On-column synthesis coupled to affinity capillary electrophoresis for the determination of binding constants of peptides to glycopeptide antibiotics

Binding constants of the glycopeptide antibiotics teicoplanin (Teic), ristocetin (Rist), and vancomycin (Van), and their derivatives to D-Ala-D-Ala terminus peptides were determined by on-column ligand and receptor synthesis coupled to affinity capillary electrophoresis (ACE) or partial filling ACE (PFACE). In the first technique, 9-fluorenylmethoxycarbonyl (Fmoc)-amino acid-D-Ala-D-Ala species are first synthesized using on-column techniques. The initial sample plug contains a D-Ala-D-Ala terminus peptide and two non-interacting standards. Plugs two and three contain solutions of Fmoc-amino acid-N-hydroxysuccinimide (NHS) ester and buffer, respectively. Upon electrophoresis, the initial D-Ala-D-Ala peptide reacts with the Fmoc-amino acid NHS ester yielding the Fmoc-amino acid D-Ala-D-Ala peptide. Continued electrophoresis results in the overlap of the glycopeptide in the running buffer and the plug of Fmoc-amino acid-D-Ala-D-Ala peptide and non-interacting markers. Subsequent analysis of the change in the electrophoretic mobility (mu) or relative migration time ratio (RMTR) of the peptide relative to the non-interacting standards, as a function of the concentration of the antibiotic, yields a value for the binding constant. In the second technique, derivatives of the glycopeptides Teic and Rist are first synthesized on-column before analysis by ACE or PFACE. After the column has been partially filled with increasing concentrations of D-Ala-D-Ala terminus peptides, a plug of buffer followed by two separate plugs of reagents are injected. The order of the reagent plugs containing the antibiotic and two non-interacting standards and the anhydride varies with the charge of the glycopeptide. Upon electrophoresis, the antibiotic reacts with the anhydride yielding a derivative of Teic or Rist. Continued electrophoresis results in the overlap of the derivatized antibiotic and the plug of D-Ala-D-Ala peptide. Analysis of the change in RMTR of the new glycopeptide relative to the non-interacting standards, as a function of the concentration of the D-Ala-D-Ala ligand yields a value for the binding constant.     

Synthesis, biological evaluation and structural characterization of novel glycopeptide analogues of nociceptin N/OFQ

To examine if the biological activity of the N/OFQ peptide, which is the native ligand of the pain-related and viable drug target NOP receptor, could be modulated by glycosylation and if such effects could be conformationally related, we have synthesized three N/OFQ glycopeptide analogues, namely: [Thr(5)-O-α-D-GalNAc-N/OFQ] (glycopeptide 1), [Ser(10)-O-α-D-GalNAc]-N/OFQ (glycopeptide 2) and [Ser(10)-O-β-D-GlcNAc]-N/OFQ] (glycopeptide 3). They were tested for biological activity in competition binding assays using the zebrafish animal model in which glycopeptide 2 exhibited a slightly improved binding affinity, whereas glycopeptide 1 showed a remarkably reduced binding affinity compared to the parent compound and glycopeptide 3. The structural analysis of these glycopeptides and the parent N/OFQ peptide by NMR and circular dichroism indicated that their aqueous solutions are mainly populated by random coil conformers. However, in membrane mimic environments a certain proportion of the molecules of all these peptides exist as α-helix structures. Interestingly, under these experimental conditions, glycopeptide 1 (glycosylated at Thr-5) exhibited a population of folded hairpin-like geometries. From these facts it is tempting to speculate that nociceptin analogues showing linear helical structures are more complementary and thus interact more efficiently with the native NOP receptor than folded structures, since glycopeptide 1 showed a significantly reduced binding affinity for the NOP receptor.     

New Insights into Glycopeptide Antibiotic Binding to Cell Wall Precursors using SPR and NMR Spectroscopy

