Influence of the charge state on the structures and interactions of vancomycin antibiotics with cell-wall analogue peptides: experimental and theoretical studies

Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties

Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.

Controlling the Evolution of Selective Vancomycin Resistance through Successful Ophthalmic Eye-Drop Preparation of Vancomycin-Loaded Nanoliposomes Using the Active-Loading Method

Vancomycin is the front-line defense and drug of choice for the most serious and life-threatening methicillin-resistant Staphylococcus aureus (MRSA) infections. However, poor vancomycin therapeutic practice limits its use, and there is a consequent rise of the threat of vancomycin resistance by complete loss of its antibacterial activity. Nanovesicles as a drug-delivery platform, with their featured capabilities of targeted delivery and cell penetration, are a promising strategy to resolve the shortcomings of vancomycin therapy. However, vancomycin's physicochemical properties challenge its effective loading. In this study, we used the ammonium sulfate gradient method to enhance vancomycin loading into liposomes. Depending on the pH difference between the extraliposomal vancomycin-Tris buffer solution (pH 9) and the intraliposomal ammonium sulfate solution (pH 5-6), vancomycin was actively and successfully loaded into liposomes (up to 65% entrapment efficiency), while the liposomal size was maintained at 155 nm. Vancomycin-loaded nanoliposomes effectively enhanced the bactericidal effect of vancomycin; the minimum inhibitory concentration (MIC) value for MRSA decreased 4.6-fold. Furthermore, they effectively inhibited and killed heteroresistant vancomycin-intermediate S.aureous (h-VISA) with an MIC of 0.338 μg mL^-1. Moreover, MRSA could not develop resistance against vancomycin that was loaded into and delivered by liposomes. Vancomycin-loaded nanoliposomes could be a feasible solution for enhancing vancomycin's therapeutic use and controlling the emerging vancomycin resistance.

UV-VUV Photofragmentation Spectroscopy of Isolated Neutral Fragile Macromolecules: A Proof-of-Principle Based on a Deprotonated Vancomycin-Peptide Noncovalent Complex

The gas phase offers the possibility to analyze organic molecules by ultraviolet-vacuum ultraviolet (UV-VUV) spectroscopy without any solvent effect or limitation in terms of spectral range due to absorption by the solvent. Up to now, the size and chemical composition of neutral molecular systems under study have been limited by the use of vaporization methods based on thermal heating. Soft sources of gas-phase thermolabile molecular systems such as electrospray or matrix-assisted laser desorption ionization are appealing alternatives to heating-based techniques, but they lead to the production of ions. In such cases, UV-VUV action spectroscopy is then the method of choice to study the electronic structure and corresponding photodynamics of these gas-phase molecular ions. However, previous investigations have shown that the UV-VUV action spectrum of a given molecular ion depends on the charge state, which in many cases might be a caveat. Here, by means of synchrotron radiation coupled to mass spectrometry and through the test case of the glycopeptide antibiotic vancomycin noncovalently bound to a deprotonated small peptide, we show that the UV-VUV photofragmentation spectrum of neutral thermally fragile organic molecules can be obtained via charge-tagging action spectroscopy.

Pharmacokinetics and pharmacodynamics of peptide antibiotics

Antimicrobial resistance is a major global health challenge. As few new efficacious antibiotics will become available in the near future, peptide antibiotics continue to be major therapeutic options for treating infections caused by multidrug-resistant pathogens. Rational use of antibiotics requires optimisation of the pharmacokinetics and pharmacodynamics for the treatment of different types of infections. Toxicodynamics must also be considered to improve the safety of antibiotic use and, where appropriate, to guide therapeutic drug monitoring. This review focuses on the pharmacokinetics/pharmacodynamics/toxicodynamics of peptide antibiotics against multidrug-resistant Gram-negative and Gram-positive pathogens. Optimising antibiotic exposure at the infection site is essential for improving their efficacy and minimising emergence of resistance.

