1
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Rice AJ, Pelton JM, Kramer NJ, Catlin DS, Nair SK, Pogorelov TV, Mitchell DA, Bowers AA. Enzymatic Pyridine Aromatization during Thiopeptide Biosynthesis. J Am Chem Soc 2022; 144:21116-21124. [PMID: 36351243 PMCID: PMC9955758 DOI: 10.1021/jacs.2c07377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thiazole-containing pyritides (thiopeptides) are ribosomally synthesized and post-translationally modified peptides (RiPPs) that have attracted interest owing to their potent biological activities and structural complexity. The class-defining feature of a thiopeptide is a six-membered, nitrogenous heterocycle formed by an enzymatic [4 + 2]-cycloaddition. In rare cases, piperidine or dehydropiperidine (DHP) is present; however, the aromatized pyridine is considerably more common. Despite significant effort, the mechanism by which the central pyridine is formed remains poorly understood. Building on our recent observation of the Bycroft-Gowland intermediate (i.e., the direct product of the [4 + 2]-cycloaddition), we interrogated thiopeptide pyridine synthases using a combination of targeted mutagenesis, kinetic assays, substrate analogs, enzyme-substrate cross-linking, and chemical rescue experiments. Collectively, our data delineate roles for several conserved residues in thiopeptide pyridine synthases. A critical tyrosine facilitates the final aromatization step of pyridine formation. This work provides a foundation for further exploration of the [4 + 2]-cycloaddition reaction and future customization of pyridine-containing macrocyclic peptides.
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Affiliation(s)
- Andrew J. Rice
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
| | - Nicholas J. Kramer
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
| | - Daniel S. Catlin
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Satish K. Nair
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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2
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Zhang Y, Vinogradov AA, Chang JS, Goto Y, Suga H. Solid-Phase-Based Synthesis of Lactazole-Like Thiopeptides. Org Lett 2022; 24:7894-7899. [DOI: 10.1021/acs.orglett.2c02870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yue Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Alexander A. Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jun Shi Chang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Nguyen DT, Le TT, Rice AJ, Hudson GA, van der Donk WA, Mitchell DA. Accessing Diverse Pyridine-Based Macrocyclic Peptides by a Two-Site Recognition Pathway. J Am Chem Soc 2022; 144:11263-11269. [PMID: 35713415 PMCID: PMC9247985 DOI: 10.1021/jacs.2c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Macrocyclic peptides
are sought-after molecular scaffolds for drug
discovery, and new methods to access diverse libraries are of increasing
interest. Here, we report the enzymatic synthesis of pyridine-based
macrocyclic peptides (pyritides) from linear precursor peptides. Pyritides
are a recently described class of ribosomally synthesized and post-translationally
modified peptides (RiPPs) and are related to the long-known thiopeptide
natural products. RiPP precursors typically contain an N-terminal
leader region that is physically engaged by the biosynthetic proteins
that catalyze modification of the C-terminal core region of the precursor
peptide. We demonstrate that pyritide-forming enzymes recognize both
the leader region and a C-terminal tripeptide motif, with each contributing
to site-selective substrate modification. Substitutions in the core
region were well-tolerated and facilitated the generation of a wide
range of pyritide analogues, with variations in macrocycle sequence
and size. A combination of the pyritide biosynthetic pathway with
azole-forming enzymes was utilized to generate a thiazole-containing
pyritide (historically known as a thiopeptide) with no similarity
in sequence and macrocycle size to the naturally encoded pyritides.
The broad substrate scope of the pyritide biosynthetic enzymes serves
as a future platform for macrocyclic peptide lead discovery and optimization.
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Affiliation(s)
- Dinh T Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tung T Le
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew J Rice
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Abstract
The past decade has seen impressive advances in understanding the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs). One of the most common modifications found in these natural products is macrocyclization, a strategy also used by medicinal chemists to improve metabolic stability and target affinity and specificity. Another tool of the peptide chemist, modification of the amides in a peptide backbone, has also been observed in RiPPs. This review discusses the molecular mechanisms of biosynthesis of a subset of macrocyclic RiPP families, chosen because of the unusual biochemistry involved: the five classes of lanthipeptides (thioether cyclization by Michael-type addition), sactipeptides and ranthipeptides (thioether cyclization by radical chemistry), thiopeptides (cyclization by [4+2] cycloaddition), and streptide (cyclization by radical C-C bond formation). In addition, the mechanisms of backbone amide methylation, backbone epimerization, and backbone thioamide formation are discussed, as well as an unusual route to small molecules by posttranslational modification.
