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Salim AA, Butler MS, Blaskovich MAT, Henderson IR, Capon RJ. Natural products as anthelmintics: safeguarding animal health. Nat Prod Rep 2023; 40:1754-1808. [PMID: 37555325 DOI: 10.1039/d3np00019b] [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: 08/10/2023]
Abstract
Covering literature to December 2022This review provides a comprehensive account of all natural products (500 compounds, including 17 semi-synthetic derivatives) described in the primary literature up to December 2022, reported to be capable of inhibiting the egg hatching, motility, larval development and/or the survival of helminths (i.e., nematodes, flukes and tapeworms). These parasitic worms infect and compromise the health and welfare, productivity and lives of commercial livestock (i.e., sheep, cattle, horses, pigs, poultry and fish), companion animals (i.e., dogs and cats) and other high value, endangered and/or exotic animals. Attention is given to chemical structures, as well as source organisms and anthelmintic properties, including the nature of bioassay target species, in vivo animal hosts, and measures of potency.
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Affiliation(s)
- Angela A Salim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia, 4072.
| | - Mark S Butler
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia, 4072.
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia, 4072.
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia, 4072.
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia, 4072.
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2
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De novo design of discrete, stable 3 10-helix peptide assemblies. Nature 2022; 607:387-392. [PMID: 35732733 DOI: 10.1038/s41586-022-04868-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/13/2022] [Indexed: 02/02/2023]
Abstract
The α-helix is pre-eminent in structural biology1 and widely exploited in protein folding2, design3 and engineering4. Although other helical peptide conformations do exist near to the α-helical region of conformational space-namely, 310-helices and π-helices5-these occur much less frequently in protein structures. Less favourable internal energies and reduced tendencies to pack into higher-order structures mean that 310-helices rarely exceed six residues in length in natural proteins, and that they tend not to form normal supersecondary, tertiary or quaternary interactions. Here we show that despite their absence in nature, synthetic peptide assemblies can be built from 310-helices. We report the rational design, solution-phase characterization and an X-ray crystal structure for water-soluble bundles of 310-helices with consolidated hydrophobic cores. The design uses six-residue repeats informed by analysing 310-helical conformations in known protein structures, and incorporates α-aminoisobutyric acid residues. Design iterations reveal a tipping point between α-helical and 310-helical folding, and identify features required for stabilizing assemblies of 310-helices. This work provides principles and rules to open opportunities for designing into this hitherto unexplored region of protein-structure space.
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3
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Rius J, Torrelles X. A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:339-347. [PMID: 34196295 PMCID: PMC8248888 DOI: 10.1107/s2053273321004915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
The incorporation of the new peakness-enhancing fast Fourier transform compatible ipp procedure (ipp = inner-pixel preservation) into the recently published SM algorithm based on |ρ| [Rius (2020). Acta Cryst A76, 489-493] improves its phasing efficiency for larger crystal structures with atomic resolution data. Its effectiveness is clearly demonstrated via a collection of test crystal structures (taken from the Protein Data Bank) either starting from random phase values or by using the randomly shifted modulus function (a Patterson-type synthesis) as initial ρ estimate. It has been found that in the presence of medium scatterers (e.g. S or Cl atoms) crystal structures with 1500 × c atoms in the unit cell (c = number of centerings) can be routinely solved. In the presence of strong scatterers like Fe, Cu or Zn atoms this number increases to around 5000 × c atoms. The implementation of this strengthened SM algorithm is simple, since it only includes a few easy-to-adjust parameters.
