Methods for the comprehensive structural elucidation of constitution and stereochemistry of lipopeptides

Characterization and Production of a Biosurfactant Viscosin from Pseudomonas sp. HN11 and its Application on Enhanced oil Recovery During oily Sludge Cleaning

Biosurfactants are renewable resources with versatile applications on environmental bioremediation and industrial processes. Pseudomonas species are one of the promising biosurfactant producers. However, besides rhamnolipids, little is known about Pseudomonas-derived biosurfactants on solubilization of polycyclic aromatic hydrocarbons (PAHs) and oily sludge treatment. In this study, Pseudomonas sp. HN11-derived biosurfactant was purified by chromatographic methods and was characterized as viscosin via bioinformatic analysis, spectrometric and spectroscopic analyses, Marfey's method and (C-H)α NMR fingerprint matching approach. Viscosin is a potent biosurfactant with critical micelle concentration of 5.79 mg/L and is stable under various stresses. Moreover, viscosin was produced at 0.42 g/L at 48 h of liquid fermentation. Further data have shown that emulsifying agent viscosin is capable of promoting the solubilization of PAHs and displays enhanced oil recovery during oily sludge treatment. More specifically, viscosin has shown significantly enhanced solubilization on fluoranthene compared with control (0.04 mg/L), 2.21 mg/L and 1.27 mg/L fluoranthene was recovered from 100 mg/L and 200 mg/L viscosin treatment, respectively. However, only 200 mg/L viscosin has significantly enhanced the solubilization of phenanthrene (0.75 mg/L) and benzo[a]pyrene (0.51 mg/L) compared to each control (0.23 mg/L for phenanthrene and 0.09 mg/L for benzo[a]pyrene). Viscosin treatment of oily sludge (recovering of 0.58 g oil) has shown a significant oil recovery compared to that of control (recovering of 0.42 g oil). This study shows the great potential of viscosin-type biosurfactant on oily sludge treatment.

Automated sample preparation with 6-Aminoquinolyl-N-hydroxysuccinimidyl carbamate and iodoacetamide derivatization reagents for enantioselective liquid chromatography tandem mass spectrometry amino acid analysis

Enantioselective amino acid analysis is gaining increasing importance in pharmaceutical, biomedical and food sciences. While there are many methods available for enantiomer separation of amino acids, the simultaneous analysis of all chiral proteinogenic amino acids by a single method with one column and a single condition is still challenging. Herein, we report an enantioselective high-performance liquid chromatography-tandem mass spectrometry (LC-MS) assay using Chiralpak QN-AX as chiral column. With 6-aminoquinolyl-N-hydrosysuccinimidyl carbamate (AQC) as derivatization reagent, efficient enantioselective separation of D- and L-amino acids using HPLC has become possible. Thiol-containing amino acids like Cys are alkylated prior to AQC-labelling. A protocol for automated sample preparation including both derivatization step and calibrator preparation is presented. For compensating matrix effects, u-13C15N-labelled internal standards (IS) were employed. The method was validated and applied to the enantioselective analysis of amino acids in a bacterial fermentation broth.

Comprehensive reversed-phase×chiral two-dimensional liquid chromatography coupled to quadrupole-time-of-flight tandem mass spectrometry with post-first dimension flow splitting for untargeted enantioselective amino acid analysis

This work describes a comprehensive achiral × chiral two-dimensional liquid chromatography separation for enantioselective amino acid analysis coupled to electrospray ionization-tandem mass spectrometry detection using data-independent acquisition. Flow splitting after the first and second dimension separation was utilized for volumetric flow reduction and for enabling a multi-detector approach (with ultraviolet, fluorescence, charged aerosol, and MS detection), respectively. Derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate provided a chromophore, a fluorophore, and an efficient mass tag for efficient ionization in positive electrospray ionization-mass spectrometry. Chiral columns often have limitations in terms of their chemoselectivity, which may be a problem when complex sample mixtures with structurally related compounds need to be separated. It can be alleviated by a reversed-phase×chiral two-dimensional-liquid chromatography setup, in which the first dimension provides the chemoselectivity and a chiral tandem column constituted of quinine-carbamate derived weak anion-exchanger and zwitterionic ion-exchanger in the second dimension separation of D- and L-amino acid enantiomers. The method was used to control the stereointegrity of the therapeutic peptide octreotide. After hydrolysis, all amino acid constituents were detected with the correct configuration and composition. Some options for flow splitting and integration of destructive detectors in the first dimension separation are outlined.

An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides

Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus l-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly, however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. Using Pseudomonas CLiPs from the Bananamide, Orfamide, and Xantholysin groups as test cases, we demonstrate and validate that the combined 1H and 13C Nuclear Magnetic Resonance (NMR) chemical shifts of CLiPs constitute a spectral fingerprint that is sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single d/l configuration. Rapid screening, involving simple matching of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, its spectral fingerprint allows to quickly verify whether a newly isolated CLiP is novel or already present in the reference collection. We show NMR fingerprinting leads to a simple approach for early on dereplication which should become more effective as more fingerprints are collected. To benefit research involving CLiPs, we have made a publicly available data repository accompanied by a 'knowledge base' at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. IMPORTANCE Pseudomonas CLiPs are ubiquitous specialized metabolites, impacting the producer's lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as a premise to their development is hindered because full structural characterization including stereochemical information requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology based on matching NMR spectral fingerprints of newly isolated CLiPs to natural and synthetic reference compounds with (un)known stereochemistry. In addition, NMR fingerprinting is shown to provide a suitable basis for structural dereplication. A publicly available reference compound repository promises to facilitate participation of the lipopeptide research community in structural assessment and dereplication of newly isolated CLiPs, which should also support further developments in genome mining for novel CLiPs.

Chiral separation of dipeptides on Cinchona-based zwitterionic chiral stationary phases under buffer-free reversed-phase conditions

Chiral zwitterion ion exchangers represent efficient chiral stationary phases for stereoselective resolution of various analytes including chiral acids, bases, and zwitterions. In this contribution, we have focused on utilization of chiral zwitterionic sorbents, denoted as ZWIX (+A) and ZWIX (-A). These are analogical chiral systems to commercially available columns, Chiralpak ZWIX (+) and Chiralpak ZWIX (-), which are usually operated with buffered mobile phases. In this contribution, we have studied the enantiorecognition power of the ZWIX (+A) and ZWIX (-A) columns on a series of dipeptides operated under buffer-free reversed-phase conditions. Retention characteristics of zwitterionic dipeptides are discussed using an electrostatically driven adsorption model, which provides a good fit with both monotonous and U-shaped curves.

Stress proteins, nonribosomal peptide synthetases, and polyketide synthases regulate carbon sources-mediated bio-demulsifying mechanisms of nitrate-reducing bacterium Gordonia sp. TD-4

Carbon sources have been reported to determine the bio-demulsifying performance and mechanisms. However, the genetic regulation of carbon sources-mediated bio-demulsification remains unclear. Here, the effects of β-oxidation, stress response, and nitrate metabolism on the demulsification of alkaline-surfactant-polymer flooding produced water by Gordonia sp. TD-4 were investigated. The results showed that competitive adsorption-derived demulsification was mediated by oil-soluble carbon sources (paraffin). Surface-active lipopeptides responsible for competitive adsorption-derived demulsification could be biosynthesized by the nonribosomal peptide synthetases and polyketide synthases using oil-soluble carbon sources. Bio-flocculation-derived demulsification was mediated by water-soluble carbon sources. Water-soluble carbon sources (sodium acetate and glucose) mediated the process of the dissimilatory reduction of nitrate to ammonia, which resulted in the variable accumulation of nitrite. The accumulated nitrite (>180 mg-N/L) stimulated stress response and induced the upregulation of chaperone-associated genes. The upregulation of chaperonins increased the cell surface hydrophobicity and the cation-dependent bio-flocculating performance, which were responsible for bio-flocculation-derived demulsification. The β-oxidation of fatty acids significantly affected both competitive adsorption-derived demulsification and bio-flocculation-derived demulsification. This study illustrates the synergistic effects of nitrogen sources and carbon sources on the regulation of bio-demulsifying mechanisms of TD-4 and identifies two key functional gene modules responsible for the regulation of bio-demulsifying mechanisms.

Enantioselective multiple heart cutting online two-dimensional liquid chromatography-mass spectrometry of all proteinogenic amino acids with second dimension chiral separations in one-minute time scales on a chiral tandem column

