stage Conversion of Diphenylphosphonate to Fluorophosphonate Probes for the Investigation of Serine Hydrolases. Cell Chem Biol 2019; 26:878-884.e8. [PMID: 30982751 DOI: 10.1016/j.chembiol.2019.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/04/2019] [Accepted: 02/27/2019] [Indexed: 01/13/2023]
Abstract
Diphenylphosphonates (DPPs) have been used for 50 years to inactivate serine hydrolases, creating adducts representative of tetrahedral intermediates of this important class of enzymes. Failure to react at active site serine residues, however, can thwart their usefulness. Here, we describe a facile route and allied mechanistic studies to highly reactive, structurally complex organofluorophosphonates (FPs) by direct fluorinative hydrolysis of DPPs. Advantages over current preparations of FPs are exemplified by the synthesis of a β-lactam-containing peptide substrate analog capable of modifying the C-terminal, dual-function thioesterase involved in nocardicin A biosynthesis. Although this serine hydrolase was found to resist modification by classic DPP inhibitors, active site selective phosphonylation by the corresponding FP occurs rapidly to form a stable adduct. This simple, late-stage method enables the ready preparation of FP probes that retain important structural motifs of native substrates, thus promoting efforts in mechanistic enzymology by accessing biologically relevant enzyme-inhibitor co-structures.
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6
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Application of the N-Dibenzyl Protective Group in the Preparation of β-Lactam Pseudopeptides. Molecules 2019; 24:molecules24071261. [PMID: 30939731 PMCID: PMC6479863 DOI: 10.3390/molecules24071261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/17/2022] Open
Abstract
Despite the great importance of β-lactam antibiotics, there is still a limited number of synthetic approaches for the formation of β-lactam⁻containing dipeptides. In this study, we report upon the stereoselective preparation of β-lactam⁻containing pseudopeptides, where different reaction conditions and NH₂ protective groups were tested to obtain compounds that contain 3-amino-azetidin-2-one. We demonstrate that the protective group is essential for the outcome of the reaction. Successful implementation of dibenzyl-protected serine-containing dipeptides through the Mitsunobu reaction can provide the desired products at high yields and stereoselectivity.
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7
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Ziesche L, Rinkel J, Dickschat JS, Schulz S. Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria. Beilstein J Org Chem 2018; 14:1309-1316. [PMID: 29977398 PMCID: PMC6009203 DOI: 10.3762/bjoc.14.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
N-Acylhomoserine lactones (AHLs) are important bacterial messengers, mediating different bacterial traits by quorum sensing in a cell-density dependent manner. AHLs are also produced by many bacteria of the marine Roseobacter group, which constitutes a large group within the marine microbiome. Often, specific mixtures of AHLs differing in chain length and oxidation status are produced by bacteria, but how the biosynthetic enzymes, LuxI homologs, are selecting the correct acyl precursors is largely unknown. We have analyzed the AHL production in Dinoroseobacter shibae and three Phaeobacter inhibens strains, revealing strain-specific mixtures. Although large differences were present between the species, the fatty acid profiles, the pool for the acyl precursors for AHL biosynthesis, were very similar. To test the acyl-chain selectivity, the three enzymes LuxI1 and LuxI2 from D. shibae DFL-12 as well as PgaI2 from P. inhibens DSM 17395 were heterologously expressed in E. coli and the enzymes isolated for in vitro incubation experiments. The enzymes readily accepted shortened acyl coenzyme A analogs, N-pantothenoylcysteamine thioesters of fatty acids (PCEs). Fifteen PCEs were synthesized, varying in chain length from C4 to C20, the degree of unsaturation and also including unusual acid esters, e.g., 2E,11Z-C18:2-PCE. The latter served as a precursor of the major AHL of D. shibae DFL-12 LuxI1, 2E,11Z-C18:2-homoserine lactone (HSL). Incubation experiments revealed that PgaI2 accepts all substrates except C4 and C20-PCE. Competition experiments demonstrated a preference of this enzyme for C10 and C12 PCEs. In contrast, the LuxI enzymes of D. shibae are more selective. While 2E,11Z-C18:2-PCE is preferentially accepted by LuxI1, all other PCEs were not, except for the shorter, saturated C10–C14-PCEs. The AHL synthase LuxI2 accepted only C14 PCE and 3-hydroxydecanoyl-PCE. In summary, chain-length selectivity in AHLs can vary between different AHL enzymes. Both, a broad substrate acceptance and tuned specificity occur in the investigated enzymes.
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Affiliation(s)
- Lisa Ziesche
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
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Payne JAE, Schoppet M, Hansen MH, Cryle MJ. Diversity of nature's assembly lines - recent discoveries in non-ribosomal peptide synthesis. MOLECULAR BIOSYSTEMS 2017; 13:9-22. [PMID: 27853778 DOI: 10.1039/c6mb00675b] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The biosynthesis of complex natural products by non-ribosomal peptide synthetases (NRPSs) and the related polyketide synthases (PKSs) represents a major source of important bioactive compounds. These large, multi-domain machineries are able to produce a fascinating range of molecules due to the nature of their modular architectures, which allows natural products to be assembled and tailored in a modular, step-wise fashion. In recent years there has been significant progress in characterising the important domains and underlying mechanisms of non-ribosomal peptide synthesis. More significantly, several studies have uncovered important examples of novel activity in many NRPS domains. These discoveries not only greatly increase the structural diversity of the possible products of NRPS machineries but - possibly more importantly - they improve our understanding of what is a highly important, yet complex, biosynthetic apparatus. In this review, several recent examples of novel NRPS function will be introduced, which highlight the range of previously uncharacterised activities that have now been detected in the biosynthesis of important natural products by these mega-enzyme synthetases.