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Affiliation(s)
- Jordi Rius
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
| | - Xavier Torrelles
- Institut de Ciència de Materials de Barcelona, CSIC, Campus de la UAB, Bellaterra, Catalonia 08193, Spain
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4
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The Emericellipsins A-E from an Alkalophilic Fungus Emericellopsis alkalina Show Potent Activity against Multidrug-Resistant Pathogenic Fungi. J Fungi (Basel) 2021; 7:jof7020153. [PMID: 33669976 PMCID: PMC7924852 DOI: 10.3390/jof7020153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 11/17/2022] Open
Abstract
Novel antimicrobial peptides with antifungal and cytotoxic activity were derived from the alkalophilic fungus Emericellopsis alkalina VKPM F1428. We previously reported that this strain produced emericellipsin A (EmiA), which has strong antifungal and cytotoxic properties. Further analyses of the metabolites obtained under a special alkaline medium resulted in the isolation of four new homologous (Emi B-E). In this work, we report the complete primary structure and detailed biological activity for the newly synthesized nonribosomal antimicrobial peptides called emericellipsins B-E. The inhibitory activity of themajor compound, EmiA, against drug-resistant pathogenic fungi was similar to that of amphotericin B (AmpB). At the same time, EmiA had no hemolytic activity towards human erythrocytes. In addition, EmiA demonstrated low cytotoxic activity towards the normal HPF line, but possessed cancer selectivity to the K-562 and HCT-116 cell lines. Emericillipsins from the alkalophilic fungus Emericellopsis alkaline are promising treatment alternatives to licensed antifungal drugs for invasive mycosis therapy, especially for multidrug-resistant aspergillosis and cryptococcosis.
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Zhao P, Xue Y, Li X, Li J, Zhao Z, Quan C, Gao W, Zu X, Bai X, Feng S. Fungi-derived lipopeptide antibiotics developed since 2000. Peptides 2019; 113:52-65. [PMID: 30738838 DOI: 10.1016/j.peptides.2019.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/12/2022]
Abstract
Lipopeptide antibiotics have linear or cyclic structures with one or more hydrocarbon tails linked to the N-terminus of a short oligopeptide that may be chemically modified and/or contain unusual amino acid residues in their structures. They possess huge potential as pharmaceutical drugs and biocontrol agents, and ˜30 representative genera of fungi are known to produce them. Some chemically synthesised derivatives have already been developed into commercial products or subjected to clinical trials, including cilofungin, caspofungin, micafungin, anidulafungin, rezafungin, emodepside, fusafungine and destruxins. This review summarizes 200 fungi-derived compounds reported since 2000, including 95 cyclic depsipeptides, 67 peptaibiotics (including 35 peptaibols, eight lipoaminopeptides, and five lipopeptaibols), and 38 non-depsipeptide and non-peptaibiotic lipopeptides. Their sources, structural sequences, antibiotic activities (e.g. antibacterial, antifungal, antiviral, antimycobacterial, antimycoplasmal, antimalarial, antileishmanial, insecticidal, antitrypanosomal and nematicidal), structure-activity relationships, mechanisms of action, and specific relevance are discussed. These compounds have attracted considerable interest within the pharmaceutical and agrochemical industries.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Xin Li
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Zhanqin Zhao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
| | - Chunshan Quan
- Department of Life Science, Dalian Nationalities University, Dalian, 116600, China
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shuxiao Feng
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471023, China
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6
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Gessmann R, Brückner H, Berg A, Petratos K. The crystal structure of the lipoaminopeptaibol helioferin, an antibiotic peptide from Mycogone rosea. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:315-320. [PMID: 29652258 DOI: 10.1107/s2059798318001857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/30/2018] [Indexed: 11/10/2022]
Abstract
The crystal structure of the natural nonapeptide antibiotic helioferin has been determined and refined to 0.9 Å resolution. Helioferin consists of helioferin A and B, which contain 2-(2'-aminopropyl)aminoethanol (Apae) and 2-[(2'-aminopropyl)methylamino]ethanol (Amae) at their respective alkanolamine termini. In addition, helioferin contains the unusual amino-acid residues α-aminoisobutyric acid (Aib) and (2S,4S,6S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoic acid (Ahmod). The amino-terminus is capped with 2-methyl-n-1-octanoic acid (M8a). The peptide crystallizes with a 1:1 molar ratio of helioferin A and B in the monoclinic space group C2, with unit-cell parameters a = 34.711, b = 10.886, c = 17.150 Å, β = 93.05°. The peptide backbone folds in a regular right-handed α-helical conformation, with eight intramolecular hydrogen bonds, all but one forming 5→1 interactions. The two aliphatic chains of the fatty-acyl (M8a) and the second residue (Ahmod) extend out of the α-helical structure in opposite directions and lead to a corkscrew-like shape of the peptide molecule. Halogen anions (Cl- and F-) have been co-crystallized with the peptide molecules, implying a positive charge at the aminoalcohol end of the peptide. In the tightly packed crystal the helices are linked head to tail via the anions by electrostatic, hydrogen-bond and van der Waals interactions, forming continuous helical rods. Two nonparallel rods (forming an angle of 118°) interact directly via hydrogen bonds and via the anions, forming a double layer. Successive double layers are held together only via van der Waals contacts. The helical axes of successive double layers are also related by an angle of 118°. The structure of helioferin reported here and the previously determined structure of the homologous leucinostatin A have a total straight length of about 21 Å, indicating a different membrane-modifying bioactivity from that of long-chain, amphiphilic peptaibols.
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Affiliation(s)
| | - Hans Brückner
- Research Center for BioSystems, Land Use and Nutrition (IFZ), Institute of Nutritional Science, Department of Food Sciences, Heinrich-Buff-Ring 26-32, 65392 Giessen, Germany
| | - Albrecht Berg
- Innovent e.V., Prüssingstrasse 27B, 07745 Jena, Germany
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7
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Gessmann R, Axford D, Brückner H, Berg A, Petratos K. A natural, single-residue substitution yields a less active peptaibiotic: the structure of bergofungin A at atomic resolution. Acta Crystallogr F Struct Biol Commun 2017; 73:95-100. [PMID: 28177320 PMCID: PMC5297930 DOI: 10.1107/s2053230x17001236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/24/2017] [Indexed: 11/11/2022] Open
Abstract
Bergofungin is a peptide antibiotic that is produced by the ascomycetous fungus Emericellopsis donezkii HKI 0059 and belongs to peptaibol subfamily 2. The crystal structure of bergofungin A has been determined and refined to 0.84 Å resolution. This is the second crystal structure of a natural 15-residue peptaibol, after that of samarosporin I. The amino-terminal phenylalanine residue in samarosporin I is exchanged to a valine residue in bergofungin A. According to agar diffusion tests, this results in a nearly inactive antibiotic peptide compared with the moderately active samarosporin I. Crystals were obtained from methanol solutions of purified bergofungin mixed with water. Although there are differences in the intramolecular hydrogen-bonding scheme of samarosporin I, the overall folding is very similar for both peptaibols, namely 310-helical at the termini and α-helical in the middle of the molecules. Bergofungin A and samarosporin I molecules are arranged in a similar way in both lattices. However, the packing of bergofungin A exhibits a second solvent channel along the twofold axis. This latter channel occurs in the vicinity of the N-terminus, where the natural substitution resides.
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Affiliation(s)
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Hans Brückner
- Department of Food Science, Institute of Nutritional Science, Research Center for BioSystems, Land Use and Nutrition (IFZ), Heinrich-Buff-Ring 26-32, 65392 Giessen, Germany
| | - Albrecht Berg
- Innovent e.V., Prüssingstrasse 27B, 07745 Jena, Germany
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8
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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9
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Pike SJ, Raftery J, Webb SJ, Clayden J. Conformational analysis of helical aminoisobutyric acid (Aib) oligomers bearing C-terminal ester Schellman motifs. Org Biomol Chem 2016; 12:4124-31. [PMID: 24831537 DOI: 10.1039/c4ob00268g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of Schellman motifs on the adoption of stable 310 helical conformations in a series of aminoisobutyric (Aib) oligomers has been studied in the solid state and solution. The destabilising effect of the Schellman motif (a local inversion of helical screw-sense due to a C-terminal ester residue) was quantified in the solid state using X-ray crystallography through analysis of the torsion angles and their deviation from those observed in an ideal 310 helix. Investigation of the intramolecular hydrogen-bonding interactions in the solid state led to the identification of a fully extended C5 conformation in one oligomer, which is a novel folding motif for Aib oligomers. The effect of ester groups with differing steric demands on intermolecular hydrogen-bonding contacts in the solid state was also ascertained. In solution, the adoption of a 310 conformation in Aib oligomers appeared to be more finely tuned, depending on a number of factors, including chain length and the steric demands of the C-terminal destabilising Schellman motif.
