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Pfeiffer IPM, Schröder MP, Mordhorst S. Opportunities and challenges of RiPP-based therapeutics. Nat Prod Rep 2024; 41:990-1019. [PMID: 38411278 DOI: 10.1039/d3np00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: up to 2024Ribosomally synthesised and post-translationally modified peptides (RiPPs) comprise a substantial group of peptide natural products exhibiting noteworthy bioactivities ranging from antiinfective to anticancer and analgesic effects. Furthermore, RiPP biosynthetic pathways represent promising production routes for complex peptide drugs, and the RiPP technology is well-suited for peptide engineering to produce derivatives with specific functions. Thus, RiPP natural products possess features that render them potentially ideal candidates for drug discovery and development. Nonetheless, only a small number of RiPP-derived compounds have successfully reached the market thus far. This review initially outlines the therapeutic opportunities that RiPP-based compounds can offer, whilst subsequently discussing the limitations that require resolution in order to fully exploit the potential of RiPPs towards the development of innovative drugs.
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Affiliation(s)
- Isabel P-M Pfeiffer
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Maria-Paula Schröder
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Silja Mordhorst
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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2
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Ramos Figueroa J, Zhu L, van der Donk WA. Unexpected Transformations during Pyrroloiminoquinone Biosynthesis. J Am Chem Soc 2024; 146:14235-14245. [PMID: 38719200 PMCID: PMC11117183 DOI: 10.1021/jacs.4c03677] [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] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/21/2024]
Abstract
Pyrroloiminoquinone-containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP- and tRNA-dependent manner catalyzed by a PEptide Aminoacyl-tRNA Ligase (PEARL). The indole of Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes from two gene clusters, which show that the previously proposed pathway is incorrect and that Nature's route toward pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, amino groups in pyrroloiminoquinones are derived from (at least) three different sources, glycine, asparagine, and leucine, all introduced in a tRNA-dependent manner. We also show that an FAD-dependent putative glycine oxidase (Amm14) is required for the process that incorporates the nitrogens from glycine and leucine and that a quinone reductase is required for the incorporation of asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes, such as the glutamyl-tRNA-dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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3
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Králová P, Soural M. Biological properties of pyrroloquinoline and pyrroloisoquinoline derivatives. Eur J Med Chem 2024; 269:116287. [PMID: 38492334 DOI: 10.1016/j.ejmech.2024.116287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/18/2024]
Abstract
In this review, we summarize pyrroloquinoline and pyrroloisoquinoline derivatives (PQs and PIQs) that act on a broad spectrum of biological targets and are used as bacteriostatic, antiviral, plasmodial, anticancer, antidiabetic and anticoagulant agents. Many of these compounds play important roles in the study of DNA and its interactions, the regulation of the cell cycle and programmed cell death. This review involves twenty-five types of skeletally analogical compounds bearing pyrrole and (iso)quinoline scaffolds with different mutual annelations.
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Affiliation(s)
- Petra Králová
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu12, 771 46, Olomouc, Czech Republic
| | - Miroslav Soural
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu12, 771 46, Olomouc, Czech Republic.
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4
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Gao ZH, Guo XY, Liu YZ, Zhang QM, Tong XJ, Qiu LH. Trinickia violacea sp. nov. and Trinickia terrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917540 DOI: 10.1099/ijsem.0.006147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
Two Gram-stain negative, aerobic and rod-shaped bacterial strains, DHOD12T and 7GSK02T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOD12T grew at 4-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.5-6.5) and in the presence of 0-1.5 % (w/v; optimum, 0-0.5 %)NaCl; while strain 7GSK02T grew at 12-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.0-6.0) and in the presence of 0-0.5 % (w/v; optimum, 0 %) NaCl. Strains DHOD12T and 7GSK02T had the highest 16S rRNA sequence similarities of 98.0 and 98.3 % with the same species Trinickia mobilis DHG64T, respectively, and 98.4 % between themselves. In the 16S rRNA phylogeny, they formed a clade that was sister to a major cluster consisting of all described Trinickia species. Phylogenomic analyses with the UBCG and PhyloPhlAn methods consistently showed that strains DHOD12T and 7GSK02T formed a clade with T. mobilis DHG64T that was a sister of a cluster containing the remainder of the Trinickia species. The DNA G+C contents of strains DHOD12T and 7GSK02T were 63.1 and 64.6 mol%, respectively. Digital DNA-DNA hybridization and average nucleotide identity values of strains DHOD12T, 7GSK02T and their closely related strains were in the ranges of 21.6-31.4 % and 77.1-86.9 %, respectively. These two strains had the same major respiratory quinone, ubiquinone-8, and both had C16 : 0, C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as their major fatty acids. Their major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genomic analysis indicated that the two strains could have the potential to degrade aromatic compounds like other Trinickia species. On the basis of phenotypic and phylogenetic results, strains DHOD12T and 7GSK02T represent two novel species of the genus Trinickia, for which the names Trinickia violacea sp. nov. (type strain DHOD12T=LMG 30258T=CGMCC 1.15436T) and Trinickia terrae sp. nov. (type strain 7GSK02T=CGMCC 1.15432T=KCTC 62468T) are proposed.
