Saturation Transfer Difference Experiments Research Articles

Structural analysis of nanosystems: Solid Sorbitan esters Nanoparticles (SSN) as a case study

Innovative approaches in nanotechnology can provide drug delivery systems with a high potential in different fields. To avoid trial and error assays as a main driving force governing new designs and, furthermore, to develop successful nanosystem optimization strategies, it is of the greatest importance to develop specific characterisation techniques beyond conventional determinations of size, zeta potential and morphology. However, the application of techniques able to determine some key characteristics, such as nanostructure (i.e., solid structure vs vesicular), and the way in which the reorganization of components takes place on these structures has been scarcely explored. The present work has been devoted to provide some insights about the potential offered by some NMR techniques to those scientists working on nanotechnological approaches. For this purpose, we selected our nanosystems based on sorbitan monooleate as a case study. We used 1H NMR methods, including a recently proposed method relying in the well-known Saturation Transfer Difference (STD) experiment for the observation of ‘invisible signals’ in large aggregates (Invisible State STD or ISSTD). Overall, these techniques revealed the presence in these nanosystems of a gradient of flexibility from an internal rigid core towards a more flexible region located on their surface, as well as the absence of water content in both regions. Such structure, corresponding to a solid nanostructure rather than a vesicular one, can explain some of the interesting properties previously observed for these innovative nanosystems, such as their high stability, and allows us to refer to these nanosystems with the term “Solid Sorbitan esters Nanoparticles” (SSN). On the basis of the valuable information provided by the mentioned characterisation techniques, it is our understanding that they could facilitate the future design of new drug delivery nanosystems as well as the improvement of existing ones and/or the development of new applications for classical drug delivery concepts.

Application of the 19F-Waterlogsy Type Experiment for NMR-Based Screening of Fluorinated Compounds

The WaterLOGSY type experiment with 19F detection was applied to observe the interaction between a fluorinated compound and a macromolecule. The proposed experiment, which was developed based on the 19F{1H} saturation transfer difference experiment, was carried out using the conventional spectrometer equipped with a single high band amplifier and a H/F/C-double tuned probe. The selective 19F detection is advantageous in screening the fluorinated compounds, considering that 19F is a sensitive nucleus in NMR spectroscopy. The effective approach to discriminate binding of the fluorinated compounds to proteins with 19F detection was demonstrated using the complex of diflunisal and human serum albumin.

Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS)

The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDO8PS) from Helicobacter pylori (HpKDO8PS) was determined alone and within various complexes, revealing an extra helix (HE) that is absent in the structures of KDO8PS from other organisms. In contrast to the metal coordination of the KDO8PS enzyme from Aquifex aeolicus, HpKDO8PS is specifically coordinated with Cd2+ or Zn2+ ions, and isothermal titration calorimetry (ITC) and differential scanning fluorimetry (DSF) revealed that Cd2+ thermally stabilizes the protein structure more efficiently than Zn2+. In the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. Using the structures of HpKDO8PS and API [arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) bisubstrate inhibitor], we generated 21 compounds showing potential HpKDO8PS-binding properties via in silico virtual screening. The capacity of three, avicularin, hyperin, and MC181, to bind to HpKDO8PS was confirmed through saturation transfer difference (STD) experiments, and we identified their specific ligand binding modes by combining competition experiments and docking simulation analysis. Hyperin was confirmed to bind to the A5P binding site, primarily via hydrophilic interaction, whereas MC181 bound to both the PEP and A5P binding sites through hydrophilic and hydrophobic interactions. These results were consistent with the epitope mapping by STD. Our results are expected to provide clues for the development of HpKDO8PS inhibitors.

(R)‐α‐trifluoromethylalanine containing short peptide in the inhibition of amyloid peptide fibrillation