Glycopeptide antibiotics, such as vancomycin and teicoplanin, are used to treat life‐threatening infections caused by multidrug‐resistant Gram‐positive pathogens. They inhibit bacterial cell wall biosynthesis by binding to the D ‐Ala‐D ‐Ala C‐terminus of peptidoglycan precursors. Vancomycin‐resistant bacteria replace the dipeptide with the D ‐Ala‐D ‐Lac depsipeptide, thus reducing the binding affinity of the antibiotics with their molecular targets. Herein, studies of the interaction of teicoplanin, teicoplanin‐like A40926, and of their semisynthetic derivatives (mideplanin, MDL63,246, dalbavancin) with peptide analogues of cell‐wall precursors by NMR spectroscopy and surface plasmon resonance (SPR) are reported. NMR spectroscopy revealed the existence of two different complexes in solution, when the different glycopeptides interact with Ac2Kd AlaD AlaOH. Despite the NMR experimental conditions, which are different from those employed for the SPR measurements, the NMR spectroscopy results parallel those deduced in the chip with respect to the drastic binding difference existing between the D ‐Ala and the D ‐Lac terminating analogues, confirming that all these antibiotics share the same primary molecular mechanism of action and resistance. Kinetic analysis of the interaction between the glycopeptide antibiotics and immobilized AcKd AlaD AlaOH by SPR suggest a dimerization process that was not observed by NMR spectroscopy in DMSO solution. Moreover, in SPR, all glycopeptides with a hydrophobic acyl chain present stronger binding with a hydrophobic surface than vancomycin, indicating that additional interactions through the employed surface are involved. In conclusion, SPR provides a tool to differentiate between vancomycin and other glycopeptides, and the calculated binding affinities at the surface seem to be more relevant to in vitro antimicrobial activity than the estimations from NMR spectroscopy analysis.     

Convenient synthesis of a glycopeptide analogue having a complex type disialyl-undecasaccharide

Described herein is a convenient synthesis of a glycopeptide analogue having an undecasaccharide and its stability towards peptide:N-glycosidase F (PNGase-F). To obtain the glycopeptide analogue, bromoacetamidyl undecasaccharide and undecapeptide containing a cysteine residue were synthesized and then a coupling reaction between haloacetamide and thiol was performed. The coupling reaction progressed smoothly at pH 7.0 in phosphate buffer and afforded the desired glycopeptide analogue. In addition, stability of the glycopeptide analogue thus obtained towards PNGase-F was investigated. The result indicated that the glycopeptide analogue was resistant to the enzymatic digestion.     

Effect of buffer on heparin binding and sensing in competitive aqueous media

Abstract

Although buffer-specific effects on molecular recognition are known in biological science, they remain rare in supramolecular chemistry. The binding between a cationic dye, mallard blue (MalB) and polyanionic heparin in aqueous NaCl (150 mM) is studied in three commonly used buffers (Tris-HCl, HEPES, Phosphate, each 10 mM). Although MalB has a very similar UV–visible spectrum in each buffer, the sensory response towards heparin was different in each case. This can be ascribed to differences in the complex formed. In Tris-HCl which has the least competitive chloride counter-anions, MalB exhibits a hypsochromic shift of 25 nm, assigned to strong binding and aggregation of the dye on heparin. In more competitive HEPES, containing a sulfonate anion, there is weaker binding and less aggregation of MalB along the heparin; the hypsochromic shift is only 15 nm. In phosphate buffer, MalB can interact quite strongly with buffer phosphate anions; although heparin binding is still observed, the hypsochromic shift associated with dye aggregation is only 5 nm. As such, specific buffer interactions with the MalB–heparin complex mediate host–guest binding and sensing. Buffer choice must be made carefully in studies of molecular recognition – we would caution against using phosphate and sulfonate containing buffers when studying electrostatic binding.     

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide’s spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.     

Investigation of the interaction mechanism of the recombinant human antibody MDJ8 and its fragments with chromatographic apatite phases

The chromatographic behaviour of a recombinant human antibody (IgG₁-subtype, κ-light chain, MW: 149.5 kD, pI: 9.3) was investigated as a function of the buffer pH and buffer type (HEPES, phosphate, borate) on fluoroapatite and hydroxyapatite stationary phases. HEPES buffer was used at pH 7.0, phosphate buffer at pH 8.2 and borate buffer between pH 8.5 and 11. Elution was by a double gradient method of first a salt gradient from 0 to 1 M NaCl in the corresponding buffer, followed by a step gradient to 0.4 M sodium phosphate. Regardless of the pH and buffer type, the antibody eluted in the NaCl gradient; capacity factors decreased with increasing pH. At pH 11 the antibody eluted in the flow-through. Retention was thus dominated by electrostatic interaction throughout the investigated pH-range. Investigation of antibody fragments obtained by papain digestion (fc- and fab-fragments) and deglycosylated fc-fragments showed that the sugar structures had no influence on the chromatographic behaviour. Instead the chromatographic behaviour was dominated by that of the fab-fragment. ζ-Potential measurements verified that the apatite surface bore a negative surface charge in the investigated pH range, while the antibody net surface charge switched from positive to negative as the pH increased. The corresponding isoionic point was a function of both the buffer concentration and the buffer species. However, above a pH of 8.3 the ζ-potential of the antibody generally was negative. Simulations of the molecular electrostatic potential of the antibody and the two fragments revealed the presence of a positively charged patch within the fab-fragment, which only disappeared above a pH of 10. Most likely this patch was responsible for the observed behaviour.     

