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Zeng R, Bian Y, Zhang X, Zhu Z, Yang B. Terahertz Spectroscopy Study of the Stereoisomers of Threonine. APPLIED SPECTROSCOPY 2022; 76:1132-1141. [PMID: 35469427 DOI: 10.1177/00037028221099958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The terahertz (THz) band contains a wealth of information about vibration and rotational energy levels, most of the vibration modes between amino acid molecules are in the THz band, so it reflects many unique absorption characteristics in the THz band. The use of terahertz time-domain spectroscopy can not only effectively identify different kinds of amino acids but also distinguish various isomers of the same amino acid due to the varied vibration modes. The absorption spectra of four stereoisomers of threonine were investigated by terahertz time-domain spectroscopy (THz-TDS) and Fourier transform infrared spectroscopy. The results show that the isomers show similarity in the infrared band, while manifest evidently the similarity between enantiomers L-threonine and D-threonine, and between L-allo-threonine and D-allo-threonine, and the difference between diastereoisomer L-threonine/D-threonine and L-allo-threonine/D-allo-threonine in the terahertz band. In order to fully understand the origin of the terahertz absorption characteristics of isomer molecules, simulation calculations were carried out in combination with density functional theory to connect the vibrational modes and molecular structures, Furthermore, the unit cell configurations of L-thr and L-allo-thr and the differences between various low-frequency vibrational modes are analyzed from the perspective of hydrogen bond configuration. By further extracting terahertz optical parameters such as refractive index and imaginary part of the dielectric constant of threonine isomers, the results show that the refractive index spectrum and dielectric loss spectrum can clearly show the response characteristics of the orientation polarization of dipole inside threonine isomers in terahertz band.
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Affiliation(s)
- Ruonan Zeng
- College of Textile Science and Engineering (International College of Silk), 12646Zhejiang Sci-Tech University, Hangzhou, China
| | - Yujing Bian
- College of Textile Science and Engineering (International College of Silk), 12646Zhejiang Sci-Tech University, Hangzhou, China
| | - Xun Zhang
- College of Textile Science and Engineering (International College of Silk), 12646Zhejiang Sci-Tech University, Hangzhou, China
| | - Zhenqi Zhu
- College of Textile Science and Engineering (International College of Silk), 12646Zhejiang Sci-Tech University, Hangzhou, China
| | - Bin Yang
- College of Textile Science and Engineering (International College of Silk), 12646Zhejiang Sci-Tech University, Hangzhou, China
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, 12646Zhejiang Sci-Tech University, Hangzhou, China
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Schnegotzki R, Wiebach V, Sánchez-Hidalgo M, Tietzmann M, zur Bonsen AB, Genilloud O, Süssmuth RD. Total Synthesis and Biosynthesis of Cyclodepsipeptide Cochinmicin I. Org Lett 2022; 24:2344-2348. [DOI: 10.1021/acs.orglett.2c00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Romina Schnegotzki
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | | | - Marina Sánchez-Hidalgo
- Department of Microbiology, Fundación MEDINA, Av. Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Marcel Tietzmann
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Andreas B. zur Bonsen
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Olga Genilloud
- Department of Microbiology, Fundación MEDINA, Av. Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Roderich D. Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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Niehs SP, Dose B, Scherlach K, Pidot SJ, Stinear TP, Hertweck C. Genome Mining Reveals Endopyrroles from a Nonribosomal Peptide Assembly Line Triggered in Fungal-Bacterial Symbiosis. ACS Chem Biol 2019; 14:1811-1818. [PMID: 31283172 DOI: 10.1021/acschembio.9b00406] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial endosymbiont (Burkholderia rhizoxinica) of the rice seedling blight fungus (Rhizopus microsporus) harbors a large number of cryptic biosynthesis gene clusters. Genome mining and sequence similarity networks based on an encoded nonribosomal peptide assembly line and the associated pyrrole-forming enzymes in the symbiont indicated that the encoded metabolites are unique among a large number of tentative pyrrole natural products in diverse and unrelated bacterial phyla. By performing comparative metabolic profiling using a mutant generated with an improved pheS Burkholderia counterselection marker, we found that the symbionts' biosynthetic pathway is mainly activated under salt stress and exclusively in symbiosis with the fungal host. The cryptic metabolites were fully characterized as novel pyrrole-substituted depsipeptides (endopyrroles). A broader survey showed that endopyrrole production is a hallmark of geographically distant endofungal bacteria, which produce the peptides solely under symbiotic conditions.