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Affiliation(s)
- Hyunji Lee
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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5
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Lu J, Li Y, Bai Z, Lv H, Wang H. Enzymatic macrocyclization of ribosomally synthesized and posttranslational modified peptides via C-S and C-C bond formation. Nat Prod Rep 2021; 38:981-992. [PMID: 33185226 DOI: 10.1039/d0np00044b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2000 to 2020 Ribosomally synthesized and posttranslational modified peptides (RiPPs) are a rapidly growing class of bioactive natural products. Many members of RiPPs contain macrocyclic structural units constructed by modification enzymes through macrocyclization of linear precursor peptides. In this study, we summarize recent progress in the macrocyclization of RiPPs by C-S and C-C bond formation with a focus on the current understanding of the enzymatic mechanisms.
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Affiliation(s)
- Jingxia Lu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Yuqing Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Zengbing Bai
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Hongmei Lv
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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6
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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7
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Vinogradov AA, Shimomura M, Kano N, Goto Y, Onaka H, Suga H. Promiscuous Enzymes Cooperate at the Substrate Level En Route to Lactazole A. J Am Chem Soc 2020; 142:13886-13897. [PMID: 32664727 DOI: 10.1021/jacs.0c05541] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs) often have relaxed specificity profiles and are able to modify diverse substrates. When several such enzymes act together during precursor peptide maturation, a multitude of products can form, yet usually the biosynthesis converges on a single natural product. For the most part, the mechanisms controlling the integrity of RiPP assembly remain elusive. Here, we investigate the biosynthesis of lactazole A, a model thiopeptide produced by five promiscuous enzymes from a ribosomal precursor peptide. Using our in vitro thiopeptide production (FIT-Laz) system, we determine the order of biosynthetic events at the individual modification level and supplement this study with substrate scope analysis for participating enzymes. Our results reveal an unusual but well-defined assembly process where cyclodehydration, dehydroalanine formation, and azoline dehydrogenation events are intertwined due to minimal substrate recognition requirements characteristic of every lactazole enzyme. Additionally, each enzyme plays a role in directing LazBF-mediated dehydroalanine formation, which emerges as the central theme of the assembly process. Cyclodehydratase LazDE discriminates a single serine residue for azoline formation, leaving the remaining five as potential dehydratase substrates. Pyridine synthase LazC exerts kinetic control over LazBF to prevent the formation of overdehydrated thiopeptides, whereas the coupling of dehydrogenation to dehydroalanine installation impedes generation of underdehydrated products. Altogether, our results indicate that substrate-level cooperation between the biosynthetic enzymes maintains the integrity of lactazole assembly. This work advances our understanding of RiPP biosynthesis processes and facilitates thiopeptide bioengineering.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Naokazu Kano
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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8
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Bogart JW, Kramer NJ, Turlik A, Bleich RM, Catlin DS, Schroeder FC, Nair SK, Williamson RT, Houk KN, Bowers AA. Interception of the Bycroft-Gowland Intermediate in the Enzymatic Macrocyclization of Thiopeptides. J Am Chem Soc 2020; 142:13170-13179. [PMID: 32609512 PMCID: PMC7429253 DOI: 10.1021/jacs.0c05639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thiopeptides are a broad class of macrocyclic, heavily modified peptide natural products that are unified by the presence of a substituted, nitrogen-containing heterocycle core. Early work indicated that this core might be fashioned from two dehydroalanines by an enzyme-catalyzed aza-[4 + 2] cycloaddition to give a cyclic-hemiaminal intermediate. This common intermediate could then follow a reductive path toward a dehydropiperidine, as in the thiopeptide thiostrepton, or an aromatization path to yield the pyridine groups observed in many other thiopeptides. Although several of the enzymes proposed to perform this cycloaddition have been reconstituted, only pyridine products have been isolated and any hemiaminal intermediates have yet to be observed. Here, we identify the conditions and substrates that decouple the cycloaddition from subsequent steps and allow interception and characterization of this long hypothesized intermediate. Transition state modeling indicates that the key amide-iminol tautomerization is the major hurdle in an otherwise energetically favorable cycloaddition. An anionic model suggests that deprotonation and polarization of this amide bond by TbtD removes this barrier and provides a sufficient driving force for facile (stepwise) cycloaddition. This work provides evidence for a mechanistic link between disparate cyclases in thiopeptide biosynthesis.
