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Yan JX, Wu Q, Maity M, Braun DR, Alas I, Wang X, Yin X, Zhu Y, Bell BA, Rajski SR, Ge Y, Richardson DD, Zhong W, Bugni TS. Rapid Unambiguous Structure Elucidation of Streptnatamide A, a New Cyclic Peptide Isolated from A Marine-derived Streptomyces sp. Chemistry 2023; 29:e202301813. [PMID: 37452377 PMCID: PMC10592287 DOI: 10.1002/chem.202301813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Cyclic peptides have been excellent source of drug leads. With the advances in discovery platforms, the pharmaceutical industry has a growing interest in cyclic peptides and has pushed several into clinical trials. However, structural complexity of cyclic peptides brings extreme challenges for structure elucidation efforts. Isotopic fine structure analysis, Nuclear magnetic resonance (NMR), and detailed tandem mass spectrometry rapidly provided peptide sequence for streptnatamide A, a cyclic peptide isolated from a marine-derived Streptomyces sp. Marfey's analysis determined the stereochemistry of all amino acids, enabling the unambiguous structure determination of this compound. A non-ribosomal peptide synthetase biosynthetic gene cluster (stp) was tentatively identified and annotated for streptnatamide A based on the in silico analysis of whole genome sequencing data. These analytical tools will be powerful tools to overcome the challenges for cyclic peptide structure elucidation and accelerate the development of bioactive cyclic peptides.
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Affiliation(s)
- Jia-Xuan Yan
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Qihao Wu
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Current address: Department of Chemistry, Institute of Biomolecular Design & Discovery, Yale University, 06516, West Haven, CT, USA
| | - Mitasree Maity
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Doug R Braun
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Imraan Alas
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Xiao Wang
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Xing Yin
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
| | - Bailey A Bell
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Scott R Rajski
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave, 53705, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, 53706, Madison, WI, USA
| | | | - Wendy Zhong
- Merck & Co., Inc., 126 E. Lincoln Ave, 07065, Rahway, NJ, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, 777 Highland Ave, 53705, Madison, WI, USA
- Lachman Institute for Pharmaceutical Development, University of Wisconsin-Madison, 600 Highland Ave, 53792, Madison, WI, USA
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Wu Z, Kim GJ, Park SY, Shon JC, Liu KH, Choi H. In Vitro Metabolism Study of Seongsanamide A in Human Liver Microsomes Using Non-Targeted Metabolomics and Feature-Based Molecular Networking. Pharmaceutics 2021; 13:pharmaceutics13071031. [PMID: 34371722 PMCID: PMC8309059 DOI: 10.3390/pharmaceutics13071031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Seongsanamide A is a bicyclic peptide with an isodityrosine residue discovered in Bacillus safensis KCTC 12796BP which exhibits anti-allergic activity in vitro and in vivo without significant cytotoxicity. The purpose of this study was to elucidate the in vitro metabolic pathway and potential for drug interactions of seongsanamide A in human liver microsomes using non-targeted metabolomics and feature-based molecular networking (FBMN) techniques. We identified four metabolites, and their structures were elucidated by interpretation of high-resolution tandem mass spectra. The primary metabolic pathway associated with seongsanamide A metabolism was hydroxylation and oxidative hydrolysis. A reaction phenotyping study was also performed using recombinant cytochrome P450 isoforms. CYP3A4 and CYP3A5 were identified as the major metabolic enzymes responsible for metabolite formation. Seongsanamide A did not inhibit the cytochrome P450 isoforms commonly involved in drug metabolism (IC50 > 10 µM). These results will contribute to further understanding the metabolism and drug interaction potential of various bicyclic peptides.
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Affiliation(s)
- Zhexue Wu
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Korea;
| | - Geum Jin Kim
- College of Pharmacy and Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
| | - So-Young Park
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-Y.P.); (J.C.S.)
| | - Jong Cheol Shon
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-Y.P.); (J.C.S.)
| | - Kwang-Hyeon Liu
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Korea;
- BK21 FOUR Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, Korea; (S.-Y.P.); (J.C.S.)
- Correspondence: (K.-H.L.); (H.C.); Tel.: +82-53-950-8567 (K.-H.L.); +82-53-810-2824 (H.C.); FAX: +82- 53-950-8557 (K.-H.L.); +82-53-810-2036 (H.C.)
| | - Hyukjae Choi
- College of Pharmacy and Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea;
- Correspondence: (K.-H.L.); (H.C.); Tel.: +82-53-950-8567 (K.-H.L.); +82-53-810-2824 (H.C.); FAX: +82- 53-950-8557 (K.-H.L.); +82-53-810-2036 (H.C.)