Mechanistic Study of Enhanced Protonation by Chromium(III) in Electrospray Ionization: A Superacid Bound to a Peptide

Addition of trivalent chromium, Cr(III), to solutions undergoing electrospray ionization (ESI) enhances protonation and leads to formation of [M + 2H]²⁺ for peptides that normally produce [M + H]⁺. This effect is explored using electronic structure calculations at the density functional theory (DFT) level to predict the energetics of various species that are potentially important to the mechanism. Gas- and solution-phase reaction free energies for glycine and its anion reacting with [Cr(III)(H₂O)₆]³⁺ and for dehydration of these species have been predicted, where glycine is used as a simple model for a peptide. For comparison, calculations were also performed with Fe(III), Al(III), Sc(III), Y(III), and La(III). Removal of water from these complexes, as would occur during the ESI desolvation process, results in species that are highly acidic. The calculated pK_a of Cr(III) with a single solvation shell is -10.8, making [Cr(III)(H₂O)₆]³⁺ a superacid that is more acidic than sulfuric acid (pK_a = -8.8). Binding to glycine requires removal of two aqua ligands, which gives [Cr(III)(H₂O)₄]³⁺ that has an extremely acidic pK_a of -28.8. Removal of additional water further enhances acidity, reaching a pK_a of -84.7 for [Cr(III)(H₂O)]³⁺. A mechanism for enhanced protonation is proposed that incorporates computational and experiment results, as well as information on the known chemistry of Cr(III), which is substitutionally inert. The initial step involves binding of [Cr(III)(H₂O)₄]³⁺ to the deprotonated C-terminus of a peptide. As the drying process during ESI strips water from the complex, the resulting superacid transfers protons to the bound peptide, eventually leading to formation of [M + 2H]²⁺.

The use of chromium(III) complexes to enhance peptide protonation by electrospray ionization mass spectrometry

The addition of trivalent chromium, Cr(III), reagents to peptide solutions can increase the intensity of doubly protonated peptides, [M + 2H]²⁺ , through electrospray ionization (ESI). Three model heptapeptides were studied: neutral (AAAAAAA), acidic (AAEEEAA), and basic (AAAKAAA). The neutral and acidic peptides form almost no 2+ ions in the absence of Cr(III). Twenty Cr(III) complexes were used as potential enhanced protonation reagents, including 11 complexes with nonlabile ligands and nine with labile ligands. The complexes that provide the most abundant [M + 2H]²⁺ , the greatest [M + 2H]²⁺ to [M + H]⁺ ratio, and the cleanest mass spectra are [Cr(H₂ O)₆ ](NO₃ )₃ ·3H₂ O and [Cr(THF)₃ ]Cl₃ . Anions in Cr(III) reagents can also affect the intensity of [M + 2H]²⁺ and the [M + 2H]²⁺ to [M + H]⁺ ratio through cation-anion interactions. The influence of anions on the extent of peptide protonation follows the trend ClO₄ ^-  ˃ SO₄ ^2-  ˃ Br^-  ˃ Cl^-  ˃ F^-  ≈ NO₃ ^- . Solvent effects and complexes with varying number of water ligands were investigated to study the importance of water in enhanced protonation. Aqueous solvent systems and Cr(III) complexes that have at least one bound water ligand in solution must be used for successful increase in the intensity of [M + 2H]²⁺ , which indicates that water is involved in the mechanism of Cr(III)-induced enhanced protonation. The ESI source design is also important because no enhanced protonation was observed using a Z-spray source. The current results suggest that this Cr(III)-induced effect occurs during the ESI desolvation process.

Optimization of electrospray ionization conditions to enhance formation of doubly protonated peptide ions with and without addition of chromium(III)

RATIONALE

Production of multiply protonated ions by electrospray ionization (ESI) is important to the analysis of peptides by mass spectrometry. For small neutral and acidic peptides, addition of chromium(III) greatly increases the intensity of doubly protonated ions. The current study examines instrumental and solution parameters that maximize peptide ion charge by ESI.