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Affiliation(s)
- Zeng-Hong Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xiu-Yin Guo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Yi-Zhi Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Qiu-Mei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xin-Jie Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
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5
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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6
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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7
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Gao Y, Li K, Zhang L, Chen C, Bai C. A Nucleophilic Chemical Probe Targeting Electrophilic Functional Groups in an Untargeted Way to Explore Cysteine Modulators in Natural Products. ACS Chem Biol 2022; 17:1685-1690. [PMID: 35766822 DOI: 10.1021/acschembio.2c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vital roles of biologically relevant cysteines have been discovered from proteins that are promising targets for new drugs or chemical tools. Therefore, new electrophilic small molecules that can covalently modulate these cysteines have attracted immense interest. Because of their extremely wide chemical diversity, electrophilic natural products (NPs) have been studied as promising sources of cysteine modulators. Previous studies have developed chemical probes to facilitate the detection and isolation of electrophilic NPs. To address the problems with the current methods, including their low sensitivity, high false-positive rate, and dependence on performing manual processing with a plethora of spectra, we report a chemical probe that can first covalently capture electrophilic NPs from natural resources and then produce sensitive reporter ion signals that are specific for the detected NPs. We applied this untargeted method to explore electrophilic NPs from natural resources and found that the complexity of electrophilic NPs was beyond our expectations. We used this chemical probe to identify a new electrophilic furanosesterterpene (BG-1) from an extract of Ginkgo biloba that targets the Cys207 of acyl-CoA thioesterase 7 (ACOT7).
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Affiliation(s)
- Yinyi Gao
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510130, China
| | - Kaili Li
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Lijun Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Chu Chen
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Sichuan Academy of Chinese Medicine Sciences, Chengdu, Sichuan 610041, China
| | - Chuan Bai
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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8
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McLaughlin MI, Yu Y, van der Donk WA. Substrate Recognition by the Peptidyl-( S)-2-mercaptoglycine Synthase TglHI during 3-Thiaglutamate Biosynthesis. ACS Chem Biol 2022; 17:930-940. [PMID: 35362960 PMCID: PMC9016710 DOI: 10.1021/acschembio.2c00087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
3-Thiaglutamate is a recently identified amino acid analog originating from cysteine. During its biosynthesis, cysteinyl-tRNA is first enzymatically appended to the C-terminus of TglA, a 50-residue ribosomally translated peptide scaffold. After hydrolytic removal of the tRNA, this cysteine residue undergoes modification on the scaffold before eventual proteolysis of the nascent 3-thiaglutamyl residue to release 3-thiaglutamate and regenerate TglA. One of the modifications of TglACys requires a complex of two polypeptides, TglH and TglI, which uses nonheme iron and O2 to catalyze the removal of the peptidyl-cysteine β-methylene group, oxidation of this Cβ atom to formate, and reattachment of the thiol group to the α carbon. Herein, we use in vitro transcription-coupled translation and expressed protein ligation to characterize the role of the TglA scaffold in TglHI recognition and determine the specificity of TglHI with respect to the C-terminal residues of its substrate TglACys. The results of these experiments establish a synthetically accessible TglACys fragment sufficient for modification by TglHI and identify the l-selenocysteine analog of TglACys, TglASec, as an inhibitor of TglHI. These insights as well as a predicted structure and native mass spectrometry data set the stage for deeper mechanistic investigation of the complex TglHI-catalyzed reaction.
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Affiliation(s)
- Martin I. McLaughlin
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yue Yu
- Department of Chemistry and 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 and 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
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9
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Müller MJ, Dorst A, Paulus C, Khan I, Sieber S. Catch-enrich-release approach for amine-containing natural products. Chem Commun (Camb) 2022; 58:12560-12563. [DOI: 10.1039/d2cc04905h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemoselective approach to extract amine-containing natural products from complex matrices. The enzymatic release from the probe affords the underivatised compounds as products.