Rational design and synthesis of water-compatible molecularly imprinted polymers for selective solid phase extraction of amiodarone

Novel water-compatible molecularly imprinted polymers (MIPs) selective for amiodarone (AD) were designed via a new methodology which relies on screening library of non-imprinted polymers (NIPs). The NIP library consisted of eighteen cross-linked co-polymers synthesized from monomers commonly used in molecular imprinting. The binding capacity of each polymer in the library was analyzed in two different solvents. Binding in water was used to assess non-specific (hydrophobic) interactions and binding in an appropriate organic solvent was used to assess specific interactions. A good correlation was found between the screening tests and modeling of monomer–template interactions performed using computational approach. Additionally, analysis of template–monomer interactions was performed using UV–vis spectroscopy. As the result, 4-vinylpyridine (4-VP) was selected as the best monomer for developing MIP for AD. The 4-VP-based polymers demonstrated imprinting factor equal 3.9. The polymers performance in SPE was evaluated using AD and its structural analogues. The recovery of AD was as high as 96% when extracted from spiked phosphate buffer (pH 4.5) solution and 82.1% from spiked serum samples. The developed MIP shown as a material with specific binding to AD, comparing to its structural analogues, 1-(2-diethylaminoethoxy)-2,6-diiodo-4-nitrobenzene and lidocaine, which shown 9.9% and 25.4% of recovery from the buffer solution, correspondingly. We believe that the screening of NIP library could be proposed as an alternative to commonly used computational and combinatorial approaches.     

Thermodynamic studies on the recognition of flexible peptides by transition-metal complexes

Strong and selective binding to a trihistidine peptide has been achieved employing Cu(2+)-histidine interactions in aqueous medium (25 mM HEPES buffer, pH 7.0). When the pattern of cupric ions on a complex matched with the pattern of histidines on the peptide, a strong and selective binding was observed. UV-vis spectroscopic studies show that the cupric ions coordinate to the histidines of the peptides. Thermodynamic studies reveal that the binding process is enthalpy driven over the entire range of working temperature (25-40 degrees C). An enthalpy-entropy compensation effect was also observed.     

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.     

Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall

Glycopeptide antibiotics, including vancomycin, form complexes via a set of five hydrogen bonds with the acyl-l-Lys-d-Ala-d-Ala portion of the peptidyl stems of the bacterial cell wall peptidoglycan. This complexation deprives the organism from the ability to cross-link peptidyl stems of the peptidoglycan, leading to bacterial cell death. Four synthetic fragments as surrogates of the components of the bacterial cell wall have been prepared in our lab in multistep syntheses. These synthetic samples were used in investigations of the thermodynamics properties (DeltaG degrees , DeltaH degrees , and TDeltaS degrees ) for the complexation with vancomycin by isothermal titration calorimetry (ITC). Complexation with the glycopeptide analogues is largely enthalpy-driven (formation of five hydrogen bonds), and in the analogues with a single peptidyl stem, the complexation is 1:1. The complexation is more complicated with an approximately 2 kDa cell wall surrogate (compound 4), which possesses two peptidyl stems. The data were suggestive of interactions between the two vancomycin molecules, with an entropic penalty attributable to restriction of molecular movements within the complex due to restriction of motion of the highly mobile acyl-d-Ala-d-Ala moiety of the peptidyl stems. These data were reconciled with the recently determined NMR solution structure for the peptidoglycan fragment 4 and its implications for the larger cell wall.     

Elucidating the Anomalous Binding Enhancement of Isoquinoline Boronic Acid for Sialic Acid Under Acidic Conditions: Expanding Biorecognition Beyond Vicinal Diols

A zwitterionic heterocyclic boronic acid based on 4-isoquinolineboronic acid (IQBA) exhibits the highest reported binding affinity for sialic acid or N-acetylneuraminic acid (Neu5Ac, K=5390±190 m ⁻¹) through the formation of a cyclic boronate ester complex under acidic conditions (pH 3). This anomalous pH-dependent binding enhancement does not occur with common neutral saccharides (e.g., glucose, fructose, sorbitiol), because it is mediated via selective complexation to a α-hydroxycarboxylate moiety forming a stable ion pair and ternary complex with Neu5Ac in phosphate buffer. IQBA expands biorecognition beyond classical vicinal diols under neutral or alkaline buffer conditions, which enables the direct analysis of Neu5Ac by native fluorescence with sub-micromolar detection limits.     