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Affiliation(s)
- Sarah J Pike
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
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10
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Abstract
Foldamers can be made more than pieces of static, conformationally uniform molecular architecture by designing into their structure the conformational dynamism characteristic of functional molecular machines. We show that these dynamic foldamers display biomimetic properties reminiscent of allosteric proteins and receptor molecules. They can translate chemical signals into conformational changes, and hence into chemical outputs such as control of reactivity and selectivity. Future developments could see dynamic foldamers operating in the membrane phase providing artificial mechanisms for communication and control that integrate synthetic chemistry into synthetic biology.
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Affiliation(s)
- Bryden A F Le Bailly
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
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11
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Pike SJ, Boddaert T, Raftery J, Webb SJ, Clayden J. Participation of non-aminoisobutyric acid (Aib) residues in the 310 helical conformation of Aib-rich foldamers: a solid state study. NEW J CHEM 2015. [DOI: 10.1039/c4nj01547a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
310 helical conformations that extend over 21 Å result when selected non-Aib terminal and central residues are incorporated into Aib-rich foldamers.
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Affiliation(s)
- Sarah J. Pike
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | | | - James Raftery
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Simon J. Webb
- School of Chemistry
- University of Manchester
- Manchester
- UK
- Manchester Institute of Biotechnology
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12
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Gessmann R, Brückner H, Petratos K. The achiral tetrapeptide Z-Aib-Aib-Aib-Gly-OtBu. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:1046-9. [PMID: 25370104 DOI: 10.1107/s2053229614022165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/07/2014] [Indexed: 11/10/2022]
Abstract
The title achiral peptide N-benzyloxycarbonyl-α-aminoisobutyryl-α-aminoisobutyryl-α-aminoisobutyrylglycine tert-butyl ester or Z-Aib-Aib-Aib-Gly-OtBu (Aib is α-aminoisobutyric acid, Z is benzyloxycarbonyl, Gly is glycine and OtBu indicates the tert-butyl ester), C26H40N4O7, is partly hydrated (0.075H2O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 310-helices. They differ in the relative orientation of the N-terminal protection group and at the C-terminus. There are two 4→1 intramolecular hydrogen bonds.
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Affiliation(s)
| | - Hans Brückner
- Department of Food Sciences, Interdisciplinary Research Centre, Justus-Liebig-University of Giessen, 35392 Giessen, Germany
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13
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Hayouka Z, Mortenson DE, Kreitler DF, Weisblum B, Forest KT, Gellman SH. Evidence for phenylalanine zipper-mediated dimerization in the X-ray crystal structure of a magainin 2 analogue. J Am Chem Soc 2013; 135:15738-15741. [PMID: 24102563 PMCID: PMC3928869 DOI: 10.1021/ja409082w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-resolution structure elucidation has been challenging for the large group of host-defense peptides that form helices on or within membranes but do not manifest a strong folding propensity in aqueous solution. Here we report the crystal structure of an analogue of the widely studied host-defense peptide magainin 2. Magainin 2 (S8A, G13A, G18A) is a designed variant that displays enhanced antibacterial activity relative to the natural peptide. The crystal structure of magainin 2 (S8A, G13A, G18A), obtained for the racemic form, features a dimerization mode that has previously been proposed to play a role in the antibacterial activity of magainin 2 and related peptides.
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Affiliation(s)
- Zvi Hayouka
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David E. Mortenson
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Dale F. Kreitler
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Bernard Weisblum
- Department of Medicine, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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14
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Orcel U, De Poli M, De Zotti M, Clayden J. The N-Terminal Nonapeptide of Cephaibols A and C: A Naturally Occurring Example of Mismatched Helical Screw-Sense Control. Chemistry 2013; 19:16357-65. [DOI: 10.1002/chem.201302648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 12/14/2022]
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15
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Shenkarev ZO, Paramonov AS, Lyukmanova EN, Gizatullina AK, Zhuravleva AV, Tagaev AA, Yakimenko ZA, Telezhinskaya IN, Kirpichnikov MP, Ovchinnikova TV, Arseniev AS. Peptaibol Antiamoebin I: Spatial Structure, Backbone Dynamics, Interaction with Bicelles and Lipid-Protein Nanodiscs, and Pore Formation in Context of Barrel-Stave Model. Chem Biodivers 2013; 10:838-63. [DOI: 10.1002/cbdv.201200421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Indexed: 11/12/2022]
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16
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Pradeille N, Tzouros M, Möhle K, Linden A, Heimgartner H. Total synthesis of the peptaibols hypomurocin A3 and hypomurocin A5, and their conformation analysis. Chem Biodivers 2013; 9:2528-58. [PMID: 23161633 DOI: 10.1002/cbdv.201200285] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Indexed: 11/06/2022]
Abstract
The total syntheses of hypomurocin A3 and hypomuricin A5 (HM A3 and HM A5, resp.) in solution phase are described. These syntheses have been successfully achieved by applying the 'azirine/oxazolone method' to introduce the two Aib-Pro units into the backbone of these undecapeptaibols in one step with methyl 2,2-dimethyl-2H-azirine-3-prolinate as the 'Aib-Pro synthon'. The coupling of Z-protected (Z=(benzyloxy)carbonyl) amino acids or peptide acids with amino acid tert-butyl esters and of peptide segments was carried out according to the TBTU (=O-(benzotriazol-1-yl)-N,N,N',N'-tetramethyluronium tetrafluoroborate) and HOBt (=1-hydroxybenzotriazole) protocol. Purification by reversed-phase HPLC gave the peptides in pure form. The products were characterized by optical rotation, NMR and IR spectroscopy, mass spectrometry, and elemental analysis. The crystal structures of HM A3 and of an octapeptide fragment of HM A5 could be obtained. An NMR analysis was also carried out with HM A3 and HM A5 to determine their conformations in solution. A global structural comparison between the three sequences of HM A1, HM A3, and HM A5 was performed, as well as the HPLC correlation of the natural HM A family and the synthetic samples.
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Affiliation(s)
- Nicolas Pradeille
- Organisch-chemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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17
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Gessmann R, Axford D, Evans G, Brückner H, Petratos K. The crystal structure of samarosporin I at atomic resolution. J Pept Sci 2012; 18:678-84. [PMID: 23019149 DOI: 10.1002/psc.2454] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 01/24/2023]
Abstract
The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15-residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀-helical and a minor fraction of α-helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10-Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16-residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed.
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De Zotti M, Biondi B, Crisma M, Hjørringgaard CU, Berg A, Brückner H, Toniolo C. Isovaline in naturally occurring peptides: A nondestructive methodology for configurational assignment. Biopolymers 2011; 98:36-49. [DOI: 10.1002/bip.21679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 05/03/2011] [Accepted: 05/10/2011] [Indexed: 11/08/2022]
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Dittrich B, Bond CS, Kalinowski R, Spackman MA, Jayatilaka D. Revised electrostatics from invariom refinement of the 18-residue peptaibol antibiotic trichotoxin A50E. CrystEngComm 2010. [DOI: 10.1039/c001072c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Andersson MA, Mikkola R, Raulio M, Kredics L, Maijala P, Salkinoja-Salonen MS. Acrebol, a novel toxic peptaibol produced by an Acremonium exuviarum indoor isolate. J Appl Microbiol 2009; 106:909-23. [PMID: 19191958 DOI: 10.1111/j.1365-2672.2008.04062.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To identify a toxin and its producer isolated from woody material in a building where the occupants experienced serious ill health symptoms. METHODS AND RESULTS Hyphal extracts of an indoor fungus, identified as the cycloheximide-tolerant species Acremonium exuviarum, inhibited motility of boar spermatozoa (EC(50) 5 +/- 2 microg of crude solids ml(-1)) and caused cytolysis of murine neuroblastoma cells (MNA) and feline fetal lung cells (FL). The responsible substances were purified and identified as two structurally similar, heat-stable, novel, toxic peptaibols, 1726 Da and 1740 Da, respectively, with amino acid sequences of Acetyl-Phe-Iva/Val-Gln-Aib-Ile-Thr-Leu-Aib-Pro-Aib-Gln-Pro-Aib-(X-X-X)-SerOH and Acetyl-Phe-Iva/Val-Gln-Aib-Ile-Thr-Leu-Val-Pro-Aib-Gln-Pro-Aib-(X-X-X)-SerOH. Purified acrebol inhibited motility of boar sperm, depleted ATP half-content in 1 day (EC(50) of 0.1 microg ml(-1), 60 nmol l(-1)) depolarised the mitochondria after 2 days, but did not affect the cellular content in NADH. This indicates mitochondrial toxicity. Plate-grown biomass of A. exuviarum BMB4 contained 0.1-1% (w/w) of acrebol, depending on the culture medium. CONCLUSIONS Acrebol paralysed the energy generation of mammalian cells suggesting that mitochondria were its target of action. SIGNIFICANCE AND IMPACT OF THE STUDY Acremonium exuviarum, as an indoor fungus, is potentially hazardous to health because of the toxic peptaibols that it produces.
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Affiliation(s)
- M A Andersson
- Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki, Finland
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Aravinda S, Shamala N, Balaram P. Aib Residues in Peptaibiotics and Synthetic Sequences: Analysis of Nonhelical Conformations. Chem Biodivers 2008; 5:1238-62. [PMID: 18649312 DOI: 10.1002/cbdv.200890112] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Shenkarev ZO, Paramonov AS, Nadezhdin KD, Bocharov EV, Kudelina IA, Skladnev DA, Tagaev AA, Yakimenko ZA, Ovchinnikova TV, Arseniev AS. Antiamoebin I in Methanol Solution: Rapid Exchange between Right-Handed and Left-Handed310-Helical Conformations. Chem Biodivers 2007; 4:1219-42. [PMID: 17589862 DOI: 10.1002/cbdv.200790106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antiamoebin I (Aam-I) is a membrane-active peptaibol antibiotic isolated from fungal species belonging to the genera Cephalosporium, Emericellopsis, Gliocladium, and Stilbella. Antiamoebin I has the amino acid sequence: Ac-Phe(1)-Aib-Aib-Aib-Iva-Gly-Leu-Aib(8)-Aib-Hyp-Gln-Iva-Hyp-Aib-Pro-Phl(16). By using the uniformly (13)C,(15)N-labeled sample of Aam-I, the set of conformationally dependent J couplings and (3h)J(NC) couplings through H-bonds were measured. Analysis of these data along with the data on magnetic nonequivalence of the (13)C(beta) nuclei (Deltadelta((13)C(beta))) in Aib and Iva residues allowed us to draw the univocal conclusion that the N-terminal part (Phe(1)-Gly(6)) of Aam-I in MeOH solution is in fast exchange between the right-handed and left-handed 3(10)-helical conformations, with an approximately equal population of both states. An additional conformational exchange process was found at the Aib(8) residue. The (15)N-NMR-relaxation and CD-spectroscopy measurements confirmed these findings. Molecular modeling and Monte Carlo simulations revealed that both exchange processes are correlated and coupled with significant hinge-bending motions around the Aib(8) residue. Our results explain relatively low activity of Aam-I with respect to other 15-amino acid residue peptaibols (for example, zervamicin) in functional and biological tests. The high dynamic 'propensity' possibly prevents both initial binding of the antiamoebin to the membrane and subsequent formation of stable ionic channels according to the barrel-stave mechanism.
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Affiliation(s)
- Zakhar O Shenkarev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Crisma M, Peggion C, Baldini C, Maclean EJ, Vedovato N, Rispoli G, Toniolo C. Crystal structure of a spin-labeled, channel-forming alamethicin analogue. Angew Chem Int Ed Engl 2007; 46:2047-50. [PMID: 17279588 DOI: 10.1002/anie.200604417] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Marco Crisma
- Istituto di Chimica Biomolecolare, CNR, Dipartimento di Scienze Chimiche, Università degli Studi di Padova via Marzolo 1, 35131 Padova, Italy.
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Crisma M, Peggion C, Baldini C, MacLean E, Vedovato N, Rispoli G, Toniolo C. Crystal Structure of a Spin-Labeled, Channel-Forming Alamethicin Analogue. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hoh F, Cerdan R, Kaas Q, Nishi Y, Chiche L, Kubo S, Chino N, Kobayashi Y, Dumas C, Aumelas A. High-resolution X-ray structure of the unexpectedly stable dimer of the [Lys(-2)-Arg(-1)-des(17-21)]endothelin-1 peptide. Biochemistry 2005; 43:15154-68. [PMID: 15568807 DOI: 10.1021/bi049098a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous structural studies on the [Lys((-2))-Arg((-1))]endothelin-1 peptide (KR-ET-1), 540-fold less potent than ET-1, strongly suggested the presence of an intramolecular Arg(-1)-Asp(8) (R(-1)-D(8)) salt bridge that was also observed in the shorter [Lys((-2))-Arg((-1))-des(17-21)]endothelin-1 derivative (KR-CSH-ET). In addition, for these two analogues, we have shown that the Lys-Arg dipeptide, which belongs to the prosequence, significantly improves the formation of the native disulfide bonds (>or=96% instead of approximately 70% for ET-1). In contrast to what was inferred from NMR data, molecular dynamics simulations suggested that such an intramolecular salt bridge would be unstable. The KR-CSH-ET peptide has now been crystallized at pH 5.0 and its high-resolution structure determined ab initio at 1.13 A using direct methods. Unexpectedly, KR-CSH-ET was shown to be a head-to-tail symmetric dimer, and the overall interface involves two intermolecular R(-1)-D(8) salt bridges, a two-stranded antiparallel beta-sheet, and hydrophobic contacts. Molecular dynamics simulations carried out on this dimer clearly showed that the two intermolecular salt bridges were in this case very stable. Sedimentation equilibrium experiments unambiguously confirmed that KR-ET-1 and KR-CSH-ET also exist as dimers in solution at pH 5.0. On the basis of the new dimeric structure, previous NMR data were reinterpreted. Structure calculations were performed using 484 intramolecular and 38 intermolecular NMR-derived constraints. The solution and the X-ray structures of the dimer are very similar (mean rmsd of 0.85 A). Since the KR dipeptide at the N-terminus of KR-CSH-ET is present in the prosequence, it can be hypothesized that similar intermolecular salt bridges could be involved in the in vivo formation of the native disulfide bonds of ET-1. Therefore, it appears to be likely that the prosequence does assist the ET-1 folding in a chaperone-like manner before successive cleavages that yield the bioactive ET-1 hormone.
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Affiliation(s)
- François Hoh
- Centre de Biochimie Structurale, UMR5048 CNRS-Université Montpellier I, UMR554 INSERM-Université Montpellier I, Faculté de Pharmacie, 15 avenue Charles Flahault, BP 14491, 34093 Montpellier-Cedex 5, France
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