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Affiliation(s)
| | - Andrea Dorst
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Constanze Paulus
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Imran Khan
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
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10
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A biosynthetic pathway to aromatic amines that uses glycyl-tRNA as nitrogen donor. Nat Chem 2022; 14:71-77. [PMID: 34725492 PMCID: PMC8758506 DOI: 10.1038/s41557-021-00802-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/27/2021] [Indexed: 11/12/2022]
Abstract
Aromatic amines in nature are typically installed with Glu or Gln as the nitrogen donor. Here we report a pathway that features glycyl-tRNA instead. During the biosynthesis of pyrroloiminoquinone-type natural products such as ammosamides, peptide-aminoacyl tRNA ligases append amino acids to the C-terminus of a ribosomally synthesized peptide. First, [Formula: see text] adds Trp in a Trp-tRNA-dependent reaction and the flavoprotein AmmC1 then carries out three hydroxylations of the indole ring of Trp. After oxidation to the corresponding ortho-hydroxy para-quinone, [Formula: see text] attaches Gly to the indole ring in a Gly-tRNA dependent fashion. Subsequent decarboxylation and hydrolysis results in an amino-substituted indole. Similar transformations are catalysed by orthologous enzymes from Bacillus halodurans. This pathway features three previously unknown biochemical processes using a ribosomally synthesized peptide as scaffold for non-ribosomal peptide extension and chemical modification to generate an amino acid-derived natural product.
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11
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Abstract
Natural products have traditionally been a fruitful source of chemical matter that has been developed into novel therapeutics. Actinomycetes and several other bacterial taxa are especially gifted in biosynthesizing natural products. However, many decades of intense bioactivity-based screening led to a large rediscovery problem, rendering industrial natural product discovery pipelines uneconomical. Numerous methods for circumventing the rediscovery problem have been developed, among them various chemistry-focused strategies, including reactivity-based screening. Emerging from the field of chemical proteomics, reactivity-based screening relies on a reactive probe that chemoselectively modifies a functional group of interest in the context of a complex biological sample. Reactivity-based probes for several distinct functional groups have been deployed to discover new polyketide and peptidic natural products. This chapter describes the protocols to conduct a reactivity-based screening campaign, including bacteria cultivation and screening of cellular extracts with phenylglyoxal-, tetrazine-, thiol-, and aminooxy-functionalized probes, which respectively target primary uriedo, electron-rich olefins, Michael acceptors, and reactive carbonyls. In addition, a recent case study is presented that employs reactivity-based screening as a component of a forward genetics screen to identify a previously unknown peptidyl arginine deiminase. We anticipate that these methods will be useful for those interested in discovering natural products that evade detection by traditional, bioassay-guided methods and others who wish to rapidly connect metabolic chemotype with genotype.
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Affiliation(s)
- Lonnie A. Harris
- Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois, Urbana, IL, United States,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States,Department of Microbiology, University of Illinois, Urbana, IL, United States,Corresponding Author: 600 S. Mathews Avenue, Roger Adams Laboratory, Rm. 361, University of Illinois, Urbana, IL 61801, 217-333-1345,
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12
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Hai Y, Wei MY, Wang CY, Gu YC, Shao CL. The intriguing chemistry and biology of sulfur-containing natural products from marine microorganisms (1987-2020). MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:488-518. [PMID: 37073258 PMCID: PMC10077240 DOI: 10.1007/s42995-021-00101-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/18/2021] [Indexed: 05/03/2023]
Abstract
Natural products derived from marine microorganisms have received great attention as a potential resource of new compound entities for drug discovery. The unique marine environment brings us a large group of sulfur-containing natural products with abundant biological functionality including antitumor, antibiotic, anti-inflammatory and antiviral activities. We reviewed all the 484 sulfur-containing natural products (non-sulfated) isolated from marine microorganisms, of which 59.9% are thioethers, 29.8% are thiazole/thiazoline-containing compounds and 10.3% are sulfoxides, sulfones, thioesters and many others. A selection of 133 compounds was further discussed on their structure-activity relationships, mechanisms of action, biosynthesis, and druggability. This is the first systematic review on sulfur-containing natural products from marine microorganisms conducted from January 1987, when the first one was reported, to December 2020. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00101-2.