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Affiliation(s)
- Jonathan W. Bogart
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nicholas J. Kramer
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Rachel M. Bleich
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel S. Catlin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Ithaca, New York 14853, USA
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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9
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Vinogradov AA, Suga H. Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem Biol 2020; 27:1032-1051. [PMID: 32698017 DOI: 10.1016/j.chembiol.2020.07.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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10
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Minimal lactazole scaffold for in vitro thiopeptide bioengineering. Nat Commun 2020; 11:2272. [PMID: 32385237 PMCID: PMC7210931 DOI: 10.1038/s41467-020-16145-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Lactazole A is a cryptic thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, we establish a platform for in vitro biosynthesis of lactazole A, referred to as the FIT-Laz system, via a combination of the flexible in vitro translation (FIT) system with recombinantly produced lactazole biosynthetic enzymes. Systematic dissection of lactazole biosynthesis reveals remarkable substrate tolerance of the biosynthetic enzymes and leads to the development of the minimal lactazole scaffold, a construct requiring only 6 post-translational modifications for macrocyclization. Efficient assembly of such minimal thiopeptides with FIT-Laz opens access to diverse lactazole analogs with 10 consecutive mutations, 14- to 62-membered macrocycles, and 18 amino acid-long tail regions, as well as to hybrid thiopeptides containing non-proteinogenic amino acids. This work suggests that the minimal lactazole scaffold is amenable to extensive bioengineering and opens possibilities to explore untapped chemical space of thiopeptides. Lactazole A is a thiopeptide from Streptomyces lactacystinaeus, encoded by a compact 9.8 kb biosynthetic gene cluster. Here, the authors show a platform for in vitro biosynthesis of lactazole A via a combination of a flexible in vitro translation system with recombinantly produced lactazole biosynthetic enzymes.
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11
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Fleming SR, Himes PM, Ghodge SV, Goto Y, Suga H, Bowers AA. Exploring the Post-translational Enzymology of PaaA by mRNA Display. J Am Chem Soc 2020; 142:5024-5028. [PMID: 32109054 DOI: 10.1021/jacs.0c01576] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PaaA is a RiPP enzyme that catalyzes the transformation of two glutamic acid residues within a substrate peptide into the bicyclic core of Pantocin A. Here, for the first time, we use mRNA display techniques to understand RiPP enzyme-substrate interactions to illuminate PaaA substrate recognition. Additionally, our data revealed insights into the enzymatic timing of glutamic acid modification. The technique developed is quite sensitive and a significant advancement over current RiPP studies and opens the door to enzyme modified mRNA display libraries for natural product-like inhibitor pans.