In this work, we present a unique, robust and fully automated analytical platform technology for the enantioselective amino acid analysis using a multiple heart cutting RPLC-enantio/stereoselective HPLC-ESI-QTOF-MS method. This 2D-LC method allows the full enantioselective separation of 20 proteinogenic AAs plus 5 isobaric analogues, namely allo-Threonine (aThr), homoserine (Hse), allo-isoleucine (aIle), tert-Leucine (Tle) and Norleucine (Nle), after pre-column derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC; AccQ). This N-terminal AA-derivatization method introduces on the one hand beneficial chromatographic properties for ¹D RP-LC (stronger retention) and ²D chiral separation (better chiral recognition), and on the other hand favorable detection properties with its chromophoric, fluorophoric, and easily ionizable quinoline mass tag. The entire separation occurs within a total 2DLC run time of 45 min, which includes the ¹D-RP run and the 68 s ²D chiral separations of 30 heart-cuts (from the ¹D-RP-run) on a chiral quinine carbamate (core-shell QNAX/fully porous ZWIX) tandem column. This relatively short overall run time was only possible by utilizing the highly efficient "smart peak parking" algorithm for the heart cuts and the resulting optimized analysis order thereof. ¹D retention time precisions of <0.21% RSD were a requirement for the time-based sampling mode and finally led to a robust, fully automated enantioselective amino acid analysis platform. This achiral-chiral 2DLC method was applied for the amino acid stereoconfiguration assignment of three peptides (aureobasidin A, a lipopeptide research sample, and octreotide) using an L-[u-¹³C¹⁵N] labelled internal AA standard mix spiked to each sample. The isotopically labelled L-AA standard allowed an easy and straightforward identification and configuration assignment, as well as the relative quantification of amino acids within the investigated peptides, allowing the direct determination of the number of respective amino acids and their chirality within a peptide.

Direct enantioselective gradient reversed-phase ultra-high performance liquid chromatography tandem mass spectrometry method for 3-hydroxy alkanoic acids in lipopeptides on an immobilized 1.6 μm amylose-based chiral stationary phase

3-Hydroxy fatty acids are important chiral building blocks of lipopeptides and metabolic intermediates of fatty acid oxidation, respectively. The analysis of the stereochemistry of such biomolecules has significant practical impact to elucidate and assign the enzymatic specificity of the biosynthesis machinery. In this work, a new mass spectrometry compatible direct chiral ultra high performance liquid chromatography separation method for 3-hydroxy fatty acids without derivatization is presented. The application of amylose tris(3,5-dimethylphenyl carbamate) based polysaccharide chiral stationary phase immobilized on 1.6 μm silica particles (CHIRALPAK IA-U) allows the enantioseparation of 3-hydroxy fatty acids under generic electrospray ionization mass spectrometry friendly reversed phase gradient elution conditions. Adequate separation factors were achieved with both acetonitrile and methanol as organic modifiers, covering hydrocarbon chain lengths between C₆ and C₁₄ . Elution orders were derived from rhamnolipid (R-95) of which enantiomerically pure or enriched (R)-3-hydroxy fatty acids were recovered after ester hydrolysis. The S-configured acids consistently eluted before the respective R-enantiomers. The method was successfully applied for the elucidation of the absolute configuration of 3-hydroxy fatty acids originating from a novel lipopeptide with unknown structure. The work furthermore demonstrates that gradient elution is a viable option also in enantioselective (ultra)high performance liquid chromatography, even for analytes with modest separation factors, although less commonly exploited.

Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining

Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.

Introducing Multifactorial Peak Crossover in Analytical and Preparative Chromatography via Computer-Assisted Modeling

Modern pharmaceutical processes can often lead to multicomponent mixtures of closely related species that are difficult to resolve under chromatographic conditions, and even worse in preparative scale settings. Despite recent improvements in column technology and instrumentation, there remains an urgent need for creating innovative approaches that address challenging coelutions of critical pair and poor chromatographic productivity of purification methods. Herein, we overcome these challenges by introducing a simple and practical technique named multifactorial peak crossover (MPC) via computer-assisted chromatographic modeling. The approach outlined here focuses on mapping the separation landscape of pharmaceutical mixtures to quickly identify spaces of peak coelution crossings which enables one to conveniently switch the elution order of target analytes. Diverse examples of MPC diagrams as a function of column temperature, mobile phase gradient or a multifactorial combination in reversed phase and ion exchange chromatography (RPLC and IEC) modes are generated using ACD Laboratories/LC Simulator software and corroborated with experimental data match (overall retention time differences of less than 1%). This powerful MPC technique allows us to gain massive productivity increases (shorter cycle time and higher sample loading) for purification of pharmaceuticals by selectively switching the elution order of target components away from undesired tailing peaks and coelution spaces. MPC chromatography dramatically reduces the time spent developing productive analytical and preparative scale separations. In addition, we illustrate how this new MPC concept can be used to gain substantial improvements of the signal-to-noise ratio, enabling straightforward ppb detection of low-level target components with direct impact in the quantitation of metabolites and potential genotoxic impurities (PGIs). These innovations are of paramount importance in order to facilitate efficient isolation, characterization, and quantitation of drug substances in the development of new medicines.

Structure elucidation of bacterial nonribosomal lipopeptides

We provide a summary of the tools, which allow elucidate the structures of nonribosomal lipopetides.

Enantioselective high-performance liquid chromatography analysis of oxygenated polyunsaturated fatty acids

Oxygenated polyunsaturated fatty acids (PUFAs)play an outstanding role in the physiological and pathological regulation of several biological processes. These oxygenated metabolites can be produced both enzimatically, yielding almost pure enantiomers, and non-enzymatically. The free radical-mediated non-enzymatic oxidation commonly produces racemic mixtures which are used as biomarkers of oxidative stress and tissue damage. The biological activity of oxygenated PUFAs is often associated with only one enantiomer, making it necessary of availing of lipidomics platforms allowing to disclose the role of single enantiomers in health and disease. Polysaccharide-based chiral stationary phases (CSPs) play a dominating part in this setting. As for the cellulose backbone, 4-methylbenzoate derivatives exhibit very high chiral recognition ability towards this class of compounds. Concerning the phenylcarbamate derivatives of cellulose and amylose, the tris(3,5-dimethylphenylcarbamate) variants show the best enantioresolving ability for a variety of oxygenated PUFAs. Moreover, also the amylose tris(5-chloro-2-methylphenylcarbamate)-based selector produces relevant chromatographic performances. The extreme versatility of those CSPs mostly depends on their compatibility with the most relevant elution modes: normal- and reversed-phase, as well as polar organic/ionic-mode. In this review article, a selection of enantioseparation studies of different oxygenated PUFAs is reported, with both tris(benzoates) and tris(phenylcarbamates) of cellulose and amylose.

Discovery of the Cyclic Lipopeptide Gacamide A by Genome Mining and Repair of the Defective GacA Regulator in Pseudomonas fluorescens Pf0-1

Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secondary metabolite gacamide A, a lipodepsipeptide that forms a new family of Pseudomonas lipopeptides. The compound has a moderate, narrow-spectrum antibiotic activity and facilitates bacterial surface motility.

Cinchona Alkaloid-Based Zwitterionic Chiral Stationary Phases Applied for Liquid Chromatographic Enantiomer Separations: An Overview

For the early 2000s, chromatographic methods applying chiral stationary phases (CSPs) became the most effective techniques for the resolution of chiral compounds on both analytical and preparative scales. High-performance liquid chromatography (HPLC) employing various types of chiral selectors covalently bonded to silica-based supports offers a state-of-the-art methodology for "chiral analysis." Although a large number of CSPs are available nowadays, the design and development of new "chiral columns" are still needed since it is obvious that in practice one needs a good portfolio of different columns to face the challenging task of enantiomeric resolutions. The development of the unique chiral anion, cation, and zwitterion exchangers achieved by Lindner and his partners serves as an expansion of the range of the efficiently applicable CSPs.In this context this overview chapter discusses and summarizes direct enantiomer separations of chiral acids and ampholytes applying zwitterionic ion exchangers derived from Cinchona alkaloids. Our aim is to provide comprehensive information on practical solutions with focus on the molecular recognition and methodological variables.

Liquid chromatographic enantiomer separations applying chiral ion-exchangers based on Cinchona alkaloids

As the understanding of the various biological actions of compounds with different stereochemistry has grown, the necessity to develop methods for the analytical qualification and quantification of chiral products has become particularly important. The last quarter of the century has seen a vast growth of diverse chiral technologies, including stereocontrolled synthesis and enantioselective separation and analysis concepts. By the introduction of covalently bonded silica-based chiral stationary phases (CSPs), the so-called direct liquid chromatographic (LC) methods of enantiomer separation became the state-of-the-art methodology. Although a large number of CSPs is available nowadays, the design and development of new chiral selectors and CSPs are still needed since it is obvious that in practice one needs a good portfolio of different CSPs and focused "chiral columns" to tackle the challenging tasks. This review discusses and summarizes direct enantiomer separations of chiral acids and ampholytes applying anionic and zwitterionic ion-exchangers derived from Cinchona alkaloids with emphasis on literature data published in the last 10 years. Our aim is to provide an overview of practical solutions, while focusing on the integration of molecular recognition and methodological variables.

Lipopeptides as therapeutics: applications and in vivo quantitative analysis

A number of novel lipopeptides have been studied for their possible therapeutic potential. These studies should be supported by the appropriate analytical tools not only for novel potential drugs but also for their metabolites, precursors and side products. Lipopeptides have specific physicochemical properties that make them successful in medical applications. However, there are some difficulties with their qualitative and quantitative analyses in biological samples. Therefore, reliable, sensitive and robust analytical methods are in high demand. The main interest of our review is to describe a selection of specific and important properties of lipopeptides, and the analytical methods currently utilized for their characterization and determination in biological samples. A comparison of the pros and cons of immunomethods versus LC-MS methods is discussed in detail.