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Affiliation(s)
- Yang Hai
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Mei-Yan Wei
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
| | - Yu-Cheng Gu
- Syngenta Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY UK
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, The Ministry of Education of China, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237 China
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13
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Tang Y, Friesen JB, Nikolić DS, Lankin DC, McAlpine JB, Chen SN, Pauli GF. Silica Gel-mediated Oxidation of Prenyl Motifs Generates Natural Product-Like Artifacts. PLANTA MEDICA 2021; 87:998-1007. [PMID: 33975359 PMCID: PMC8867998 DOI: 10.1055/a-1472-6164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Prenyl moieties are commonly encountered in the natural products of terpenoid and mixed biosynthetic origin. The reactivity of unsaturated prenyl motifs is less recognized and shown here to affect the acyclic Rhodiola rosea monoterpene glycoside, kenposide A (8: ), which oxidizes readily on silica gel when exposed to air. The major degradation product mediated under these conditions was a new aldehyde, 9: . Exhibiting a shortened carbon skeleton formed through the breakdown of the terminal isopropenyl group, 9: is prone to acetalization in protic solvents. Further investigation of minor degradation products of both 8: and 8-prenylapigenin (8-PA, 12: ), a flavonoid with an ortho-prenyl substituent, revealed that the aldehyde formation was likely realized through epoxidation and subsequent cleavage at the prenyl olefinic bond. Employment of 1H NMR full spin analysis (HiFSA) achieved the assignment of all chemical shifts and coupling constants of the investigated terpenoids and facilitated the structural validation of the degradation product, 9: . This study indicates that prenylated compounds are generally susceptible to oxidative degradation, particularly in the presence of catalytic mediators, but also under physiological conditions. Such oxidative artifact/metabolite formation leads to a series of compounds with prenyl-derived (cyclic) partial structures that are analogous to species formed during Phase I metabolism in vivo. Phytochemical and pharmacological studies should take precautions or at least consider the impact of (unavoidable) exposure of prenyl-containing compounds to catalytic and/or oxidative conditions.
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Affiliation(s)
- Yu Tang
- UIC/NIH Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
| | - J. Brent Friesen
- Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
- Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University, River Forest, United States
| | - Dejan S. Nikolić
- UIC/NIH Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
| | - David C. Lankin
- UIC/NIH Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
| | - James B. McAlpine
- Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
| | - Shao-Nong Chen
- UIC/NIH Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
- Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
| | - Guido F. Pauli
- UIC/NIH Center for Botanical Dietary Supplements Research, Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
- Center for Natural Product Technologies (CENAPT), Pharmacognosy Institute, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, United States
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14
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Coussens NP, Auld DS, Thielman JR, Wagner BK, Dahlin JL. Addressing Compound Reactivity and Aggregation Assay Interferences: Case Studies of Biochemical High-Throughput Screening Campaigns Benefiting from the National Institutes of Health Assay Guidance Manual Guidelines. SLAS DISCOVERY 2021; 26:1280-1290. [PMID: 34218710 DOI: 10.1177/24725552211026239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Compound-dependent assay interferences represent a continued burden in drug and chemical probe discovery. The open-source National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) Assay Guidance Manual (AGM) established an "Assay Artifacts and Interferences" section to address different sources of artifacts and interferences in biological assays. In addition to the frequent introduction of new chapters in this important topic area, older chapters are periodically updated by experts from academia, industry, and government to include new technologies and practices. Section chapters describe many best practices for mitigating and identifying compound-dependent assay interferences. Using two previously reported biochemical high-throughput screening campaigns for small-molecule inhibitors of the epigenetic targets Rtt109 and NSD2, the authors review best practices and direct readers to high-yield resources in the AGM and elsewhere for the mitigation and identification of compound-dependent reactivity and aggregation assay interferences.