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Affiliation(s)
- Steven R Fleming
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Paul M Himes
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Swapnil V Ghodge
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Early Discovery Biochemistry Department, Genentech Inc., South San Francisco, California 94114, United States
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,JST, PRESTO, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,JST, CREST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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12
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Bogart JW, Bowers AA. Dehydroamino acids: chemical multi-tools for late-stage diversification. Org Biomol Chem 2019; 17:3653-3669. [PMID: 30849157 PMCID: PMC6637761 DOI: 10.1039/c8ob03155j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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13
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Lichman BR, O'Connor SE, Kries H. Biocatalytic Strategies towards [4+2] Cycloadditions. Chemistry 2019; 25:6864-6877. [DOI: 10.1002/chem.201805412] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Benjamin R. Lichman
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
- Current address: Department of Biology; University of York; York YO10 5YW UK
| | - Sarah E. O'Connor
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
| | - Hajo Kries
- Independent Junior Research Group, Biosynthetic Design of Natural Products; Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena); Beutenbergstr. 11a 07745 Jena Germany
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14
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Akasapu S, Hinds AB, Powell WC, Walczak MA. Total synthesis of micrococcin P1 and thiocillin I enabled by Mo(vi) catalyst. Chem Sci 2019; 10:1971-1975. [PMID: 30881626 PMCID: PMC6383332 DOI: 10.1039/c8sc04885a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/03/2018] [Indexed: 12/05/2022] Open
Abstract
Thiopeptides are a class of potent antibiotics with promising therapeutic potential. We developed a novel Mo(vi)-oxide/picolinic acid catalyst for the cyclodehydration of cysteine peptides to form thiazoline heterocycles. With this powerful tool in hand, we completed the total syntheses of two representative thiopeptide antibiotics: micrococcin P1 and thiocillin I. These two concise syntheses (15 steps, longest linear sequence) feature a C-H activation strategy to install the trisubstituted pyridine core and thiazole groups. The synthetic material displays promising antimicrobial properties measured against a series of Gram-positive bacteria.
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Affiliation(s)
- Siddhartha Akasapu
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
| | - Aaron B Hinds
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
| | - Wyatt C Powell
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
| | - Maciej A Walczak
- Department of Chemistry , University of Colorado , Boulder , CO 80309 , USA .
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15
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Bogart JW, Bowers AA. Thiopeptide Pyridine Synthase TbtD Catalyzes an Intermolecular Formal Aza-Diels-Alder Reaction. J Am Chem Soc 2019; 141:1842-1846. [PMID: 30653303 DOI: 10.1021/jacs.8b11852] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thiopeptide pyridine synthases catalyze a multistep reaction involving a unique and nonspontaneous intramolecular aza-[4 + 2] cycloaddition between two dehydroalanines to forge a trisubstituted pyridine core. We discovered that the in vitro activity of pyridine synthases from the thiocillin and thiomuracin pathways are significantly enhanced by general base catalysis and that this broadly expands the enzymes substrate tolerance. Remarkably, TbtD is competent to perform an intermolecular cyclization in addition to its cognate intramolecular reaction, underscoring its versatility as a biocatalyst. These data provide evidence that pyridine synthases use a two-site substrate recognition model to engage and process their substrates.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27514 , United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27514 , United States
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16
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Fleming SR, Bartges TE, Vinogradov AA, Kirkpatrick CL, Goto Y, Suga H, Hicks LM, Bowers AA. Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides. J Am Chem Soc 2019; 141:758-762. [PMID: 30602112 DOI: 10.1021/jacs.8b11521] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Thiopeptides are natural antibiotics that are fashioned from short peptides by multiple layers of post-translational modification. Their biosynthesis, in particular the pyridine synthases that form the macrocyclic antibiotic core, has attracted intensive research but is complicated by the challenges of reconstituting multiple-pathway enzymes. By combining select RiPP enzymes with cell free expression and flexizyme-based codon reprogramming, we have developed a benchtop biosynthesis of thiopeptide scaffolds. This strategy side-steps several challenges related to the investigation of thiopeptide enzymes and allows access to analytical quantities of new thiopeptide analogs. We further demonstrate that this strategy can be used to validate the activity of new pyridine synthases without the need to reconstitute the cognate prior pathway enzymes.
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Affiliation(s)
- Steven R Fleming
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Tessa E Bartges
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo 113-0033 , Japan.,JST , PRESTO , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Christine L Kirkpatrick
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo 113-0033 , Japan.,JST , PRESTO , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science , The University of Tokyo , Bunkyo-ku , Tokyo 113-0033 , Japan.,JST , CREST , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Leslie M Hicks
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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17
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Arbour CA, Stockdill JL. A mild capping method for SPPS on the N-methyl diaminobenzoyl linker: Synthesis of an N-acyl urea appended C. elegans neuropeptide. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.08.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Goto Y, Suga H. Engineering of RiPP pathways for the production of artificial peptides bearing various non-proteinogenic structures. Curr Opin Chem Biol 2018; 46:82-90. [DOI: 10.1016/j.cbpa.2018.06.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 11/15/2022]
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19
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Hudson GA, Mitchell DA. RiPP antibiotics: biosynthesis and engineering potential. Curr Opin Microbiol 2018; 45:61-69. [PMID: 29533845 PMCID: PMC6131089 DOI: 10.1016/j.mib.2018.02.010] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/23/2018] [Indexed: 01/14/2023]
Abstract
The threat of antibiotic resistant bacterial infections continues to underscore the need for new treatment options. Historically, small molecule metabolites from microbes have provided a rich source of antibiotic compounds, and as a result, significant effort has been invested in engineering the responsible biosynthetic pathways to generate novel analogs with attractive pharmacological properties. Unfortunately, biosynthetic stringency has limited the capacity of non-ribosomal peptide synthetases and polyketide synthases from producing substantially different analogs in large numbers. Another class of natural products, the ribosomally synthesized and post-translationally modified peptides (RiPPs), have rapidly expanded in recent years with many natively displaying potent antibiotic activity. RiPP biosynthetic pathways are modular and intrinsically tolerant to alternative substrates. Several prominent RiPPs with antibiotic activity will be covered in this review with a focus on their biosynthetic plasticity. While only a few RiPP enzymes have been thoroughly investigated mechanistically, this knowledge has already been harnessed to generate new-to-nature compounds. Through the use of synthetic biology approaches, on-going efforts in RiPP engineering hold great promise in unlocking the potential of this natural product class.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States; Department of Microbiology, University of Illinois, 600 S Mathews Ave, Urbana, IL 61801, United States.
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20
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Post-translational site-selective protein backbone α-deuteration. Nat Chem Biol 2018; 14:955-963. [DOI: 10.1038/s41589-018-0128-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/19/2018] [Indexed: 01/29/2023]
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21
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Yang L, Ma H, Han L, Liu P, Shen H, Li C, Li Y. Sequence Features of Sequence-Controlled Polymers Synthesized by 1,1-Diphenylethylene Derivatives with Similar Reactivity during Living Anionic Polymerization. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01491] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lincan Yang
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Hongwei Ma
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Li Han
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Pibo Liu
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Heyu Shen
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Chao Li
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Yang Li
- State Key Laboratory of Fine Chemicals, Department of Polymer Science and Engineering, Liaoning Key Laboratory of Polymer Science and Engineering, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
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22
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Abstract
Enzymes in biosynthetic pathways, especially in plant and microbial metabolism, generate structural and functional group complexity in small molecules by conversion of acyclic frameworks to cyclic scaffolds via short, efficient routes. The distinct chemical logic used by several distinct classes of cyclases, oxidative and non-oxidative, has recently been elucidated by genome mining, heterologous expression, and genetic and mechanistic analyses. These include enzymes performing pericyclic transformations, pyran synthases, tandem acting epoxygenases, and epoxide "hydrolases", as well as oxygenases and radical S-adenosylmethionine enzymes that involve rearrangements of substrate radicals under aerobic or anaerobic conditions.
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
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23
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Li X, Zheng Q, Yin J, Liu W, Gao S. Chemo-enzymatic synthesis of equisetin. Chem Commun (Camb) 2018; 53:4695-4697. [PMID: 28401214 DOI: 10.1039/c7cc01929g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We here report that the biosynthesis of equisetin, a fungal tetramate natural product with potent anti-infectious activity, relies on Fsa2, a Diels-Alderase that constructs the trans-decalin system of the molecule in a stereo-selective manner. This finding led to the development of a concise chemo-enzymatic route toward the synthesis of equisetin, which involves facile preparation of a linear polyene precursor via 7-steps and Fsa2 activity for equisetin maturation through an intramolecular Diels-Alder reaction, thus exemplifying the significance of the combination of chemical and biological methods to achieve structurally complex cyclic natural products and their derivatives.
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Affiliation(s)
- Xiaojun Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 3663N Zhongshan Road, Shanghai 200062, China.
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24
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Zheng Q, Fang H, Liu W. Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 2018; 15:3376-3390. [PMID: 28358161 DOI: 10.1039/c7ob00466d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins. Since the biosynthetic gene clusters of thiopeptides were first discovered in 2009, several research studies regarding the biochemistry and enzymology of thiopeptide biosyntheses have been reported, indicating that their characteristic framework is constructed via a cascade of common PTMs and that additional specific PTMs diversify the molecules. In this review, we primarily summarize recent advances in understanding the biosynthesis of thiopeptide antibiotics and propose some potential applications based on our insights into the biosynthetic logic and machinery.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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25
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Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis. Proc Natl Acad Sci U S A 2017; 114:12928-12933. [PMID: 29158402 DOI: 10.1073/pnas.1716035114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The [4+2] cycloaddition reaction is an enabling transformation in modern synthetic organic chemistry, but there are only limited examples of dedicated natural enzymes that can catalyze this transformation. Thiopeptides (or more formally thiazolyl peptides) are a class of thiazole-containing, highly modified, macrocyclic secondary metabolites made from ribosomally synthesized precursor peptides. The characteristic feature of these natural products is a six-membered nitrogenous heterocycle that is assembled via a formal [4+2] cycloaddition between two dehydroalanine (Dha) residues. This heteroannulation is entirely contingent on enzyme activity, although the mechanism of the requisite pyridine/dehydropiperidine synthase remains to be elucidated. The unusual aza-cylic product is distinct from the more common carbocyclic products of synthetic and biosynthetic [4+2] cycloaddition reactions. To elucidate the mechanism of cycloaddition, we have determined atomic resolution structures of the pyridine synthases involved in the biosynthesis of the thiopeptides thiomuracin (TbtD) and GE2270A (PbtD), in complex with substrates and product analogs. Structure-guided biochemical, mutational, computational, and binding studies elucidate active-site features that explain how orthologs can generate rigid macrocyclic scaffolds of different sizes. Notably, the pyridine synthases show structural similarity to the elimination domain of lanthipeptide dehydratases, wherein insertions of secondary structural elements result in the formation of a distinct active site that catalyzes different chemistry. Comparative analysis identifies other catalysts that contain a shared core protein fold but whose active sites are located in entirely different regions, illustrating a principle predicted from efforts in de novo protein design.
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26
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Ding W, Ji W, Wu Y, Wu R, Liu WQ, Mo T, Zhao J, Ma X, Zhang W, Xu P, Deng Z, Tang B, Yu Y, Zhang Q. Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ. Nat Commun 2017; 8:437. [PMID: 28874663 PMCID: PMC5585349 DOI: 10.1038/s41467-017-00439-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/28/2017] [Indexed: 01/10/2023] Open
Abstract
Nosiheptide is a prototypal thiopeptide antibiotic, containing an indole side ring in addition to its thiopeptide-characteristic macrocylic scaffold. This indole ring is derived from 3-methyl-2-indolic acid (MIA), a product of the radical S-adenosylmethionine enzyme NosL, but how MIA is incorporated into nosiheptide biosynthesis remains to be investigated. Here we report functional dissection of a series of enzymes involved in nosiheptide biosynthesis. We show NosI activates MIA and transfers it to the phosphopantetheinyl arm of a carrier protein NosJ. NosN then acts on the NosJ-bound MIA and installs a methyl group on the indole C4, and the resulting dimethylindolyl moiety is released from NosJ by a hydrolase-like enzyme NosK. Surface plasmon resonance analysis show that the molecular complex of NosJ with NosN is much more stable than those with other enzymes, revealing an elegant biosynthetic strategy in which the reaction flux is controlled by protein-protein interactions with different binding affinities.Thiopeptides such as nosiheptide are clinically-interesting antimicrobial natural products. Here the authors show the functional dissection of a series of enzymes involved in nosiheptide biosynthesis, revealing a unique biosynthetic pathway that centers on a previously-unknown carrier protein.
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Affiliation(s)
- Wei Ding
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng, 224002, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wenjuan Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yujie Wu
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Runze Wu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Wan-Qiu Liu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Junfeng Zhao
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaoyan Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng, 224002, China.
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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27
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Gober JG, Ghodge SV, Bogart JW, Wever WJ, Watkins RR, Brustad EM, Bowers AA. P450-Mediated Non-natural Cyclopropanation of Dehydroalanine-Containing Thiopeptides. ACS Chem Biol 2017; 12:1726-1731. [PMID: 28535034 DOI: 10.1021/acschembio.7b00358] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiopeptides are a growing class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Many biosynthetic enzymes for RiPPs, especially thiopeptides, are promiscuous and can accept a wide range of peptide substrates with different amino acid sequences; thus, these enzymes have been used as tools to generate new natural product derivatives. Here, we explore an alternative route to molecular complexity by engineering thiopeptide tailoring enzymes to do new or non-native chemistry. We explore cytochrome P450 enzymes as biocatalysts for cyclopropanation of dehydroalanines, chemical motifs found widely in thiopeptides and other RiPP-based natural products. We find that P450TbtJ1 and P450TbtJ2 selectively cyclopropanate dehydroalanines in a number of complex thiopeptide-based substrates and convert them into 1-amino-2-cyclopropane carboxylic acids (ACCAs), which are important pharmacophores. This chemistry takes advantage of the innate affinity of these biosynthetic enzymes for their substrates and enables incorporation of new pharmacophores into thiopeptide architectures. This work also presents a strategy for diversification of natural products through rationally repurposing biosynthetic enzymes as non-natural biocatalysts.
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Affiliation(s)
- Joshua G. Gober
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Swapnil V. Ghodge
- Division
of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Jonathan W. Bogart
- Division
of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Walter J. Wever
- Division
of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Richard R. Watkins
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Eric M. Brustad
- Department
of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Albert A. Bowers
- Division
of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
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28
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Lin Z, He Q, Liu W. Bio-inspired engineering of thiopeptide antibiotics advances the expansion of molecular diversity and utility. Curr Opin Biotechnol 2017; 48:210-219. [PMID: 28672170 DOI: 10.1016/j.copbio.2017.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 02/08/2023]
Abstract
Thiopeptide antibiotics, which are a class of sulfur-rich and highly modified peptide natural products, exhibit a wide variety of important biological properties. These antibiotics are ribosomally synthesized and arise from post-translational modifications, exemplifying a process through which nature develops the structural complexity from Ser/Thr and Cys-rich precursor peptides. Following a brief review of the knowledge gained from nature in terms of the formation of a common thiopeptide scaffold and its specialization to individual members, we highlight the significance of bio-inspired engineering, which has greatly expanded the molecular diversity and utility of thiopeptide antibiotics regarding the search for clinically useful agents, investigation into new mechanisms of action and access to typically 'inaccessible' biosynthetic processes over the past two years.
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Affiliation(s)
- Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qingli He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China.
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29
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Elucidating and engineering thiopeptide biosynthesis. World J Microbiol Biotechnol 2017; 33:119. [DOI: 10.1007/s11274-017-2283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/03/2017] [Indexed: 01/15/2023]
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30
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Zhang Z, Hudson GA, Mahanta N, Tietz JI, van der Donk WA, Mitchell DA. Biosynthetic Timing and Substrate Specificity for the Thiopeptide Thiomuracin. J Am Chem Soc 2016; 138:15511-15514. [PMID: 27700071 PMCID: PMC5148741 DOI: 10.1021/jacs.6b08987] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The biosynthesis of the thiopeptide thiomuracin is a well-orchestrated process involving a multitude of posttranslational modifications. We show that six Cys residues of a precursor peptide are first cyclodehydrated and oxidized to thiazoles in an ordered, but nonlinear fashion that is leader-peptide-dependent. Then four alcohols are glutamylated and converted to alkenes in a C-to-N terminal directional process that is leader-peptide-independent. Finally, two of these alkenes undergo a formal [4 + 2] cycloaddition to form a trithiazole-substituted pyridine macrocycle. We describe here the factors that govern the substrate specificity and order of biosynthetic events that turn a ribosomal peptide into a powerful antibiotic.
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Affiliation(s)
- Zhengan Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Jonathan I. Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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