METHODS

The neutral and basic heptapeptides AAAAAAA (A7) and AAAKAAA (A3KA3) were used as test compounds and electrosprayed from a solution containing chromium(III) nitrate at a peptide to metal molar ratio of 1:10. Positive ion mode experiments were performed on a Bruker HCTultra PTM Discovery System quadrupole ion trap mass spectrometer. Source voltages and drying/nebulizer gases were systematically altered. The effects of rinsing, brand, and color of plastic microcentrifuge tubes (vials) employed were also investigated.

RESULTS

Nebulizer gas pressure and drying gas flow rate are crucial parameters for production of [M + 2H]²⁺ , while drying gas temperature alone has minimal effect. Optimization of the capillary exit and skimmer voltages are important both to maximize [M + 2H]²⁺ and reduce unwanted ion dissociation. Protonation is enhanced and fewer impurity peaks are observed when solutions are prepared in colorless plastic vials that have been rinsed briefly with propan-2-ol (isopropanol).

CONCLUSIONS

Optimization of instrument and sample preparation factors for enhanced protonation with and without Cr(III) is necessary to allow maximum formation of [M + 2H]²⁺ . Proteomics researchers should find these procedures to be of use for increasing multiply protonated signal intensity even in the absence of Cr(III). Copyright © 2017 John Wiley & Sons, Ltd.

Surface-induced dissociation: a unique tool for studying energetics and kinetics of the gas-phase fragmentation of large ions

Surface-induced dissociation (SID) is a valuable tool for investigating the activation and dissociation of large ions in tandem mass spectrometry. This account summarizes key findings from studies of the energetics and mechanisms of complex ion dissociation in which SID experiments were combined with Rice-Ramsperger-Kassel-Marcus modeling of the experimental data. These studies used time- and collision-energy-resolved SID experiments and SID combined with resonant ejection of selected fragment ions on a specially designed Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Fast-ion activation by collision with a surface combined with the long and variable timescale of FT-ICR mass spectrometry is perfectly suited to studying the energetics and dynamics of complex ion dissociation in the gas phase. Modeling of time- and collision-energy-resolved SID enables the accurate determination of energy and entropy effects in the dissociation process. It has been demonstrated that entropy effects play an important role in determining the dissociation rates of both covalent and noncovalent bonds in large gaseous ions. SID studies have provided important insights on the competition between charge-directed and charge-remote fragmentation in even-electron peptide ions and the role of the charge and radical site on the energetics of the dissociation of odd-electron peptide ions. Furthermore, this work examined factors that affect the strength of noncovalent binding, as well as the competition between covalent and noncovalent bond cleavages and between proton and electron transfer in model systems. Finally, SID studies have been used to understand the factors affecting nucleation and growth of clusters in solution and in the gas phase.

Conformational changes of peptidoglycan fragments during their interactions with vancomycin

Six complexes of vancomycin and peptidoglycan precursors were studied via molecular dynamics simulations. The interactions between the antibiotic and peptidoglycan fragments were identified and described in detail. All six studied modifications of the peptidoglycan precursor resulted in a weakening of the interaction with vancomycin when comparing to the native D-Ala-D-Ala-terminated fragment. It was confirmed that the N-terminus of the vancomycin is directly responsible for peptidoglycan recognition and antimicrobial activity. In simulated systems, the saccharide part of the antibiotic interacts with peptide precursors, thus it could also be important for antimicrobial activity. The complex terminated with D-Lac is the only one in which there is a weak interaction with the sugar moiety in the simulated systems. Analysis of conformational changes is a major scope of this work. The lack of interactions resulting from modification of the peptidoglycan precursors (D-Lac, D-Ser or other substitution) would be counterbalanced by proper modifications of the vancomycin moiety, especially the saccharide part of vancomycin.

Competition between covalent and noncovalent bond cleavages in dissociation of phosphopeptide-amine complexes

Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (X = S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. For systems examined in this study, covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel.