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Konno S, Tanaka M, Mizuguchi T, Toyokai H, Taguchi A, Taniguchi A, Hayashi Y. Peptide mixed phosphonates for covalent complex formation with thioesterases in nonribosomal peptide synthetases. J Pept Sci 2024; 30:e3532. [PMID: 37423887 DOI: 10.1002/psc.3532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/11/2023]
Abstract
Natural macrocyclic peptides derived from microorganisms are medicinal resources that are important for the development of new therapeutic agents. Most of these molecules are biosynthesized by a nonribosomal peptide synthetase (NRPS). The thioesterase (TE) domain in NRPS is responsible for the macrocyclization of mature linear peptide thioesters in a final biosynthetic step. NRPS-TEs can cyclize synthetic linear peptide analogs and can be utilized as biocatalysts for the preparation of natural product derivatives. Although the structures and enzymatic activities of TEs have been investigated, the substrate recognition and substrate-TE interaction during the macrocyclization step are still unknown. To understand the TE-mediated macrocyclization, here we report the development of a substrate-based analog with mixed phosphonate warheads, which can react irreversibly with the Ser residue at the active site of TE. We have demonstrated that the tyrocidine A linear peptide (TLP) with a p-nitrophenyl phosphonate (PNP) enables efficient complex formation with tyrocidine synthetase C (TycC)-TE containing tyrocidine synthetase.
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Affiliation(s)
- Sho Konno
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Miyu Tanaka
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tomoe Mizuguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Haruka Toyokai
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
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2
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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3
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Zhang GF, Han LJ, Guan CF, Ding CR. SO 2F 2-Mediated Fluorination of P(O)-H and P(O)-OH Compounds under Mild Conditions. J Org Chem 2023; 88:13142-13148. [PMID: 37654092 DOI: 10.1021/acs.joc.3c01364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
With the increasing relevance of organophosphorus fluorine compounds in the pharmaceutical industry, their synthesis has attracted great attention. Herein, we report an efficient fluorination strategy for P(O)-H and P(O)-OH compounds using sulfuryl fluoride as the fluorination reagent. Avoiding the use of expensive or complex prepreparation reagents for fluoridation, this strategy could conveniently construct a variety of fluorophosphonates and phosphonofluoridates under mild conditions and without additional oxidants.
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Affiliation(s)
- Guo-Fu Zhang
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P. R. China
| | - Lin-Jun Han
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P. R. China
| | - Chen-Fei Guan
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P. R. China
| | - Cheng-Rong Ding
- College of Chemical Engineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P. R. China
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Li QW, Zhang XY, Lu L, Wu ZQ, Li J, Li GZ, Sun K, Yang S, Yang B. TFAA/DMSO‐promoted fluorination of P(O)−H and P(O)−OH compounds: Compatible Access to Fluorophosphonates and Phosphonofluoridates. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202101254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | | | | | - Kai Sun
- Anyang Normal University CHINA
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5
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Zhang Y, Chen W, Tan T, Gu Y, Zhang S, Li J, Wang Y, Hou W, Yang G, Ma P, Xu H. Palladium-catalyzed one-pot phosphorylation of phenols mediated by sulfuryl fluoride. Chem Commun (Camb) 2021; 57:4588-4591. [PMID: 33956028 DOI: 10.1039/d1cc00769f] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report a general palladium-catalyzed one-pot procedure for the synthesis of phosphonates, phosphinates and phosphine oxides from phenols mediated by sulfuryl fluoride. It features mild conditions, broad substrate scope, high functionality tolerance and water insensitivity. The utility of this procedure has been well demonstrated by gram-scale synthesis, sequential synthesis of click chemistry building blocks, late-stage decoration of drugs and natural products and on-DNA synthesis of phosphine oxide for a DNA-encoded library (DEL).
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Affiliation(s)
- Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China and Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China and Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China and Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China and Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China and Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China. and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China and Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China and University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Hou
- College of Pharmaceutical Science, and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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6
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Wang C, Zhang L, Mou Z, Feng W, Li Z, Yang H, Chen X, Lv S, Li Z. Direct 18F-Labeling of Biomolecules via Spontaneous Site-Specific Nucleophilic Substitution by F - on Phosphonate Prostheses. Org Lett 2021; 23:4261-4266. [PMID: 33942615 DOI: 10.1021/acs.orglett.1c01211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We describe a high radiochemical yield late-stage direct 18F-labeling of bare biomolecules containing common active groups. Spontaneity and site-selectivity are attributed to the remarkably higher rates of nucleophilic substitution reactions on phosphonates than on other electrophiles by F- at various hydrogen bond forms. Rapid access to many medicinally significant 18F-labeled biomolecules is achieved at 21-68% radiochemical yields and 35.9-55.1 GBq μmol-1 molar activities both manually or automatically.
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Affiliation(s)
- Chao Wang
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Lei Zhang
- Tianjin Engineering Technology Centre of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University, Tianjin 300384, P.R. China
| | - Zhaobiao Mou
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Wanru Feng
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Zhongjing Li
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Hongzhang Yang
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Xueyuan Chen
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Shengji Lv
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
| | - Zijing Li
- Centre for Molecular Imaging and Translational Medicine, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian 361102, P.R. China
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7
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Dutra JK, Foley TL, Huang Z, Fisher EL, Lachapelle EA, Mahapatra S, Ogilvie K, Butler TW, Bellenger J, Devraj Majmudar J, Am Ende CW. Fluorophosphonates on-Demand: A General and Simplified Approach toward Fluorophosphonate Synthesis. Chembiochem 2021; 22:1769-1774. [PMID: 33491295 DOI: 10.1002/cbic.202000852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/23/2021] [Indexed: 11/08/2022]
Abstract
Herein, we report a general and simplified synthesis of fluorophosphonates directly from p-nitrophenylphosphonates. This FP on-demand reaction is mediated by a commercially available polymer-supported fluoride reagent that produces a variety (25 examples) of fluorophosphonates in high yields while only requiring reagent filtration for pure fluorophosphonate isolation. This reaction protocol facilitates the rapid profiling of serine hydrolases with diverse and novel sets of activated phosphonates with differential proteome reactivity. Moreover, slight modification of the procedure into a reaction-to-assay format has enabled additional screening efficiency.
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Affiliation(s)
- Jason K Dutra
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Timothy L Foley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Zhen Huang
- Pfizer Worldwide Research and Development, 1 Portland St, Cambridge, MA 02139, USA
| | - Ethan L Fisher
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Erik A Lachapelle
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Subham Mahapatra
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Kevin Ogilvie
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Todd W Butler
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | | | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
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8
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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: 9] [Impact Index Per Article: 1.8] [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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