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Guan F, You Y, Li X, Robinson MA. A comprehensive approach to detecting multitudinous bioactive peptides in equine plasma and urine using hydrophilic interaction liquid chromatography coupled to high resolution mass spectrometry. Drug Test Anal 2019; 11:1308-1325. [PMID: 31250565 DOI: 10.1002/dta.2671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/02/2019] [Accepted: 06/19/2019] [Indexed: 12/12/2022]
Abstract
Bioactive peptides possess pharmacological effects and can be illicitly used in sports. To deter such misuse, an untargeted method using high resolution mass spectrometry (HRMS) has been developed for comprehensive detection of multitudinous exogenous peptides in equine plasma and urine. Forty-four peptides were extracted using mixed-mode solid-phase extraction (SPE) from plasma and urine, separated with a hydrophilic interaction liquid chromatography (HILIC) column, and detected on an HRMS instrument. Ammonium formate as a mobile phase additive had effects on HILIC retention and charge state distribution of the peptides. The acetonitrile percentage in the reconstitution solution affected the solubility of peptide neat standards and peptides in plasma and urine extracts differently. The stability of the peptides in plasma at ambient temperature was assessed. The limit of detection (LOD) was 10-50 pg/mL for most of the peptides in plasma, and ≤ 500 pg/mL for the remaining. LOD was 100-400 pg/mL for the majority of the analytes in urine, and ≤ 4000 pg/mL for the others. The method was used successfully to analyze incurred plasma and urine samples from research horses administered dermorphin. Even in the absence of reference standards, dermorphin metabolites (aFGYPS-NH2 , YaFG, and YaF) were identified. These results demonstrate that data generated with this method can be retrospectively reviewed for peptides that are unknown at the time of sample analysis without requiring re-analysis of the sample. This method provides a powerful novel tool for detection of numerous bioactive peptides and their metabolites in equine plasma and urine for doping control.
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Affiliation(s)
- Fuyu Guan
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA, 19348, USA.,Pennsylvania Equine Toxicology and Research Laboratory, 220 East Rosedale Avenue, West Chester, PA, 19382, USA
| | - Youwen You
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA, 19348, USA.,Pennsylvania Equine Toxicology and Research Laboratory, 220 East Rosedale Avenue, West Chester, PA, 19382, USA
| | - Xiaoqing Li
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA, 19348, USA.,Pennsylvania Equine Toxicology and Research Laboratory, 220 East Rosedale Avenue, West Chester, PA, 19382, USA
| | - Mary A Robinson
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA, 19348, USA.,Pennsylvania Equine Toxicology and Research Laboratory, 220 East Rosedale Avenue, West Chester, PA, 19382, USA
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Knolhoff AM, Zheng J, McFarland MA, Luo Y, Callahan JH, Brown EW, Croley TR. Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1768-1779. [PMID: 26250559 DOI: 10.1007/s13361-015-1190-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/24/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to exhibit antimicrobial activity against a number of pathogens, such as E. coli, Salmonella, and methicillin-resistant Staphylococcus aureus (MRSA). The responsible antimicrobial compounds were isolated from these Paenibacillus strains and a combination of low and high resolution mass spectrometry with multiple-stage tandem mass spectrometry was used for identification. A group of closely related cyclic lipopeptides was identified, differing primarily by fatty acid chain length and one of two possible amino acid substitutions. Variation in the fatty acid length resulted in mass differences of 14 Da and yielded groups of related MS(n) spectra. Despite the inherent complexity of MS/MS spectra of cyclic compounds, straightforward analysis of these spectra was accomplished by determining differences in complementary product ion series between compounds that differ in molecular weight by 14 Da. The primary peptide sequence assignment was confirmed through genome mining; the combination of these analytical tools represents a workflow that can be used for the identification of complex antibiotics. The compounds also share amino acid sequence similarity to a previously identified broad-spectrum antibiotic isolated from Paenibacillus. The presence of such a wide distribution of related compounds produced by the same organism represents a novel class of broad-spectrum antibiotic compounds.
