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Asano A, Minami C, Matsuoka S, Kato T, Doi M. An Ornithine-Free Gramicidin S Analogue Using Norleucine, Cyclo(Val-Nle-Leu-D-Phe-Pro) 2, Forms Helically Aligned β-Sheets. Chem Pharm Bull (Tokyo) 2021; 69:1097-1103. [PMID: 34719592 DOI: 10.1248/cpb.c21-00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of an ornithine (Orn)-free Gramicidin S (GS) analogue, cyclo(Val-Nle-Leu-D-Phe-Pro)2 (NGS), was studied. Its circular dichroism (CD) spectrum showed that NGS has a structure similar to GS, though the value of [θ] indicated smaller β-turn and sheet populations. This is probably because the Nle side chain could not form intramolecular hydrogen bonds stabilizing the sheet structure. The chemical shift perturbation of αH and JNH-αH were similar in GS and NGS. Three independent NGS molecules formed intramolecular β-sheet structures in crystal. The turn structures of D-Phe-Pro moieties were classed as type II' β-turns, but one part was unclassed. The molecules were arranged in a twisting manner, which resulted in the formation of a helical sheet. Similar structural characteristics were observed previously in a Leu-type, Orn-free GS analogue and in GS trifluoroacetic acid salt.
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Affiliation(s)
- Akiko Asano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Chisato Minami
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Shiori Matsuoka
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
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Asano A, Matsuoka S, Minami C, Kato T, Doi M. [Leu 2]Gramicidin S preserves the structural properties of its parent peptide and forms helically aligned β-sheets. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:1336-1343. [PMID: 31589149 DOI: 10.1107/s2053229619011872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/28/2019] [Indexed: 11/11/2022]
Abstract
For crystallographic analysis, Leu was substituted for Orn in Gramicidin S (LGS) to suppress interactions with hydrophilic solvent molecules, which increased the flexibility of the Orn side chains, leading to disorder within the crystals. The asymmetric unit (C62H94N10O10·1.296C3H8O·1.403H2O) contains three LGS molecules (A, B and C) forming β-turn and intramolecular β-sheet structures. With the exception of one motif in molecule C, D-Phe-Pro turn motifs (Phe is phenylalanine and Pro is proline) were classed as type II' β-turns. The peptide backbones twist slightly to the right along the long axis of the molecule. The puckering of Pro is in a Cγ-endo or twisted Cγ-endo-Cβ-exo form. Flanking molecules are arranged such that the angles (A...B = 104°, B...C = 139° and C...A = 117°) form helical β-sheets. Solvent molecules interact with the peptide backbones supporting the β-sheets. The forms of the replacement Leu side chains are consistent with the e-form of the Orn side chain in GS analogues. No hydrophilic region composed of solvent molecules, such as that observed in Gramicidin S hydrochloride (GS·HCl) crystals, was found. The perturbation of αH chemical shifts and coupling constants of CONH showed that the structural properties of GS·HCl and LGS are similar to each other in solution. CD spectra also supported the structural similarity. With the sequence cyclo(-Val-Leu-Leu-D-Phe-Pro-)2 (Val is valine and Leu is leucine), LGS lacks the amphiphilicity and antimicrobial activity of parental Gramicidin S (GS). However, the structure of LGS reflects the structural characteristics of GS and no disordering inconvenient for structural analysis was found. Thus, LGS could be a novel scaffold useful for studying β-turn and sheet structures.
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Affiliation(s)
- Akiko Asano
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shiori Matsuoka
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Chisato Minami
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Takuma Kato
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Mitsinobu Doi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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ASANO A, DOI M. Crystal Structure of Gramicidin S Hydrochloride at 1.1 Å Resolution. X-RAY STRUCTURE ANALYSIS ONLINE 2019. [DOI: 10.2116/xraystruct.35.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Legrand B, Mathieu L, Lebrun A, Andriamanarivo S, Lisowski V, Masurier N, Zirah S, Kang YK, Martinez J, Maillard LT. Thiazole-Based γ-Building Blocks as Reverse-Turn Mimetic to Design a Gramicidin S Analogue: Conformational and Biological Evaluation. Chemistry 2014; 20:6713-20. [DOI: 10.1002/chem.201402190] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 01/09/2023]
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Loll PJ, Upton EC, Nahoum V, Economou NJ, Cocklin S. The high resolution structure of tyrocidine A reveals an amphipathic dimer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1199-207. [PMID: 24530898 DOI: 10.1016/j.bbamem.2014.01.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/20/2014] [Accepted: 01/27/2014] [Indexed: 11/28/2022]
Abstract
Tyrocidine A, one of the first antibiotics ever to be discovered, is a cyclic decapeptide that binds to membranes of target bacteria, disrupting their integrity. It is active against a broad spectrum of Gram-positive organisms, and has recently engendered interest as a potential scaffold for the development of new drugs to combat antibiotic-resistant pathogens. We present here the X-ray crystal structure of tyrocidine A at a resolution of 0.95Å. The structure reveals that tyrocidine forms an intimate and highly amphipathic homodimer made up of four beta strands that associate into a single, highly curved antiparallel beta sheet. We used surface plasmon resonance and potassium efflux assays to demonstrate that tyrocidine binds tightly to mimetics of bacterial membranes with an apparent dissociation constant (K(D)) of 10 μM, and efficiently permeabilizes bacterial cells at concentrations equal to and below the K(D). Using variant forms of tyrocidine in which the fluorescent probe p-cyano-phenylalanine had been inserted on either the polar or apolar face of the molecule, we performed fluorescence quenching experiments, using both water-soluble and membrane-embedded quenchers. The quenching results, together with the structure, strongly support a membrane association model in which the convex, apolar face of tyrocidine's beta sheet is oriented toward the membrane interior, while the concave, polar face is presented to the aqueous phase.
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Affiliation(s)
- Patrick J Loll
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Elizabeth C Upton
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Virginie Nahoum
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Nicoleta J Economou
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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Kawai M, Yamamura H, Tanaka R, Umemoto H, Ohmizo C, Higuchi S, Katsu T. Proline residue-modified polycationic analogs of gramicidin S with high antibacterial activity against both Gram-positive and Gram-negative bacteria and low hemolytic activity*. ACTA ACUST UNITED AC 2008; 65:98-104. [PMID: 15686540 DOI: 10.1111/j.1399-3011.2004.00204.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Novel polycationic analogs of the cyclic decapeptide antibiotic, gramicidin S, possessing NH(2), D/L-Phe-NH or L-Lys-NH groups at the 4alpha- or 4beta-positions of the L-Pro residues, were synthesized. While L-Pro(4alpha/beta-NH(2))-containing analogs exhibited much weaker antibacterial activity, the D/L-Phe and L-Lys-substituted analogs exhibited higher antibacterial activity against Gram-negative bacteria than the parent gramicidin S. All of these additional amino group-containing analogs showed substantially reduced toxicity against human blood cells.
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Affiliation(s)
- M Kawai
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan.
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Oku H, Yamada K, Katakai R. Conformational change from antiparallel beta-sheet to alpha-helix in a series of depsipeptide, -(Leu-Leu-Lac)(n)-: syntheses, spectroscopic studies, and crystal structures of Boc-Leu-Lac-OEt and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2). Biopolymers 2008; 89:270-83. [PMID: 18067154 DOI: 10.1002/bip.20904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The depsipeptides Boc-Leu-Lac-OEt (1) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2) (2 and 3, respectively) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized and studied by crystallographic, CD spectroscopic, and ESI-MS analyses. In the packing cells, those three compounds adopt beta-strand conformations. Each molecule is linked into a dimer (1) or an infinite assembly (2 and 3) by tight hydrogen bonds of the type NH...O==C. Interestingly, the hexamer, 3 shows the first example of antiparallel pleated beta-sheet crystal structure for a depsipeptide molecule. In the packing cells, especially for 3, the ester groups O--C==O are perpendicularly oriented to the amide groups NH--C==O and beta-sheet planes to avoid the interaction between --O--(ester) and O==C. Therefore, when the chain length become longer, the O...O==C repulsion interaction works as a beta-sheet breaker and hence promotes an alpha-helical structure as observed for Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (4) (Oku et al. Biopolymers 2004, 75, 242-254) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 4-6) (5-7) (Katakai et al., Biopolymers 1996, 38, 285-290), in which the O...O==C repulsion does not cause significant structural changes in alpha-helical main chains. Therefore from the structural and spectroscopic analyses, we have found governing factors for the specificity in the beta-sheet and alpha-helix decision in this series of depsipeptides, -(Leu-Leu-Lac)(n)-.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Gunma, Japan.
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Doi M, Ichimiya Y, Asano A. H– D-Phe– D-Pro–Gly methyl ester hydrochloride monohydrate. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o704. [PMID: 21202095 PMCID: PMC2961031 DOI: 10.1107/s160053680800528x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 02/25/2008] [Indexed: 12/04/2022]
Abstract
The conformation of the title tripeptide methyl ester hydrochloride monohydrate, 1-[2-(methoxycarbonylmethylaminocarbonyl)pyrrolidin-1-ylcarbonyl]-2-phenylethanaminium chloride monohydrate, C17H24N3O4+·Cl−·H2O, is extended, but the structure cannot be classified as any typical secondary structure. Interactions through water molecules and chloride ions were formed, in addition to peptide–peptide hydrogen bonds, stabilizing the molecular packing. In comparison with the previous β-turn structure of the Phe–d-Pro–Gly analogue [Doi, Ichimiya & Asano (2007 ▶). Acta Cryst. E63, o4691], it was suggested that the difference between the chiralities of Phe and Pro residues of the title compound is important to induce the β-turn structure.
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Xiao J, Weisblum B, Wipf P. Trisubstituted (E)-alkene dipeptide isosteres as beta-turn promoters in the gramicidin S cyclodecapeptide scaffold. Org Lett 2007; 8:4731-4. [PMID: 17020289 PMCID: PMC2631548 DOI: 10.1021/ol0617704] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A concise synthesis of a gramicidin S analogue with trisubstituted (E)-alkene dipeptide isostere (TEADI) replacements at both d-Phe-Pro positions was realized. Conformational analysis demonstrated that TEADIs can serve as type II beta-turn promoters in a cyclic scaffold and successfully mimic a proline residue.
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Affiliation(s)
- Jingbo Xiao
- Department of Chemistry and Center for Chemical Methodologies & Library, Development, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Bernard Weisblum
- Pharmacology Department, University of Wisconsin Medical School, 1300 University Avenue, Madison, Wisconsin 53706
| | - Peter Wipf
- Department of Chemistry and Center for Chemical Methodologies & Library, Development, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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Smith AW, Tokmakoff A. Amide I two-dimensional infrared spectroscopy of beta-hairpin peptides. J Chem Phys 2007; 126:045109. [PMID: 17286519 DOI: 10.1063/1.2428300] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this report, spectral simulations and isotope labeling are used to describe the two-dimensional IR spectroscopy of beta-hairpin peptides in the amide I spectral region. 2D IR spectra of Gramicidin S, PG12, Trpzip2 (TZ2), and TZ2-T3(*)T10(*), a dual (13)C(') isotope label, are qualitatively described by a model based on the widely used local mode amide I Hamiltonian. The authors' model includes methods for calculating site energies for individual amide oscillators on the basis of hydrogen bonding, nearest neighbor and long-range coupling between sites, and disorder in the site energy. The dependence of the spectral features on the peptide backbone structure is described using disorder-averaged eigenstates, which are visualized by mapping back onto the local amide I sites. beta-hairpin IR spectra are dominated by delocalized vibrations that vary by the phase of adjacent oscillators parallel and perpendicular to the strands. The dominant nu(perpendicular) band is sensitive to the length of the hairpin and the amount of twisting in the backbone structure, while the nu(parallel) band is composed of several low symmetry modes that delocalize along the strands. The spectra of TZ2-T3(*)T10(*) are used to compare coupling models, from which we conclude that transition charge coupling is superior to transition dipole coupling for amide groups directly hydrogen bound across the beta strands. The 2D IR spectra of TZ2-T3(*)T10(*) are used to resolve the redshifted amide I band and extract the site energy of the labeled groups. This allows the authors to compare several methods for calculating the site energies used in excitonic treatments of the amide I band. Gramicidin S is studied in dimethyl sulfoxide to test the role of solvent on the spectral simulations.
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Affiliation(s)
- Adam W Smith
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Zuo R, Wood TK. Inhibiting mild steel corrosion from sulfate-reducing and iron-oxidizing bacteria using gramicidin-S-producing biofilms. Appl Microbiol Biotechnol 2004; 65:747-53. [PMID: 15278311 DOI: 10.1007/s00253-004-1651-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 04/08/2004] [Accepted: 04/23/2004] [Indexed: 11/29/2022]
Abstract
A gramicidin-S-producing Bacillus brevis 18-3 biofilm was shown to reduce corrosion rates of mild steel by inhibiting both the sulfate-reducing bacterium Desulfosporosinus orientis and the iron-oxidizing bacterium Leptothrix discophora SP-6. When L. discophora SP-6 was introduced along with D. orientis to a non-antimicrobial-producing biofilm control, Paenibacillus polymyxa ATCC 10401, a corrosive synergy was created and mild steel coupons underwent more severe corrosion than when only D. orientis was present, showing a 2.3-fold increase via electrochemical impedance spectroscopy (EIS) and a 1.8-fold difference via mass-loss measurements. However, when a gramicidin-S-producing, protective B. brevis 18-3 biofilm was established on mild steel, the metal coupons were protected against the simultaneous attack of D. orientis and L. discophora SP-6. EIS data showed that the protective B. brevis 18-3 biofilm decreased the corrosion rate about 20-fold compared with the non-gramicidin-producing P. polymyxa ATCC 10401 biofilm control. The mass loss for the protected mild steel coupons was also significantly lower than that for the unprotected ones (4-fold decrease). Scanning electron microscope images corroborated the corrosion inhibition by the gramicidin-S-producing B. brevis biofilm on mild steel by showing that the metal surface remained untarnished, i.e., the polishing grooves were still visible after exposure to the simultaneous attack of the sulfate-reducing bacterium and the iron-oxidizing bacterium.
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Affiliation(s)
- Rongjun Zuo
- Department of Chemical Engineering, University of Connecticut, Storrs, CT 06269-3222, USA
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Bach H, Gutnick D. Chapter 9 Potential applications of bioemulsifiers in the oil industry. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-2991(04)80150-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Abstract
Although most antibiotics do not need metal ions for their biological activities, there are a number of antibiotics that require metal ions to function properly, such as bleomycin (BLM), streptonigrin (SN), and bacitracin. The coordinated metal ions in these antibiotics play an important role in maintaining proper structure and/or function of these antibiotics. Removal of the metal ions from these antibiotics can cause changes in structure and/or function of these antibiotics. Similar to the case of "metalloproteins," these antibiotics are dubbed "metalloantibiotics" which are the title subjects of this review. Metalloantibiotics can interact with several different kinds of biomolecules, including DNA, RNA, proteins, receptors, and lipids, rendering their unique and specific bioactivities. In addition to the microbial-originated metalloantibiotics, many metalloantibiotic derivatives and metal complexes of synthetic ligands also show antibacterial, antiviral, and anti-neoplastic activities which are also briefly discussed to provide a broad sense of the term "metalloantibiotics."
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Affiliation(s)
- Li-June Ming
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, Tampa, Florida 33620-5250, USA.
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