The extracellular deposition of insoluble amyloid fibrils resulting from the aggregation of the amyloid-β (Aβ) is a pathological feature of neuronal loss in Alzheimer's disease (AD). Numerous small molecules have been reported to interfere with the process of Aβ aggregation. Compounds containing aromatic structures, hydrophobic amino acids and/or the α-aminoisobutyric acid (Aib) as β-sheet breaker elements have been reported to be effective inhibitors of Aβ aggregation. We synthesized two peptides, one containing the Aib amino acid and the other including its trifluoromethylated analog (R)-α-Trifluoromethylalanine ((R)-Tfm-Alanine) and we evaluated the impact of these peptides on Aβ amyloid formation. The compounds were tested by standard methods such as thioflavin-T fluorescence spectroscopy and transmission electron microscopy but also by circular dichroism, liquid state nuclear magnetic resonance (NMR) and NMR saturation transfer difference (STD) experiments to further characterize the effect of the two molecules on Aβ structure and on the kinetics of depletion of monomeric, soluble Aβ. Our results demonstrate that the peptide containing Aib reduces the quantity of aggregates containing β-sheet structure but slightly inhibits Aβ fibril formation, while the molecule including the trifluoromethyl (Tfm) group slows down the kinetics of Aβ fibril formation, delays the random coil to β-sheet structure transition and induces a change in the oligomerization pathway. These results suggest that the hydrophobic Tfm group has a better affinity with Aβ than the methyl groups of the Aib and that this Tfm group is effective and important in preventing the Aβ aggregation.

Polarization Transfer from Ligands Hyperpolarized by Dissolution Dynamic Nuclear Polarization for Screening in Drug Discovery.

Nuclear magnetic resonance (NMR) spectroscopy is a valuable technique for ligand screening, because it exhibits high specificity toward chemical structure and interactions. Dissolution dynamic nuclear polarization (DNP) is a recent advance in NMR methodology that enables the creation of non-equilibrium spin states, which can dramatically increase NMR sensitivity. Here, the transfer of such spin polarization from hyperpolarized ligand to protein is observed. Mixing hyperpolarized benzamidine with the serine protease trypsin, a "fingerprint" of enhanced protein signals is observed, which shows a different intensity profile than the equilibrium NMR spectrum of the protein, but coincides closely to the frequency profile of a saturation transfer difference (STD) NMR experiment. The DNP experiment benefits from hyperpolarization and enables observation of all frequencies in a single, rapid experiment. Based on these merits, it is an interesting alternative to the widely used STD experiment for identification of protein-ligand interactions.

1H NMR Study of the Adsorption Mechanism for Ti-Binding Peptide on TiO2 Nanoparticles

The interaction mechanism of Ti-binding peptide (TBP:RKLPDA) and TiO2 nanoparticles was studied at the atomic level by NMR. Saturation transfer difference (STD) experiments were performed to identify the interaction sites of TBP with TiO2 surface. Water molecules on TiO2 nanoparticle surface were selectively saturated as a function of time. The initial slopes of STD amplitude build-up curve against saturation time were calculated for TBP proton peaks and the relative values of initial slopes were compared to be R Hδ 100% as a standard, K Hε 91%, L Hδ 16%, P Hβ 26%, D Hβ 22% and A Hβ 9%, showing that residues R and K have the strongest effect of saturation transfer from the bound water molecules. This result suggests 1st residue R and 2nd K directly contact to TiO2 surface. The zeta potential of TiO2 nanoparticles was measured to be −23 mV in average, indicating that the TiO2 surface is negatively charged. Thus, both positively charged guanidine group of R and amino group of K must play a key role in interaction with the TiO2 surface by electrostatic force. NOESY experiment for TBP/TiO2 mixture and ROESY experiment for TBP alone in aqueous solution were performed. The averaged backbone RMSD of ten best matched structures were 0.76±0.19Å for TiO2 bound TBP and 1.37±0.34Å for free TBP. The calculated structures of TiO2-bound TBP were more converged than those of free TBP, indicated that conformations of TBP are restricted to much more extend when it is adsorbed to the TiO2 surface.

Kinetics of intramolecular chemical exchange by initial growth rates of spin saturation transfer difference experiments (SSTD NMR).

We report here the Initial Growth Rates SSTD NMR method, as a new powerful tool to obtain the kinetic parameters of intramolecular chemical exchange in challenging small organic and organometallic molecules.

Exploring NMR methods as a tool to select suitable fluorescent nucleotide analogues

Fluorescent analogues provide important tools for biochemical/biophysical research. However, the analogues contain chemical modifications much larger than those known to affect ligand-binding, such as the inversion of a carbon centre or substitution of an atom. We lack experimental tools and protocols to select the most appropriate fluorescent analogue. Herein, we use several NMR spectroscopy methods, including Saturation Transfer Difference (STD), STD competition and transferred nuclear Overhauser effect spectroscopy (Tr-NOESY), as tools to select appropriate fluorescent probes. Annexin A6 (AnxA6) is a ubiquitous protein that forms in vitro GTP-induced ion channels. We used this protein as a model and screened guanosine triphosphate (GTP) and four fluorescent analogues against AnxA6. STD reported that the GTP moiety of all ligands made similar contacts with the protein, despite additional interactions between the fluorescent tags and AnxA6. Competition STD experiments verified that the analogues and GTP bind to the same site. Tr-NOESY indicated that the bound conformation of the base relative to ribose is altered for some analogues compared to GTP. MANT-GTP or the BODIPY thioester of guanosine 5'-O-(3-thiotriphosphate) are the most suitable fluorescent analogues for AnxA6, according to NMR. These results reveal NMR as a useful technique to select and design proper fluorescent tags for biochemical/biophysical assays.