On-column ligand synthesis coupled to partial-filling affinity capillary electrophoresis to estimate binding constants of ligands to a receptor

This paper describes a two-step procedure whereby on-column ligand synthesis and partial-filling affinity capillary electrophoresis (PFACE) are sequentially coupled to each other to determine the binding constants of 9-fluorenylmethoxy carbonyl (Fmoc)-amino acid-D-Ala-D-Ala species to vancomycin (Van) from Streptomyces orientalis. In this technique four separate plugs of sample are injected onto the capillary column and electrophoresed. The initial sample plug contains a D-Ala-D-Ala terminus peptide and two non-interacting standards. Plugs two and three contain solutions of Fmoc-amino acid-N-hydroxysuccinimide (NHS) ester and running buffer, respectively. The fourth sample plug contains an increasing concentration of Van partially-filled onto the capillary column. Upon electrophoresis the initial D-Ala-D-Ala peptide reacts with the Fmoc-amino acid NHS ester yielding the Fmoc-amino acid D-Ala-D-Ala peptide. Continued electrophoresis results in the overlap of the plugs of Van and Fmoc-amino acid-D-Ala-D-Ala peptide and non-interacting markers. Analysis of the change in the relative migration time ratio of the Fmoc-amino acid-D-Ala-D-Ala peptide relative to the non-interacting standards, as a function of the concentration of Van, yields a value for the binding constant. These values agree well with those estimated using other binding and ACE techniques.     

Anionic phospholipid coatings in capillary electrochromatography. Binding of Ca2+ to phospholipid phosphate group

Anionic phospholipids phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidylserine (PS) were examined for their effect on 1-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcholine (POPC)-containing liposomes used as coating material in capillary electrochromatography. Liposome solvent was N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES) buffer at pH 7.4 with and without 3 mM of CaCl2. The background electrolyte solution was HEPES buffer at pH 7.4. The net charge, size, and short-term stability of the liposomes were measured with a Zetasizer. Results showed that calcium interacts with all liposomes but most strongly with POPC/PA. The relative migration times, retention factors, and resolution of the model analytes (one cationic, three uncharged ions, and one anionic) were studied. All liposomes successfully coated the silica capillary. Without calcium the strongest interaction and best separation of the analytes were with the POPC/PI and POPC/PS coatings, while interactions with the POPC/PA coating were weak. Calcium enhanced the interactions of the model analytes with all coatings, and the interactions were then strongest with the POPC/PA coating. In the presence of calcium there appears to be a slight reorganization of the coating with increasing number of runs. Our results indicate strong interactions between calcium and the phosphate groups in phospholipids and demonstrate the significant role of the phospholipid polar head group in phospholipid coatings on silica surfaces.     

Frontal analysis microchip capillary electrophoresis to study the binding of ligands to receptors derivatized on magnetic beads

The model binding of the glycopeptide antibiotic teicoplanin (Teic) from Actinoplanes teichomyceticus, immobilized on magnetic microspheres, to d-Ala-d-Ala terminus peptides was assessed using microchip capillary electrophoresis (MCE) with continuous frontal analysis (FA). Teic is closely related to vancomycin (Van), historically, the drug of last resort used to treat many Gram-positive bacterial infections. Glycopeptide antibiotics inhibit bacterial growth by binding to the d-Ala-d-Ala terminus on the cell wall of Gram-positive bacteria via hydrogen bonds, thereby preventing the enzyme-mediated cross-linking of peptidoglycan and eventual cell death. In this work direct and competitive bead-based assays in a microfluidic chip are demonstrated. The binding constants obtained using the technique are comparable with values reported in the literature.     

A mechanistic study of sialic acid mutarotation: implications for mutarotase enzymes

The mutarotation of N-acetylneuraminic acid (Neu5Ac) proceeds by four kinetically distinct pathways: (i) the acid-catalyzed reaction of neutral Neu5Ac; (ii) the spontaneous reaction of the carboxylic acid (the kinetically equivalent acid-catalyzed reaction on the anion being ruled out by the solvent deuterium kinetic isotope effect of 3.74 ± 0.68); (iii) a spontaneous, water-catalyzed, reaction of the anion; and (iv) a specific-base catalyzed reaction of the anion. The magnitude of the solvent kinetic isotope effect, k(H2O)/k(D2O) = 4.48 ± 0.74 is consistent with a ring-opening transition state in which a water molecule is deprotonating the anomeric hydroxyl group in concert with strengthening solvation of the ring oxygen atom. The mechanistic implications for Neu5Ac mutarotases are discussed.     