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Affiliation(s)
- Ann M Knolhoff
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA.
| | - Jie Zheng
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Melinda A McFarland
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Yan Luo
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - John H Callahan
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Eric W Brown
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
| | - Timothy R Croley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, HFS-707, 5100 Paint Branch Pkwy, College Park, MD, 20740, USA
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Jia C, Wu Z, Lietz CB, Liang Z, Cui Q, Li L. Gas-phase ion isomer analysis reveals the mechanism of peptide sequence scrambling. Anal Chem 2013; 86:2917-24. [PMID: 24313304 DOI: 10.1021/ac401578p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values, which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M → (c)b) pathway is less energetically (or kinetically) favored.
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Affiliation(s)
- Chenxi Jia
- School of Pharmacy and ‡Department of Chemistry, University of Wisconsin-Madison , 777 Highland Avenue, Madison, Wisconsin 53705, United States
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Kai M, González I, Genilloud O, Singh SB, Svatoš A. Direct mass spectrometric screening of antibiotics from bacterial surfaces using liquid extraction surface analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2477-82. [PMID: 22976215 DOI: 10.1002/rcm.6365] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
RATIONALE There is a need to find new antibiotic agents to fight resistant pathogenic bacteria. To search successfully for novel antibiotics from bacteria cultivated under diverse conditions, we need a fast and cost-effective screening method. METHODS A combination of Liquid Extraction Surface Analysis (LESA), automated chip-based nanoelectrospray ionization, and high-resolution mass or tandem mass spectrometry using an Orbitrap XL was tested as the screening platform. Actinobacteria, known to produce well-recognized thiazolyl peptide antibiotics, were cultivated on a plate of solid medium and the antibiotics were extracted by organic solvent mixtures from the surface of colonies grown on the plate and analyzed using mass spectrometry (MS). RESULTS LESA combined with high-resolution MS is a powerful tool with which to extract and detect thiazolyl peptide antibiotics from different Actinobacteria. Known antibiotics were correctly detected with high mass accuracy (<4 ppm) and structurally characterized using tandem mass spectra. Our method is the first step toward the development of a novel high-throughput extraction and identification tool for antibiotics in particular and natural products in general. CONCLUSIONS The method described in this paper is suitable for (1) screening the natural products produced by bacterial colonies on cultivation plates within the first 2 min following extraction and (2) detecting antibiotics at high mass accuracy; the cost is around 2 Euro per sample.
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Affiliation(s)
- Marco Kai
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
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Esposito S, Deventer K, Goeman J, Van der Eycken J, Van Eenoo P. Synthesis and characterization of the N-terminal acetylated 17-23 fragment of thymosin beta 4 identified in TB-500, a product suspected to possess doping potential. Drug Test Anal 2012; 4:733-8. [DOI: 10.1002/dta.1402] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/12/2012] [Accepted: 07/12/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Simone Esposito
- Doping Control Laboratory (DoCoLab); Department of Clinical Chemistry, Microbiology and Immunology; Ghent University (UGent); Technologiepark 30; B-9052; Zwijnaarde; Belgium
| | - Koen Deventer
- Doping Control Laboratory (DoCoLab); Department of Clinical Chemistry, Microbiology and Immunology; Ghent University (UGent); Technologiepark 30; B-9052; Zwijnaarde; Belgium
| | - Jan Goeman
- Laboratory for Organic and Bioorganic Synthesis; Department of Organic Chemistry; Ghent University; Krijgslaan 281 (S4); B-9000; Ghent; Belgium
| | - Johan Van der Eycken
- Laboratory for Organic and Bioorganic Synthesis; Department of Organic Chemistry; Ghent University; Krijgslaan 281 (S4); B-9000; Ghent; Belgium
| | - Peter Van Eenoo
- Doping Control Laboratory (DoCoLab); Department of Clinical Chemistry, Microbiology and Immunology; Ghent University (UGent); Technologiepark 30; B-9052; Zwijnaarde; Belgium
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Abstract
Historically, dope-testing methods have been developed to target specific and known threats to the integrity of sport. Traditionally, the source of new analytical targets for which testing was required were derived almost exclusively from the pharmaceutical industry. More recently, the emergence of designer drugs, such as tetrahydrogestrinone that are specifically intended to evade detection, or novel chemicals intended to circumvent laws controlling the sale and distribution of recreational drugs, such as anabolic steroids, stimulants and cannabinoids, have become a significant issue. In this review, we shall consider the emergence of designer drugs and the response of dope-testing laboratories to these new threats, in particular developments in analytical methods, instrumentation and research intended to detect their abuse, and we consider the likely future impact of these approaches.
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