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Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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Quorum Quenching Strategy Targeting Gram-Positive Pathogenic Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 901:109-30. [PMID: 27167409 DOI: 10.1007/5584_2016_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Quorum sensing (QS) is a cell density-dependent regulatory system that orchestrates the group behavior of unicellular organisms by synchronizing the expression of certain gene(s) within the clonal community of same species. Bacterial pathogens often employ QS system to establish efficiently an infection. A large part of low GC Gram-positive bacteria belonging to phylum Firmicutes use thiolactone/lactone peptides as communication signals so-called autoinducing peptides (AIPs) to coordinate QS circuit. In particular, QS of staphylococci, enterococci, and clostridia have been intensively studied in terms of alternative target of anti-pathogenic chemotherapy independent of bactericidal antibiotics. Thus far, a number of quorum quenching (QQ) agents that targeting the QS circuit of these Gram-positive pathogens have been developed by random screening of natural compounds or rationale design of AIP antagonists. This review summarizes those QQ agents and previews their potential as post-antibiotic drugs.
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Desouky SE, Shojima A, Singh RP, Matsufuji T, Igarashi Y, Suzuki T, Yamagaki T, Okubo KI, Ohtani K, Sonomoto K, Nakayama J. Cyclodepsipeptides produced by actinomycetes inhibit cyclic-peptide-mediated quorum sensing in Gram-positive bacteria. FEMS Microbiol Lett 2015; 362:fnv109. [PMID: 26149266 DOI: 10.1093/femsle/fnv109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2015] [Indexed: 12/18/2022] Open
Abstract
Cyclic peptides are commonly used as quorum-sensing autoinducers in Gram-positive Firmicutes bacteria. Well-studied examples of such molecules are thiolactone and lactone, used to regulate the expression of a series of virulence genes in the agr system of Staphylococcus aureus and the fsr system of Enterococcus faecalis, respectively. Three cyclodepsipeptides WS9326A, WS9326B and cochinmicin II/III were identified as a result of screening actinomycetes culture extracts for activity against the agr/fsr system. These molecules are already known as receptor antagonists, the first two for tachykinin and the last one for endothelin. WS9326A also inhibited the transcription of pfoA regulated by the VirSR two-component system in Clostridium perfringens. Receptor-binding assays using a fluorescence-labeled autoinducer (FITC-GBAP) showed that WS9326A and WS9326B act as receptor antagonists in this system. In addition, an ex vivo assay showed that WS9326B substantially attenuated the toxicity of S. aureus for human corneal epithelial cells. These results suggest that these three natural cyclodepsipeptides have therapeutic potential for targeting the cyclic peptide-mediated quorum sensing of Gram-positive pathogens.
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Affiliation(s)
- Said E Desouky
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Department of Botany and Microbiology, Faculty of Science, Al-azhar University, 11884 Nasr, Cairo, Egypt
| | - Akane Shojima
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Ravindra Pal Singh
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takahisa Matsufuji
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Takashi Suzuki
- Department of Ophthalmology, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Tohru Yamagaki
- Suntory Foundation for Life Sciences, Bioorganic Research Institute, 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka 618-8503, Japan
| | - Ken-Ichi Okubo
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Kaori Ohtani
- Department of Bacteriology, University of Kanazawa, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8203, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan Laboratory of Functional Food Design, Department of Functional Metabolic Design, Bio-Architecture Center, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
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Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
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Banerjee R, Sudarslal S, Ranganayaki RS, Raghothama S. Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides. Org Biomol Chem 2011; 9:6234-45. [PMID: 21826329 DOI: 10.1039/c1ob05392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical 'b-ion' series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the 'b' or/and the 'y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the 'y-type'. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.
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Affiliation(s)
- Raja Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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8
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Friedman M, Levin CE. Nutritional and medicinal aspects of D-amino acids. Amino Acids 2011; 42:1553-82. [PMID: 21519915 DOI: 10.1007/s00726-011-0915-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/06/2011] [Indexed: 02/07/2023]
Abstract
This paper reviews and interprets a method for determining the nutritional value of D-amino acids, D-peptides, and amino acid derivatives using a growth assay in mice fed a synthetic all-amino acid diet. A large number of experiments were carried out in which a molar equivalent of the test compound replaced a nutritionally essential amino acid such as L-lysine (L-Lys), L-methionine (L-Met), L-phenylalanine (L-Phe), and L-tryptophan (L-Trp) as well as the semi-essential amino acids L-cysteine (L-Cys) and L-tyrosine (L-Tyr). The results show wide-ranging variations in the biological utilization of test substances. The method is generally applicable to the determination of the biological utilization and safety of any amino acid derivative as a potential nutritional source of the corresponding L-amino acid. Because the organism is forced to use the D-amino acid or amino acid derivative as the sole source of the essential or semi-essential amino acid being replaced, and because a free amino acid diet allows better control of composition, the use of all-amino-acid diets for such determinations may be preferable to protein-based diets. Also covered are brief summaries of the widely scattered literature on dietary and pharmacological aspects of 27 individual D-amino acids, D-peptides, and isomeric amino acid derivatives and suggested research needs in each of these areas. The described results provide a valuable record and resource for further progress on the multifaceted aspects of D-amino acids in food and biological samples.
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Affiliation(s)
- Mendel Friedman
- Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA.
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10
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Cody WL, Doherty AM. The development of potent peptide agonists and antagonists for the endothelin receptors. Biopolymers 1995; 37:89-104. [PMID: 7893949 DOI: 10.1002/bip.360370205] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The endothelins (ETs), sarafotoxins (SRTXs), vasoactive intestinal contractor (VIC), and bibrotoxin are a family of potent vasoconstrictor peptides. All peptides in this family possess 21 amino acids arranged in a unique bicyclic motif formed between cystine bridges in the 1-15 and 3-11 positions. Since the discovery of endothelin-1 (ET-1) in 1988, significant effort has been focused on the understanding of its structure-activity relationships. The identification of endothelin receptor subtypes has led to the discovery/design of potent peptide agonists and antagonists, along with nonpeptide antagonists of endothelin with varying levels of potency and receptor subtype selectivity. In keeping with the theme of this journal, this review will focus only on the development of peptidic-based agonists and antagonists of endothelin in addition to their applications in understanding the physiological and/or pathophysiological role of endothelin and its isopeptides.
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Affiliation(s)
- W L Cody
- Parke-Davis Pharmaceutical Research Division, Warner-Lambert Company, Ann Arbor, Michigan 48105
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Warner TD, Battistini B, Doherty AM, Corder R. Endothelin receptor antagonists: actions and rationale for their development. Biochem Pharmacol 1994; 48:625-35. [PMID: 8080434 DOI: 10.1016/0006-2952(94)90038-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- T D Warner
- William Harvey Research Institute, Medical College of St. Bartholomew's Hospital, London, U.K
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Bradley EK, Ng SC, Simon RJ, Spellmeyer DC. Synthesis, molecular modelling, and NMR structure determination of four cyclic peptide antagonists of endothelin. Bioorg Med Chem 1994; 2:279-96. [PMID: 7922139 DOI: 10.1016/s0968-0896(00)82171-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A combined distance geometry and molecular mechanics/dynamics (MM/MD) protocol was unable to predict the active conformation of the cyclic pentapeptide inhibitor of endothelin-1 receptor, BQ-123, and two analogues. However, the MM/MD method alone is sufficient to predict the solution conformation of a third analogue. In that one case, the combination of proline at residue 3 and an N alpha-methyl substitution at residue 5 provides enough internal constraints to eliminate conformational flexibility seen in the other three analogues. For this constrained analogue, the 50 lowest energy conformations (out of a set of 500 DGEOM-generated, MM/MD minimized conformations) differ by no more than 3.9 kcal/mol. Thirty three of these 50 conformations have backbone atom RMSDs of less than 0.33 A, relative to the lowest energy conformation. The accuracy of this MM/MD model is verified by determining the solution structure of each of the four analogues with 2D NMR techniques. Each of the cyclic pentapeptides has a well defined solution conformation where a proline residue is clearly in a gamma-turn, leaving the remaining residues in a loose beta-turn. All four experimental NMR conformations agree closely with the MM/MD model.
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Hunt JT, Lee VG, McMullen D, Liu EC, Bolgar M, Delaney CL, Festin SM, Floyd DM, Hedberg A, Natarajan S. Structure-activity studies of endothelin leading to novel peptide ETA antagonists. Bioorg Med Chem 1993; 1:59-65. [PMID: 8081838 DOI: 10.1016/s0968-0896(00)82103-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
With the goal of producing receptor antagonists, numerous monocyclic and bicyclic endothelin analogs were prepared and tested for vasoconstrictor activity, receptor affinity and functional antagonist activity. Bis-penicillamine endothelin analogs containing Ala or Asn at position 18 were functional antagonists, with Ki values of 20-40 nM but KB values of about 1 microM (e.g., [Pen1,11, Nle7, Ala18]-endothelin-1, Ki = 42 nM, KB = 1.2 microM). While these peptides are antagonists at the ETA receptor, they appear to be at least partial agonists at another receptor subtype.
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Affiliation(s)
- J T Hunt
- Department of Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000
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