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Affiliation(s)
- Nathan P Coussens
- Molecular Pharmacology Laboratories, Division of Cancer Treatment and Diagnosis Laboratory Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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15
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Luo J, Yang D, Hindra, Adhikari A, Dong LB, Ye F, Yan X, Rader C, Shen B. Discovery of ammosesters by mining the Streptomyces uncialis DCA2648 genome revealing new insight into ammosamide biosynthesis. J Ind Microbiol Biotechnol 2021; 48:6185047. [PMID: 33982054 PMCID: PMC8210675 DOI: 10.1093/jimb/kuab027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/18/2021] [Indexed: 11/28/2022]
Abstract
The ammosamides (AMMs) are a family of pyrroloquinoline alkaloids that exhibits a wide variety of bioactivities. A biosynthetic gene cluster (BGC) that is highly homologous in both gene content and genetic organization to the amm BGC was identified by mining the Streptomyces uncialis DCA2648 genome, leading to the discovery of a sub-family of new AMM congeners, named ammosesters (AMEs). The AMEs feature a C-4a methyl ester, differing from the C-4a amide functional group characteristic to AMMs, and exhibit modest cytotoxicity against a broad spectrum of human cancer cell lines, expanding the structure-activity relationship for the pyrroloquinoline family of natural products. Comparative analysis of the ame and amm BGCs supports the use of a scaffold peptide as an emerging paradigm for the biosynthesis of the pyrroloquinoline family of natural products. AME and AMM biosynthesis diverges from a common intermediate by evolving the pathway-specific Ame24 O-methyltransferase and Amm20 amide synthetase, respectively. These findings will surely inspire future efforts to mimic Nature's combinatorial biosynthetic strategies for natural product structural diversity.
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Affiliation(s)
| | | | | | - Ajeeth Adhikari
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Liao-Bin Dong
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Fei Ye
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Correspondence should be addressed to: Ben Shen. Phone: +1-561-228-2456. Fax: +1-561-228-2472. E-mail:
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16
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Hughes CC. Chemical labeling strategies for small molecule natural product detection and isolation. Nat Prod Rep 2021; 38:1684-1705. [PMID: 33629087 DOI: 10.1039/d0np00034e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: Up to 2020.It is widely accepted that small molecule natural products (NPs) evolved to carry out a particular ecological function and that these finely-tuned molecules can sometimes be appropriated for the treatment of disease in humans. Unfortunately, for the natural products chemist, NPs did not evolve to possess favorable physicochemical properties needed for HPLC-MS analysis. The process known as derivatization, whereby an NP in a complex mixture is decorated with a nonnatural moiety using a derivatizing agent (DA), arose from this sad state of affairs. Here, NPs are freed from the limitations of natural functionality and endowed, usually with some degree of chemoselectivity, with additional structural features that make HPLC-MS analysis more informative. DAs that selectively label amines, carboxylic acids, alcohols, phenols, thiols, ketones, and aldehydes, terminal alkynes, electrophiles, conjugated alkenes, and isocyanides have been developed and will be discussed here in detail. Although usually employed for targeted metabolomics, chemical labeling strategies have been effectively applied to uncharacterized NP extracts and may play an increasing role in the detection and isolation of certain classes of NPs in the future.
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Affiliation(s)
- Chambers C Hughes
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany 72076.
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17
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Wu HB, Wu HB, Kuang MS, Lan HP, Wen YX, Liu TT. Novel Bithiophene Dimers from Echinops latifolius as Potential Antifungal and Nematicidal Agents. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11939-11945. [PMID: 33059450 DOI: 10.1021/acs.jafc.0c00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Three novel dimeric bithiophenes, echinbithiophenedimers A-C (1-3), along with two known thiophenes, 4 and 5, were obtained from Echinops latifolius, and their structures were identified through extensive spectroscopic analysis and electronic circular dichroism calculations. Compounds 1-3 possessed new carbon skeletons; they are dimeric bithiophenes with 1 and 2 featuring an unprecedented 1,3-dioxolane ring system and 3 featuring an unusual 1,4-dioxane ring. These compounds are the first examples of bithiophene dimers furnished by different cyclic diethers. Dimeric bithiophenes 1-3 had good antifungal activities against five phytopathogenic fungi, and compound 3 showed excellent activity against Alternaria alternate and Pyricularia oryzae, with a minimal inhibitory concentration value of 8 μg/mL, which was close to or higher than that of carbendazim. Moreover, its effect on the mycelial morphology was observed by scanning electron microscopy. Compounds 1-3, which were demonstrated to be nonphototoxic thiophenes, exhibited better nematicidal activity than the commercial nematicide ethoprophos against Meloidogyne incognita. This study revealed that dimeric bithiophenes containing 1,3-dioxolane or 1,4-dioxane rings could be used as novel antifungal and nematicidal agents for controlling plant fungal and nematode pathogens.