Self-association of daunomycin antibiotic in various buffer solutions

The self-association of an antitumor antibiotic, daunomycin (DAU), in various buffer solutions, including water-salt solutions, phosphate buffer, HEPES, and TRIS, was studied by 1D and 2D ¹H NMR spectroscopy at 500 MHz. The two-dimensional NOESY spectra and the concentration and temperature dependences of the chemical shifts of antibiotic protons in the solvents studied showed that the self-association parameters of DAU were independent of the type of buffer solutions. The most probable two spatial structures of the dimer of DAU in solution were constructed by the method of molecular mechanics. The mutual orientation of the chromophores was parallel in one structure and antiparallel in the other.     

Chemoselective elaboration of O-linked glycopeptide mimetics by alkylation of 3-thioGalNAc.

A critical branch point in mucin-type oligosaccharides is the beta 1-->3 glycosidic linkage to the core alpha-N-acetylgalactosamine (GalNAc) residue. We report here a strategy for the synthesis of O-linked glycopeptide analogues that replaces this linkage with a thioether amenable to construction by chemoselective ligation. The key building block was a 2-azido-3-thiogalactose-Thr analogue that was incorporated into a peptide by fluorenylmethoxycarbonyl (Fmoc)-based solid-phase peptide synthesis. Higher order oligosaccharides were readily generated by alkylation of the corresponding 3-thioGalNAc with N-bromoacetamido sugars. The rapid assembly of "core 1"and "core 3" O-linked glycopeptide mimetics was accomplished in this fashion.     

Speciation of cyclo(Pro-Gly)<Subscript>3</Subscript> and its divalent metal-ion complexes by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to study the binding of selected group II and divalent transition-metal ions by cyclo(Pro-Gly)3 (CPG3), a model ion carrier peptide. Metal salts (CatXn) were combined with the peptide (M) at a molar ratio of 1:10 M/Cat in aqueous solvents containing 50% vol/vol acetonitrile or methanol and 1 or 10 mM ammonium acetate (NH4Ac). Species detected include [M+H]+, [M+Cat-H]+, [M2+Cat]2+, [M+Cat+Ac]+, and [M+Cat+X]+. The relative stabilities of complexes formed with different cations (Mg2+, Ca2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, and Zn2+) were determined from the abundance of 1:1 and 2:1 M/Cat species relative to that of the unbound peptide. The largest metal ions (Ca2+, Sr2+, and Mn2+) formed the most stable complexes. Reducing the buffer concentration increased the overall extent of metal binding. Results show that the binding specificity of CPG3 depends upon the size of the metal ion and its propensity for electrostatic interaction with oxygen atoms. Product ion tandem mass spectrometry of [M+H]+ and [M+Cu-H]+ confirmed the cyclic structure of the peptide, although the initial site(s) of metal attachment could not be determined.     

Solid peptide nanoparticles--structural characterization and quantification of cargo encapsulation

CD3ac, an uncharged and strongly hydrophobic 10 amino acid peptide (Ac-LK(Ac)-LK(Ac)-LK(Ac)-LW-DL-LW-DL-LW-DL-LW-NH2) was synthesized and purified. The peptide readily dissolves in ethanol and--upon solvent exchange to water--assembles into solid spherical particles with diameters of around 500 nm and low size-polydispersity. CD3ac self-assembles in a convenient one-step-process in the absence of a templating two-phase solvent system or any other templating agents. Circular dichroism reveals a gramicidin-like secondary structure, which can be attributed to the presence of D-leucine, whereas LCD3ac, a peptide of identical constitution yet composed entirely of L-amino acids precipitates amorphously. The unacetylated derivative of LCD3ac (LCD3) displays α-helical character in circular dichroism. During the process of bead formation, CD3ac can take up and enrich water-soluble and--insoluble cargo compounds, which is exemplified by the encapsulation of rose bengal (RB) and 5-carboxy-fluorescein (CF), two xanthene derivatives. We confirmed their presence in CD3ac beads by confocal fluorescence microscopy and quantified the encapsulation efficiency by absorption measurements of dissolved RB-containing peptide bead suspensions. Loaded CD3ac beads consist of up to 40 mol-% RB, which corresponds to a logarithmic partition coefficient of 2.95. To the best of our knowledge CD3ac is the first peptide synthesized by Fmoc chemistry which forms solid particles in the nano- and micrometer size range and holds promise for drug delivery applications.