A practical synthesis of gramicidin s and sugar amino Acid containing analogues

A practical gram-scale and high-yielding synthesis of the antimicrobial peptide gramicidin S is presented. An Fmoc-based solid-phase peptide synthesis protocol is employed for the generation of the linear decapeptide precursor, which is cyclized in solution to afford the target compound. The versatility of our method is demonstrated by the construction of eight gramicidin S analogues (15a-h) having nonproteinogenic sugar amino acid residues (4-7) incorporated in the turn regions.     

Synthesis of gramicidin S and its analogues via an on-resin macrolactamization assisted by a predisposed conformation of the linear precursors

A simple and efficient preparation of gramicidin S and its analogues is described. It involves solid-phase peptide synthesis and on-resin macrolactamization without side chain protection, affording cyclic products in high yield and high purity. The high specificity of the cyclization reaction was shown to originate in the formation of a pre-organized conformation of the linear biosynthetic precursor of gramicidin S. This facile method will provide convenient access to the analogues of the natural product for functional optimization to counter microbial resistance.     

On the photoionization of large molecules

There is no apparent limit to the size of a molecule for which photoionization can occur. It is argued that it is difficult to obtain useful photoionization mass spectra of peptides (above ～ 2000 u), proteins, and oligonucleotides, because of the high internal energy of these polar molecules as a result of the desorption event and because vibrationally excited radical cations readily fragment. Evidence to support this hypothesis is presented from the 118-nm single-photon ionization (SPI) mass spectra of the cyclic decapeptide gramicidin S and of fullerenes, from null SPI results with the linear peptides substance P and gramicidin D and oligonucleotides, and from a variety of data found in the literature. The literature data include mass spectra from jet-cooled peptides, perfluorinated polyethers, collisional ionization of small neutral peptides, and the ultraviolet photoelectron spectroscopy of polymeric solids.     

The iterative gramicidin s thioesterase catalyzes peptide ligation and cyclization

Here, we present a comprehensive in vitro characterization of the excised iterative, bimodular PCP-TE of the gramicidin S synthetase GrsB, which is able to act both as a ligation and a cyclization catalyst. Using the native pentapeptidyl-thioester substrates, GrsB PCP-TE catalyzes the dimerization and subsequent formation of the decapeptide lactam gramicidin S. Interestingly, the detection of linear decapeptidyl-SNAC as an enzyme-dependent intermediate supports the iterative mechanism in vivo, in which two pentapeptides, one bound as an ester to the active site serine of the TE domain and the second bound as a thioester to the adjacent pan-PCP, are ligated to a decapeptidyl-pan-PCP that subsequently transferred to the adjacent TE domain and cyclized. Moreover, GrsB PCP-TE can handle different substrates length, leading not only to dimerization, but also to trimerization and the formation of different ring sizes.     

Solvent-free thermocyclization of the unactivated linear gramicidin S precursor and analogues

A convenient thermocyclization of the linear gramicidin S precursor and its analogues is demonstrated. With the preorganized β-sheet conformation, the unactivated linear precursors can cyclize into the corresponding head-to-tail cyclic products in high yield after being heated under solvent-free conditions.     

Facile solid-phase synthesis of cyclic decapeptide antibiotic streptocidins A-D

Total synthesis of decapeptide antibiotics streptocidins A-D from Streptomyces sp. Tü 6071 was accomplished for the first time by solid-phase peptide synthesis followed by traceless cyclization of the activated linear precursors, without protection of nucleophilic side chain. Synthetic products were equally active as the natural products isolated from the bacterial source and found to possess similar bacterial selectivity as other members in the amphipathic antimicrobial cyclic decapeptide family.     

Optimized protocol for synthesis of cyclic gramicidin S: starting amino acid is key to high yield

[structures: see text] A simple and highly efficient Fmoc solid-phase protocol for synthesizing the antimicrobial decapeptide gramicidin S and various labeled analogues is presented. When preparing the linear precursor peptides (1a-e), a systematic permutation of the starting amino acid within the cyclic sequence gave different yields between 51% and 93%. Also the subsequent step of cyclization gave widely diverging yields between 26% and 74%, depending again on the starting amino acid. The ease of cyclization was found to correlate with the tendency of the respective linear precursor peptide to assume a preorganized conformation, as observed by circular dichroism. The overall yield is thus critically dependent on the starting amino acid and can be raised from 20% to 70% using (D)Phe. The choice of coupling agent and its counterion was found to play only a marginal role. Irrespective of being able to assume a preorganized conformation, none of the linear precursor peptides exhibited any antimicrobial or hemolytic activity. Using the optimized protocol, which involves only simple Fmoc-couplings and requires no intermittent purification steps, several gramicidin S analogues (3-8) containing 19F-labeled phenylglycine derivatives and/or 15N-labeled amino acids were synthesized for solid-state NMR structure analysis.     

Synthesis and Controlled Polymerisation of a Novel Gramicidin S Analogue

Summary: The controlled polymerisation of a bulky, peptide‐based monomer was investigated. The cyclic β‐sheet forming decapeptide gramicidin S was modified with a methacrylate handle and subsequently polymerised via atom transfer radical polymerisation (ATRP), to yield a well‐defined gramicidin‐S‐containing polymer. The secondary structure of the peptide moiety was retained within the resulting polymer, as indicated by IR spectroscopy. This is the first example of the use of ATRP to create a synthetic polymer with a cyclic peptide as a side chain.

The gramicidin S based monomers synthesised here were then polymerised by ATRP.     

Inhibiting and Reversing Amyloid‐β Peptide (1–40) Fibril Formation with Gramicidin S and Engineered Analogues

In Alzheimer’s disease, amyloid‐β (Aβ) peptides aggregate into extracellular fibrillar deposits. Although these deposits may not be the prime cause of the neurodegeneration that characterizes this disease, inhibition or dissolution of amyloid fibril formation by Aβ peptides is likely to affect its development. ThT fluorescence measurements and AFM images showed that the natural antibiotic gramicidin S significantly inhibited Aβ amyloid formation in vitro and could dissolve amyloids that had formed in the absence of the antibiotic. In silico docking suggested that gramicidin S, a cyclic decapeptide that adopts a β‐sheet conformation, binds to the Aβ peptide hairpin‐stacked fibril through β‐sheet interactions. This may explain why gramicidin S reduces fibril formation. Analogues of gramicidin S were also tested. An analogue with a potency that was four‐times higher than that of the natural product was identified.     

Extra amino group-containing gramicidin S analogs possessing outer membrane-permeabilizing activity

Novel (2S,4R)- and (2S,4S)-4-aminoproline residue-containing analogs of the cyclic decapeptide antibiotic gramicidin S were synthesized, which exhibited marked permeabilizing activity on the outer membrane of gram-negative bacteria.     

Facile synthesis of Gramicidin S via cyclication of a linear pentapeptide

Azide and N-hydroxysuccinimide ester of five pentapeptides related to gramicidin S (cyclic decapeptide) were cyclized to determine the ratio of dimer to monomer in the cyclization product, the pentapeptide derivative with D-Phe as C-terminus giving the dimer in good yield.     

Synthesis of tyrocidine A and its analogues by spontaneous cyclization in aqueous solution

[reaction: see text] Head-to-tail cyclization of peptides is a multistep process involving tedious C-terminal activation and side chain protection. Here we report a facile, quantitative cyclization method in aqueous ammonia solution for the total syntheses of the cyclic decapeptide antibiotic Tyrocidine A and its analogues from their fully deprotected linear thioester precursors on a solid support. This novel aqueous method is conformation-dependent and may be applicable to syntheses of other natural cyclic peptides.     

Bead diffusion assay for discovering antimicrobial cyclic peptides

A combinatorial library of 15,536 cyclic decapeptide analogues of tyrocidine A and gramicidin S was prepared on photocleavable TentaGel beads. The beads were photolyzed without solvent, and spread onto an agar plate inoculated with bacterial lawn. Clear zones were formed around beads carrying antimicrobially active peptides such as E18 c(kVOrnLfThiYOrnLq), which inhibited growth of B. subtilis and selected MRSA strains.     

Ion mobility-mass spectrometry applied to cyclic peptide analysis: Conformational preferences of gramicidin S and linear analogs in the gas phase

In this paper, we present an investigation of the gas-phase structural differences between cyclic and linear peptide ions by matrix-assisted laser desorption ionization-ion mobility-mass spectrometry. Specifically, data is shown for gramicidin S (cyclo-VOLFPVOLFP where phenylalanines are D rather than L-type amino acids and the O designates the non-standard amino acid ornithine) and five linear gramicidin S analogues. Results are interpreted as evidence for a beta-sheet (or beta-hairpin) conformational preference in both linear-protonated and sodiated-cyclic gramicidin S gas-phase peptides, and a preference for the protonated-cyclic peptide to adopt a collapsed, random coil-type conformation. A comparison with solution-phase circular dichroism measurements is performed, and structures similar to those observed in the gas phase appear to be favored in low-dielectric solvents such as 2,2,2-triflouroethanol. The utility of ion mobility-mass spectrometry (IM-MS) as a means of rapidly distinguishing between linear and cyclic peptide forms in also discussed.     

Stereochemistry of protected ornithine side chains of gramicidin S derivatives: X-ray crystal structure of the bis-Boc-tetra-N-methyl derivative of gramicidin S

An X-ray crystallographic analysis of the bis-Ndelta-Boc-tetra-Nalpha-methyl derivative of gramicidin S, cyclo(-Val-MeOrn(Boc)-Leu-d-MePhe-Pro-)2, was undertaken successfully (R-factor = 0.088). As expected, the main chain adopts an antiparallel pleated beta-sheet conformation, but the pleated sheet is slightly twisted, and the sense of twisting is opposite to that found in the reported crystal structures of the gramicidin S-urea complex and the bis-Ndelta-(trichloroacetyl) and bis-Ndelta-(m-bromobenzoyl) derivatives of gramicidin S. In agreement with the observed resistance toward N-methylation, the urethane NH groups of the protected Orn side chains are hydrogen bonded to the carbonyl groups of the d-Phe residues. However, the side-chain-main-chain hydrogen bonding is in the i --> i - 3 mode, although hydrogen bonding in the i --> i + 2 mode was deduced from a 1H NMR study of protected gramicidin S derivatives and was actually found in the crystal structures of the diacylated gramicidin S.     

Conformational Structures of a Decapeptide Validated by First Principles Calculations and Cold Ion Spectroscopy

Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculated from first‐ principles and measured in a wide spectral range using infrared (IR)–UV double resonance cold ion spectroscopy. All the 522 vibrational modes of each conformer were calculated quantum mechanically and compared with the experiment without any recourse to an empirical scaling. The study demonstrates that first‐principles calculations, when accounting for vibrational anharmonicity, can reproduce high‐resolution experimental spectra well enough for validating structures of molecules as large as of 200 atoms. The validated accurate structures of the peptide may serve as templates for in silico drug design and absolute calibration of ion mobility measurements.     

Wavelength-selective fluorescence in ion channels formed by gramicidin A in membranes

Gramicidins are linear peptides that form ion channels that are specific for monovalent cations in membranes. The tryptophan residues in the gramicidin channel play a crucial role in the organization and function of the channel. The natural mixture of gramicidins, denoted as gramicidin A’, consists of mostly gramicidin A, but also contains gramicidins B, C and D as minor components. We have previously shown that the tryptophan residues in ion channels formed by the naturally occurring peptide, gramicidin A’, display wavelength-dependent fluorescence characteristics due to the motionally restricted environment in which they are localized. In order to check the influence of ground-state heterogeneity in the observed wavelength-selective fluorescence of gramicidin A’ in membranes, we performed similar experiments with pure gramicidin A in model membranes. Our results show that the observed wavelength-selective fluorescence characteristics of naturally occurring gramicidin A’ are not due to ground-state heterogeneity.     

Gramicidin A interaction at a dioleoyl phosphatidylcholine monolayer on a mercury drop electrode

A biosensor where the sensing surface is a fluid dioleyl phosphatidylcholine monolayer (DOPC) deposited on a mercury drop was used. The lipid monolayer was held in 0.1 M NaCl and a concentration of gramicidin A in the range 0-12 nM was used. Electrochemical impedance spectroscopy in the frequency range 0.1-65 kHz was employed to investigate how the defect-free monolayer responds to interactions of gramicidin A in solution.The data was analyzed both with multivariate data analysis and classical electrochemical methods. The principal component analysis of the resulting impedance spectra gave a linear dependence on the concentration of gramicidin A. An increasing permittivity was observed in the low-frequency regime with increasing concentration of gramicidin A in solution.     

Conformation of gramicidin-A in CTAB micellar media

Gramicidin A (gA) is a linear pentadecapeptide, which exhibits various conformations depending on the environment. The conformational behavior of gA in spherical and rod-shaped cationic micelles formed by cetyltrimethylammonium bromide (CTAB) surfactant has been studied using circular dichroism (CD) and fluorescence spectroscopy, and a probable structure of gramicidin A in CTAB media has been proposed. A CD study shows that gramicidin A assumes beta(6.3) helical structure in cationic spherical as well as rod-shaped CTAB micellar media. Modeling studies show the flexibility of the side chain conformation particularly in tryptophan-9. Study of intrinsic fluorescence of tryptophans in gramicidin A indicates three distinct environments for the four-tryptophan residues in CTAB media.     

Gramicidin S Derivatives Containing cis‐ and trans‐Morpholine Amino Acids (MAAs) as Turn Mimetics

The cyclic decapeptide gramicidin S (GS) was used as a model for the evaluation of four turn mimetics. For this purpose, one of the D ‐Phe‐Pro two‐residue turn motifs in the rigid cyclic β‐hairpin structure of GS was replaced with morpholine amino acids (MAA 2 – 5 ), differing in stereochemistry and length of the side‐chain. The conformational properties of the thus obtained GS analogues ( 6 – 9 ) was assessed by using NMR spectroscopy and X‐ray crystallography, and correlated with their biological properties (antimicrobial and hemolytic activity). We show that compound 8 , containing the dipeptide isostere trans‐MAA 4 , has an apparent high structural resemblance with GS and that its antibacterial activity against a panel of Gram positive and ‐negative bacterial strains is better than the derivatives 6 , 7 and 9 .