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Affiliation(s)
- Jennifer A E Payne
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
| | - Melanie Schoppet
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
| | | | - Max J Cryle
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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Roberts DM, Bartel C, Scott A, Ivison D, Simpson TJ, Cox RJ. Substrate selectivity of an isolated enoyl reductase catalytic domain from an iterative highly reducing fungal polyketide synthase reveals key components of programming. Chem Sci 2017; 8:1116-1126. [PMID: 28451251 PMCID: PMC5369529 DOI: 10.1039/c6sc03496a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
A cis-acting enoyl reductase (ER) catalytic domain was isolated from a fungal highly reducing iterative polyketide synthase (HR-iPKS) for the first time and studied in vitro. The ER from the squalestatin tetraketide synthase forms a discrete dimeric protein in solution. The ER shows broad substrate selectivity, reducing enoyl species including both natural and unnatural substrates. Pantetheine-bound substrate thiolesters reacted much faster than the corresponding SNAC thiolesters. The unnatural substrates included Z-olefins, 2-ethyl olefins and pentaketides. Methylation of the substrate modifies the activity of the ER such that the 2,4-dimethyl oct-2-enoyl substrate fits into the active site but cannot be reduced. A new NMR-based assay was developed for the direct observation of the stereochemical preferences at the 4' position of the NADPH cofactor and the C-2 and C-3 positions of the substrates. The assay reveals that the fungal iPKS ER-catalysed reaction is stereochemically identical to that of the vertebrate FAS (vFAS) at the cofactor 4' position and the substrate 3-position, but the high stereoselectivity displayed by intact SQTKS is lost such that reprotonation at the 2-position is unselective by the isolated ER. A 3D model of ER was consistent with these observations and showed that the ER may sequester its final substrate to prevent further chain extension. The results support a developing model for programming by HR-iPKS in which competition for substrates between restrictive and permissive catalytic domains chaperones the growing polyketide to completion, while allowing for errors and evolution.
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Affiliation(s)
- Douglas M Roberts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK
- Institute for Organic Chemistry , BMWZ , Leibniz Universität Hannover , Schneiderberg 1b , 30167 , Hannover , Germany .
| | - Christoph Bartel
- Institute for Organic Chemistry , BMWZ , Leibniz Universität Hannover , Schneiderberg 1b , 30167 , Hannover , Germany .
| | - Alan Scott
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK
| | - David Ivison
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK
| | - Russell J Cox
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK
- Institute for Organic Chemistry , BMWZ , Leibniz Universität Hannover , Schneiderberg 1b , 30167 , Hannover , Germany .
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10
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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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11
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Agarwal V, Diethelm S, Ray L, Garg N, Awakawa T, Dorrestein PC, Moore BS. Chemoenzymatic Synthesis of Acyl Coenzyme A Substrates Enables in Situ Labeling of Small Molecules and Proteins. Org Lett 2015; 17:4452-5. [PMID: 26333306 DOI: 10.1021/acs.orglett.5b02113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A chemoenzymatic approach to generate fully functional acyl coenzyme A molecules that are then used as substrates to drive in situ acyl transfer reactions is described. Mass spectrometry based assays to verify the identity of acyl coenzyme A enzymatic products are also illustrated. The approach is responsive to a diverse array of carboxylic acids that can be elaborated to their corresponding coenzyme A thioesters, with potential applications in wide-ranging chemical biology studies that utilize acyl coenzyme A substrates.
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Affiliation(s)
| | | | | | | | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Tokyo 113-0033, Japan
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12
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Furukawa S, Fukuyama T, Matsui A, Kuratsu M, Nakaya R, Ineyama T, Ueda H, Ryu I. Coupling-Reagent-Free Synthesis of Dipeptides and Tripeptides Using Amino Acid Ionic Liquids. Chemistry 2015. [DOI: 10.1002/chem.201501783] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Gaudelli NM, Townsend CA. Epimerization and substrate gating by a TE domain in β-lactam antibiotic biosynthesis. Nat Chem Biol 2014; 10:251-8. [PMID: 24531841 PMCID: PMC3961552 DOI: 10.1038/nchembio.1456] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/30/2013] [Indexed: 12/01/2022]
Abstract
Nonribosomal peptide synthetases are versatile engines of bioactive natural product biosynthesis that function according to the multiple carrier thiotemplate mechanism. C-terminal thioesterase (TE) domains of these giant modular proteins typically catalyze product release by hydrolysis or macrocyclization. We now report an unprecedented, dual-function TE that is involved in the biosynthesis of nocardicin A, which is the paradigm monocyclic β-lactam antibiotic. Contrary to our expectation, a stereodefined series of potential peptide substrates for the nocardicin TE domain failed to undergo hydrolysis. The stringent discrimination against peptide intermediates was overcome by prior monocyclic β-lactam formation at an L-seryl site. Kinetic data are interpreted such that the TE domain acts as a gatekeeper to hold the assembling peptide on an upstream domain until β-lactam formation takes place and then rapidly catalyzes epimerization, which has not been observed previously as a TE catalytic function, and thioesterase cleavage to discharge a fully fledged pentapeptide β-lactam harboring nocardicin G, the universal precursor of the nocardicins.
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Affiliation(s)
- Nicole M. Gaudelli
- 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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15
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Abstract
A membrane transport system functions only when activated by a chemical fuel.
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Affiliation(s)
- A. K. Dambenieks
- Department of Chemistry
- University of Victoria
- Victoria, Canada V8W 3P6
| | - P. H. Q. Vu
- Department of Chemistry
- University of Victoria
- Victoria, Canada V8W 3P6
| | - T. M. Fyles
- Department of Chemistry
- University of Victoria
- Victoria, Canada V8W 3P6
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