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Affiliation(s)
- Hai-Bo Wu
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, People's Republic of China
| | - Hai-Bin Wu
- Shandong Institute of Pomology, Tai'an 271000, People's Republic of China
| | - Ming-Shan Kuang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, People's Republic of China
| | - Hui-Peng Lan
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, People's Republic of China
| | - Yu-Xin Wen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, People's Republic of China
| | - Ting-Ting Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
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18
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Xu T, Chen W, Zhou J, Dai J, Li Y, Zhao Y. Virtual Screening for Reactive Natural Products and Their Probable Artifacts of Solvolysis and Oxidation. Biomolecules 2020; 10:E1486. [PMID: 33121010 PMCID: PMC7692644 DOI: 10.3390/biom10111486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
Chemically unstable natural products are prone to show their reactivity in the procedures of extraction, purification, or identification and turn into contaminants as so-called "artifacts". However, identification of artifacts requires considerable investments in technical equipment, time, and human resources. For revealing these reactive natural products and their artifacts by computational approaches, we set up a virtual screening system to seek cases in a biochemical database. The screening system is based on deep learning models of predicting the two main classifications of conversion reactions from natural products to artifacts, namely solvolysis and oxidation. A set of result data was reviewed for checking validity of the screening system, and we screened out a batch of reactive natural products and their probable artifacts. This work provides some insights into the formations of natural product artifacts, and the result data may act as warnings regarding the improper handling of biological matrixes in multicomponent extraction.
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Affiliation(s)
- Tingjun Xu
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China; (W.C.); (J.Z.); (J.D.); (Y.L.); (Y.Z.)
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19
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Shi WY, Ding YN, Liu C, Zheng N, Gou XY, Li M, Zhang Z, Liu HC, Niu ZJ, Liang YM. Three-component ruthenium-catalyzed remote C-H functionalization of 8-aminoquinoline amides. Chem Commun (Camb) 2020; 56:12729-12732. [PMID: 32966378 DOI: 10.1039/d0cc05491g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Multicomponent reactions can efficiently construct complex molecular structures from simple precursors. Herein, a novel ruthenium-catalyzed three-component highly selective remote C-H functionalization of 8-aminoquinoline amides has been described. The reaction tolerates a wide range of functional groups, producing arylation/difluoroalkylation products of olefins with potential biological activity and pharmaceutical value. Radical scavenging and radical clock experiments show that a free radical process is involved and a H/D exchange experiment suggests that the reaction might involve ortho-C-H activation of the aromatic ring. A possible mechanism is proposed.
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Affiliation(s)
- Wei-Yu Shi
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Ya-Nan Ding
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Ce Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Nian Zheng
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Xue-Ya Gou
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Ming Li
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Zhe Zhang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Hong-Chao Liu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Zhi-Jie Niu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
| | - Yong-Min Liang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China.
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20
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Kuranaga T, Minote M, Morimoto R, Pan C, Ogawa H, Kakeya H. Highly Sensitive Labeling Reagents for Scarce Natural Products. ACS Chem Biol 2020; 15:2499-2506. [PMID: 32865386 DOI: 10.1021/acschembio.0c00517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Scarce natural products that possess unique biological activities have been ideal drug leads for decades. However, their identification and structural determinations are problematic owing to sample amount limitation. Inspired by an extremely rare natural product yaku'amide B (10), highly sensitive labeling reagents that would be powerful tools for scarce natural product chemistry were designed and synthesized in this study. By fusion with the key structural motif for the structural revision of 10, the detection sensitivities of amino acid labeling reagents were drastically enhanced in LC-MS analysis. These advanced labeling reagents enabled the detection of infinitesimal amounts of amino acids and peptide hydrolysates. This sensitivity-enhancement design concept was also applicable to reagents for labeling saccharides and reactivity-guided isolation of electrophilic natural products. Details of these reagents, including their practical preparations and extended applications, are also provided.
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Affiliation(s)
- Takefumi Kuranaga
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mayuri Minote
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryota Morimoto
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chengqian Pan
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Haruka Ogawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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21
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Wen C, Zhong R, Qin Z, Zhao M, Li J. Regioselective remote C5 cyanoalkoxylation and cyanoalkylation of 8-aminoquinolines with azobisisobutyronitrile. Chem Commun (Camb) 2020; 56:9529-9532. [PMID: 32687138 DOI: 10.1039/d0cc00014k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficient regioselective C-H cyanoalkoxylation and cyanoalkylation of 8-aminoquinoline derivatives at the C5 position have been achieved under O2 and N2 atmospheres, respectively. Using 2,2'-azobisisobutyronitrile (AIBN) as a radical precursor, the protocols afforded the corresponding products in moderate to good yields with broad substrate generality through Cu(OAc)2 or NiSO4 catalysis. Furthermore, the single electron transfer (SET) mechanism was proposed via a radical coupling pathway.