Comparative Binding Effects of Aspirin and Anti-Inflammatory Cu Complex in the Active Site of LOX-1

(1)H NMR Saturation Transfer Difference (STD) experiments were applied to study the binding of aspirin and of an anti-inflammatory complex of Cu(I), namely [Cu(tpp)(pmt)](2) [pmt = 2-mercaptopyrimidine), synthesized in an attempt to develop novel metallotherapeutic molecules. While aspirin showed only very weak binding, the complex [Cu(tpp)(pmt)](2) clearly favored binding to LOX-1. In silico docking experiments in LOX-1 showed that aspirin does only weakly bind to LOX-1, while the complex binds with high affinity. In addition, docking experiments and molecular dynamics (MD) simulations showed that the complex binds via hydrogen bonding (HB), to an allosteric site of LOX-1, revealing that this enzyme has more than one accessible site for complex metallotherapeutic molecules. When aspirin was added in the solution containing LOX and the complex [Cu(tpp)(pmt)](2), the former was shown to hinder the binding of the Cu complex significantly. This may be interpreted as the copper complex aiding the transfer of aspirin through an acid-base reaction at the LOX enzyme which subsequently blocks its binding.

The Structure of Myristoylated Mason-Pfizer Monkey Virus Matrix Protein and the Role of Phosphatidylinositol-(4,5)-Bisphosphate in Its Membrane Binding

We determined the solution structure of myristoylated Mason-Pfizer monkey virus matrix protein by NMR spectroscopy. The myristoyl group is buried inside the protein and causes a slight reorientation of the helices. This reorientation leads to the creation of a binding site for phosphatidylinositols. The interaction between the matrix protein and phosphatidylinositols carrying C(8) fatty acid chains was monitored by observation of concentration-dependent chemical shift changes of the affected amino acid residues, a saturation transfer difference experiment and changes in (31)P chemical shifts. No differences in the binding mode or affinity were observed with differently phosphorylated phosphatidylinositols. The structure of the matrix protein-phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)] complex was then calculated with HADDOCK software based on the intermolecular nuclear Overhauser enhancement contacts between the ligand and the matrix protein obtained from a (13)C-filtered/(13)C-edited nuclear Overhauser enhancement spectroscopy experiment. PI(4,5)P(2) binding was not strong enough for triggering of the myristoyl-switch. The structural changes of the myristoylated matrix protein were also found to result in a drop in the oligomerization capacity of the protein.

Determining the Role of the Aromatic Ring of N‐Arylmethyl ent‐conduramine F‐1 in their Interactions with α‐Glucosidases by Saturation Transfer Difference NMR Spectroscopy Experiments

Glucosidases are a group of enzymes responsible of the glycosidic bond cleavage with different specificities depending on the number of monosaccharides, the position of cleavage, and the configuration of the hydroxy groups in their substrates. In particular, inhibitors of α-1,4-glucosidases have generated great interest as potential therapeutic agents for the treatment of type II diabetes (e.g., miglitol (N-2-hydroxyethyl-1-deoxynojirimycin), Glyset, Diastabol, Glucobay),1, 2 obesity,3 hepatitis B and C4, 5 and other viral diseases,6 and cancer.7

Synthesis, Dihydrofolate Reductase Inhibition, Anti-proliferative Testing, and Saturation Transfer Difference 1H-NMR Study of Some New 2-Substituted-4,6-diaminopyrimidine Derivatives

A series of 2-substituted-4,6-diaminipyrimidine derivatives were synthesized and evaluated for their dihydrofolate reductase (DHFR) inhibitory activity. Saturation transfer difference (STD) (1)H-NMR experiments were used to probe the binding characteristics of the compounds with human DHFR enzyme. The most potent molecules, 12 and 15, in enzyme assay study showed the best results in STD experiments indicating their intimate interaction with the receptor. The docking studies were followed to explain the structural basis for the observed interaction between the ligands and DHFR. All the compounds were also assayed in vitro for their growth inhibitory activity on MCF-7, HepG2, SKHep1, and Hela tumor cell lines. Compounds 16, 17, and 22 demonstrated the most potent in vitro anti-proliferative activity among the others.

Saturation Transfer Difference NMR Experiments of Membrane Proteins in Living Cells under HR‐MAS Conditions: The Interaction of the SGLT1 Co‐transporter with Its Ligands

With the magic roundabout: A new methodology that combines high-resolution magic angle spinning (HR-MAS) techniques with saturation transfer difference (STD) NMR spectroscopy is described. This approach significantly improves the versatility of the STD experiment, and expands its use for samples containing living cells derived from solid tissues (see figure).

Sugar-based peptidomimetics inhibit amyloid β-peptide aggregation

Alzheimer’s disease is characterized by the oligomerization and amyloid fibril formation of amyloid β-peptide (Aβ). We describe a novel class of small water-soluble Aβ binding peptidomimetics based on two hydrophobic Ala-Val and Val-Leu dipeptides linked to a d-glucopyranosyl scaffold through aminoalkyl and carboxyethyl links in C1 and C6 positions. These compounds combine the targeting of hydrophobic recognition interfaces with an original hydrophilic sugar β-breakage strategy. These molecules were shown, by fluorescence thioflavin-T assays, to dramatically slow down the kinetics of amyloid fibril formation even at a low peptidomimetics to Aβ ratio of 0.1:1. Electron microscopy images revealed that the peptidomimetics efficiently reduced the amount of typical amyloid fibrils. NMR saturation transfer difference experiments indicated that these molecules interact with Aβ aggregated species through their hydrophobic amino acid residues. This inhibition effect was found to be sequence-specific since these molecules did not alter the kinetics of aggregation of another amyloid peptide, IAPP, involved in type 2 diabetes mellitus.

Determination of the binding epitope of lidocaine with AGP: minimizing the effects of nonspecific binding in saturation transfer difference experiments

The ligand epitope map and the effect of nonspecific binding is assessed for lidocaine binding to α(1)-acid glycoprotein using the saturation transfer difference nuclear magnetic resonance experiment performed as a function of the ligand/protein ratio. The experimental design tested two different approaches for preparing solutions with various ligand/protein ratios; holding the protein concentration constant and increasing the ligand concentration; and holding the ligand concentration constant while decreasing the protein concentration. Nonspecific binding effects were more prevalent in experiments in which the ligand concentration was increased, although spectra with higher signal-to-noise ratios were obtained under these conditions. The epitope map determined for achiral lidocaine is compared with previously determined results for the (R)- and (S)-enantiomers of propranolol. The weaker binding affinity of lidocaine may be partially attributed to steric hindrance by the lidocaine N-ethyl groups which may prevent close contact of the lidocaine amine with the negatively charged amino acids at the apex of the protein binding pocket.

A NMR reverse diffusion filter for the simplification of spectra of complex mixtures and the study of drug receptor interactions

A reverse diffusion filter NMR experiment (Drev) is proposed for the study of small molecules in binding with macromolecules. The filtering efficiency of Drev to eliminate the signals of the macromolecule is shown to be superior to conventional transverse relaxation filters at least for macromolecules containing a significant fraction of flexible residues. The Drev filter was also a useful complement for ligand-based NMR screening in combination with saturation transfer difference experiments.

Dynamic aspects of antibody:oligosaccharide complexes characterized by molecular dynamics simulations and saturation transfer difference nuclear magnetic resonance

Carbohydrates are likely to maintain significant conformational flexibility in antibody (Ab):carbohydrate complexes. As demonstrated herein for the protective monoclonal Ab (mAb) F22-4 recognizing the Shigella flexneri 2a O-antigen (O-Ag) and numerous synthetic oligosaccharide fragments thereof, the combination of molecular dynamics simulations and nuclear magnetic resonance saturation transfer difference experiments, supported by physicochemical analysis, allows us to determine the binding epitope and its various contributions to affinity without using any modified oligosaccharides. Moreover, the methods used provide insights into ligand flexibility in the complex, thus enabling a better understanding of the Ab affinities observed for a representative set of synthetic O-Ag fragments. Additionally, these complementary pieces of information give evidence to the ability of the studied mAb to recognize internal as well as terminal epitopes of its cognate polysaccharide antigen. Hence, we show that an appropriate combination of computational and experimental methods provides a basis to explore carbohydrate functional mimicry and receptor binding. The strategy may facilitate the design of either ligands or carbohydrate recognition domains, according to needed improvements of the natural carbohydrate:receptor properties.

Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding

Saturation transfer difference (STD) NMR has emerged as one of the most popular ligand-based NMR techniques for the study of protein−ligand interactions. The success of this technique is a consequence of its robustness and the fact that it is focused on the signals of the ligand, without any need of processing NMR information about the receptor and only using small quantities of nonlabeled macromolecule. Moreover, the attractiveness of this experiment is also extendable to the classroom. In the context of a practical NMR class, this experiment is ideal to illustrate some fundamental NMR concepts, such as the nuclear Overhauser effect and relaxation in a multidisciplinary context, bridging chemistry and biochemistry with a taste of medicinal chemistry.We use the readily available human serum albumin (HSA), 6-d,l-methyl-tryptophan (6-CH3-Trp), and 7- d,l-methyl-tryptophan (7-CH3-Trp) to introduce the STD-NMR experiment and to illustrate its applicability for ligand screening, mapping of binding moieties, and determination of the dissociation constant, in a context that can be explored or adapted to the student’s course level and topic (chemistry or biochemistry). We also cover the most important theoretical aspects of the STD experiment, calling attention to some of its limitations and drawbacks without a complex theoretical approach.

Interactions of Poly(amidoamine) Dendrimers with Human Serum Albumin: Binding Constants and Mechanisms

The interactions of nanomaterials with plasma proteins have a significant impact on their in vivo transport and fate in biological fluids. This article discusses the binding of human serum albumin (HSA) to poly(amidoamine) [PAMAM] dendrimers. We use protein-coated silica particles to measure the HSA binding constants (K(b)) of a homologous series of 19 PAMAM dendrimers in aqueous solutions at physiological pH (7.4) as a function of dendrimer generation, terminal group, and core chemistry. To gain insight into the mechanisms of HSA binding to PAMAM dendrimers, we combined (1)H NMR, saturation transfer difference (STD) NMR, and NMR diffusion ordered spectroscopy (DOSY) of dendrimer-HSA complexes with atomistic molecular dynamics (MD) simulations of dendrimer conformation in aqueous solutions. The binding measurements show that the HSA binding constants (K(b)) of PAMAM dendrimers depend on dendrimer size and terminal group chemistry. The NMR (1)H and DOSY experiments indicate that the interactions between HSA and PAMAM dendrimers are relatively weak. The (1)H NMR STD experiments and MD simulations suggest that the inner shell protons of the dendrimers groups interact more strongly with HSA proteins. These interactions, which are consistently observed for different dendrimer generations (G0-NH(2)vs G4-NH(2)) and terminal groups (G4-NH(2)vs G4-OH with amidoethanol groups), suggest that PAMAM dendrimers adopt backfolded configurations as they form weak complexes with HSA proteins in aqueous solutions at physiological pH (7.4).

Identifying Components in Dissolved Humic Acid That Bind Organofluorine Contaminants using 1H{19F} Reverse Heteronuclear Saturation Transfer Difference NMR Spectroscopy

Interactions between dissolved peat humic acid and two structurally dissimilar organofluorine compounds, perfluoro-2-naphthol and perfluoro-octanoic acid, are probed using a novel (1)H{(19)F} Nuclear Magnetic Resonance (NMR) Spectroscopy technique based on the Saturation Transfer Difference (STD) experiment. This technique is used here to show selectively only those regions of the (1)H NMR spectrum of humic acid that arise from chemical constituents interacting with perfluorinated organic compounds. This approach provides a tool for high-resolution analysis of interactions between contaminants and soil organic matter (SOM) directly at the molecular level. Soil organic matter is a chemically heterogeneous mixture, and traditional techniques used to study sorption or binding phenomenon are unable to resolve multiple processes occurring simultaneously at distinct chemical moieties. Here, multiple interaction domains are identified based on known chemical constituents of humic acid, most notably from lignin- and protein-derived material. Specifically, perfluoro-2-naphthol is shown to interact with lignin, protein, and aliphatic material; however, preference is exhibited for lignin-derived domains, while perfluoro-octanoic acid exhibits near exclusive preference for the protein-derived domains of humic acid.