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Affiliation(s)
- Chunxia Wen
- Department of Organic Chemistry, College of Chemistry, Jilin University, Jiefang Road 2519, Changchun, 130023, China.
| | - Ronglin Zhong
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Zengxin Qin
- Department of Organic Chemistry, College of Chemistry, Jilin University, Jiefang Road 2519, Changchun, 130023, China.
| | - Mengfei Zhao
- Department of Organic Chemistry, College of Chemistry, Jilin University, Jiefang Road 2519, Changchun, 130023, China.
| | - Jizhen Li
- Department of Organic Chemistry, College of Chemistry, Jilin University, Jiefang Road 2519, Changchun, 130023, China.
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22
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Jiang Q, Zhu Z, Shou P, Teng F, Zhu Y, Zhao H, Yang B. Targeting pharmacophore with probe-reactivity-guided fractionation to precisely identify electrophilic sesquiterpenes and its activity of anti-TNBC. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:322-332. [PMID: 31849131 DOI: 10.1002/pca.2898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Innovative strategy is urgently needed to precisely discover novel natural products as lead compounds for development of new drugs against orphan diseases such as triple-negative breast cancer (TNBC). Herein, we describe a targeting pharmacophore with probe-reactivity-guided strategy for the discovery of electrophilic sesquiterpene (ES), a class of bioactive natural product. OBJECTIVE This study aimed to identify pharmacophore, based on pharmacophore with probe-reactivity-guided strategy for precisely discovering ESs from ethyl acetate extract of Eupatorium chinense L. (EEEChL) METHODOLOGY: MTT assay combined with ultra-performance liquid chromatography (UPLC) analysis was used to identify pharmacophore. UPLC-mass spectrometry (MS) was applied to carefully compare the intrinsic reactivity characteristics of two chemoselective nucleophilic probes: glutathione (GSH) and 4-bromothiophenol (BTP) reaction with ESs. ESs was isolated and identified from EEEChL by phytochemical methods. Furthermore, stoichiometric ratio and binding site of one typical ES 8β-[4'-hydroxytigloyloxy]-5-desoxy-8-desacyleuparotin (HDDE) reaction with BTP were studied by UPLC-quadrupole time-of-flight (Q-TOF)-MS and two-dimensional nuclear magnetic resonance (NMR). RESULTS Eleven ESs were identified from EEEChL, MTT assay illustrated that all of the 11 ESs possess fairly good anti-TNBC activity CONCLUSIONS: Electrophilic groups were confirmed as pharmacophore of bioactive compounds contained in EEEChL. An optimised halogenated aromatic probe BTP furnishes ES-BTP conjugates that are highly conspicuous via MS by virtue of a unique isotopic bromine signature, conjugates also have a considerable separation on C18 column. The new probe-reactivity-guided strategy can effectively improve the traditional bioassay-guided approaches, and significantly increase the probability of obtaining designated bioactive compounds.
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Affiliation(s)
- QingLi Jiang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - ZhiHui Zhu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - PanTing Shou
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - Fei Teng
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - Ying Zhu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - HuaJun Zhao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
| | - Bo Yang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, No. 260 Baichuan Street, Hangzhou, 311402, P. R. China
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23
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Capon RJ. Extracting value: mechanistic insights into the formation of natural product artifacts – case studies in marine natural products. Nat Prod Rep 2020; 37:55-79. [DOI: 10.1039/c9np00013e] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review highlights the importance of valuing natural product handling artifacts, to open a new window into, and provide a unique perspective of, bioactive chemical space.
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Affiliation(s)
- Robert J. Capon
- Division of Chemistry and Structural Biology
- Institute for Molecular Bioscience
- The University of Queensland
- St Lucia
- Australia
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24
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Gao D, Zhou T, Da LT, Bruhn T, Guo LL, Chen YH, Xu J, Xu MJ. Characterization and Nonenzymatic Transformation of Three Types of Alkaloids from Streptomyces albogriseolus MGR072 and Discovery of Inhibitors of Indoleamine 2,3-Dioxygenase. Org Lett 2019; 21:8577-8581. [DOI: 10.1021/acs.orglett.9b03149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Du Gao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ting Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Torsten Bruhn
- German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Li-Li Guo
- State Key Laboratory of Molecular Developmental Biology, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yu-Hang Chen
- State Key Laboratory of Molecular Developmental Biology, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
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25
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Castro-Falcón G, Millán-Aguiñaga N, Roullier C, Jensen PR, Hughes CC. Nitrosopyridine Probe To Detect Polyketide Natural Products with Conjugated Alkenes: Discovery of Novodaryamide and Nocarditriene. ACS Chem Biol 2018; 13:3097-3106. [PMID: 30272441 DOI: 10.1021/acschembio.8b00598] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An optimized nitroso-based probe that facilitates the discovery of conjugated alkene-containing natural products in unprocessed extracts was developed. It chemoselectively reacts with conjugated olefins via a nitroso-Diels-Alder cyclization to yield derivatives with a distinct chromophore and an isotopically unique bromine atom that can be rapidly identified using liquid chromatography/mass spectrometry and a bioinformatics tool called MeHaloCoA (Marine Halogenated Compound Analysis). The probe is ideally employed when genome-mining techniques identify strains containing polyketide gene clusters with two or more repeating KS-AT-DH-KR-ACP domain sequences, which are required for the biosynthesis of conjugated alkenes. Comparing the reactivity and spectral properties of five brominated arylnitroso reagents with model compounds spiramycin, bufalin, rapamycin, and rifampicin led to the identification of 5-bromo-2-nitrosopyridine as the most suitable probe structure. The utility of the dienophile probe was then demonstrated in bacterial extracts. Tylactone, novodaryamide and daryamide A, piperazimycin A, and the saccharamonopyrones A and B were cleanly labeled in extracts from their respective bacterial producers, in high regioselectivity but with varying degrees of diastereoselectivity. Further application of the method led to the discovery of a new natural product called nocarditriene, containing an unprecedented epoxy-2,3,4,5-tetrahydropyridine structure, from marine-derived Nocardiopsis strain CNY-503.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Catherine Roullier
- Mer Molécules Santé - EA2160, Université de Nantes, 44035 Nantes-cedex 1, France
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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26
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Li HL, Kanai M, Kuninobu Y. Iridium/Bipyridine-Catalyzed ortho-Selective C–H Borylation of Phenol and Aniline Derivatives. Org Lett 2017; 19:5944-5947. [DOI: 10.1021/acs.orglett.7b02936] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hong-Liang Li
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- ERATO, Japan Science
and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoichiro Kuninobu
- ERATO, Japan Science
and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Institute
for Materials Chemistry and Engineering, Kyushu University, 6-1
Kasugakoen, Kasuga-shi, Fukuoka 816-8580, Japan
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27
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Rivera-Chávez J, Raja HA, Graf TN, Gallagher JM, Metri P, Xue D, Pearce CJ, Oberlies NH. Prealamethicin F50 and related peptaibols from Trichoderma arundinaceum: Validation of their authenticity via in situ chemical analysis. RSC Adv 2017; 7:45733-45751. [PMID: 29379602 PMCID: PMC5786278 DOI: 10.1039/c7ra09602j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the field of natural products chemistry, a common question pertains to the authenticity of an isolated compound, i.e. are the interesting side chains biosynthesized naturally or an artefact of the isolation/purification processes? The droplet-liquid microjunction-surface sampling probe (droplet-LMJ-SSP) coupled to a hyphenated system (UPLC-UV-HRESIMS) empowers the analysis of natural product sources in situ, providing data on the biosynthetic timing and spatial distribution of secondary metabolites. In this study the droplet-LMJ-SSP was utilized to validate the authenticity of two new peptaibols (2 and 3) as biosynthesized secondary metabolites, even though both them had structural features that could be perceived as artefacts. Compounds 2 and 3 were isolated from the scaled up fermentation of Trichoderma arundinaceum (strain MSX70741), along with a new member of the trichobrevin BIII complex (1), and four known compounds (4-7). The structures of the isolates were established using a set of spectroscopic and spectrometric methods, and their absolute configurations were determined by Marfey's analysis. The cytotoxic activity of compounds 1, 3, 4 and 6 was evaluated against a panel of cancer cell lines, where cytotoxic activity in the single digit μM range was observed.
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Affiliation(s)
- José Rivera-Chávez
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Tyler N Graf
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jacklyn M Gallagher
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Prashant Metri
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Ding Xue
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | | | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
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