Second-generation mimics of ganglioside GM1 oligosaccharide: a three-dimensional view of their interactions with bacterial enterotoxins by NMR and computational methods

As a step to delineate a strategy of ligand design for cholera toxin (CT), NMR studies were performed on several mimics of the GM1 ganglioside oligosaccharide. The conformation of these analogues was investigated first in solution and then upon binding to cholera toxin by transferred nuclear Overhauser effect (TR-NOE) measurements. It was demonstrated that CT selects a conformation similar to the global minima of the free saccharides from the ensemble of presented conformations. No evidence of major conformational distortions was obtained, but one or two of the available conformers of the hydroxyacid side chain appear to be selected in the bound state. The NMR data were interpreted with the aid of computer models, generated and analyzed by using a combination of different approaches (MacroModels' MC/EM and MC/SD, Autodock, and GRID). Analysis of the NMR data supported by computational studies allowed us to interpret the experimental observations and to derive workable models of the ligand:toxin complexes. These models suggest that the higher affinity of the (R)-lactic acid derivative 3 may stem from lipophilic interactions with a hydrophobic area in the toxin binding site located in the vicinity of the sialic acid side chain binding region of the CT:GM1 complex, and formed by the side chain of Ile-58 and Lys-34. Thus, the models obtained have allowed us to make useful design suggestions for the improvement of ligand affinity.     

Agostic interactions in d0 metal alkyl complexes

The phenomenon of agostic interactions is reviewed and the nature of the interaction is revisited. A historical perspective is followed by an overview of experimental techniques used to diagnose agostic behavior, and previous interpretations of agostic bonding are presented. A series of simple metal alkyl complexes is considered and a new model for the phenomenon in d(0) systems is developed which sets them apart from agostic late-transition-metal complexes. Factors such as the valence electron count and coordination number of the metal center are revealed to be unimportant in facilitating the interaction in most d(0) systems. The charge density distribution in several transition-metal alkyl complexes is explored by experimental and theoretical techniques, including the powerful "Atoms in Molecules" approach. Local charge concentrations are shown to play an important role in the agostic interaction. Finally, we demonstrate for the first time a way to manipulate and control the magnitude and disposition of such local charge concentrations, and hence the strength of agostic interactions in d(0) metal alkyl complexes.     

The dilemma of CrIIINiII exchange interactions: ferromagnetism versus antiferromagnetism

The sign of the exchange interaction in dinuclear Cr(III)Ni(II) complexes was analyzed using theoretical methods based on density functional theory. This approach allowed us to reproduce the experimental J values correctly. In addition, the Kahn-Briat model, which uses the square of the sum of the overlaps between the magnetic orbitals to correlate with the exchange coupling constant, provided a reasonable correlation between the different types of Cr(III)Ni(II) complexes when using biorthogonalized orbitals. We also examined the exchange interactions in two polynuclear Cr(III)Ni(II) complexes: a Cr(7)Ni ring and an S-shaped Cr(12)Ni(3) complex. We concluded that both systems exhibit antiferromagentic interactions, and that the Cr(III)···Ni(II) interactions are similar in value to the C(III)···Cr(III) exchange couplings.     

Experimental measurement of carbohydrate-aromatic stacking in water by using a dangling-ended DNA model system

Protein-carbohydrate recognition is of fundamental importance for a large number of biological processes; carbohydrate-aromatic stacking is a widespread, but poorly understood, structural motif in this recognition. We describe, for the first time, the measurement of carbohydrate-aromatic interactions from their contribution to the stability of a dangling-ended DNA model system. We observe clear differences in the energetics of the interactions of several monosaccharides with a benzene moiety depending on the number of hydroxy groups, the stereochemistry, and the presence of a methyl group in the pyranose ring. A fucose-benzene pair is the most stabilizing of the studied series (-0.4 Kcal mol(-1)) and this interaction can be placed in the same range as other more studied interactions with aromatic residues of proteins, such as Phe-Phe, Phe-Met, or Phe-His. The noncovalent forces involved seem to be dispersion forces and nonconventional hydrogen bonds, whereas hydrophobic effects do not seem to drive the interaction.     

The nature of intermolecular CuI...CuI interactions: a combined theoretical and structural database analysis

The nature of intermolecular interactions between dicoordinate Cu(I) ions is analyzed by means of combined theoretical and structural database studies. Energetically stable Cu(I).Cu(I) interactions are only found when the two monomers involved in the interaction are neutral or carry opposite charges, thus allowing us to speak of bonding between the components of the bimolecular aggregate. A perturbative evaluation of the components of the intermolecular interaction energies, by means the IMPT scheme of Stone, indicates that both the Coulombic and dispersion forces are important in determining the Cu(I).Cu(I) bonding interactions, because only a small part of that energy is attributable to Cu.Cu interactions, while a large component results from Cu.ligand interactions. The electrostatic component is the dominant one by far in the interaction between charged monomers, while in the interaction between neutral complexes, the electrostatic component is found to be of the same order of magnitude as the dispersion term. Bimolecular aggregates that have like charges are repulsive by themselves, and their presence in the solid state results from anion.cation interactions with ions external to this aggregate. In these cases, the short-contact Cu.Cu interactions here should be more properly called counterion-mediated Cu.Cu bonds.     

A theoretical study of anion-pi interactions in seven-membered rings.

Several complexes of tropylium (1) with anions are optimized at the RI-MP2(full)/6-31++G** level of theory. This binding unit can interact very favorably with anions, and it combines the strength of the electrostatic interaction with the directionality of the anion-pi interaction. The complexes of 1 with anions are characterized by means of the Bader theory of "atoms-in-molecules," and the physical nature of the interaction has been analyzed by means of the molecular interaction potential with polarization tool. Experimental evidence of anion-pi interactions involving seven-membered rings has been found in the solid state.     

Noncovalent keystone interactions controlling biomembrane structure

There is a biomedical need to develop molecular recognition systems that selectively target the interfaces of protein and lipid aggregates in biomembranes. This is an extremely challenging problem in supramolecular chemistry because the biological membrane is a complex dynamic assembly of multifarious molecular components with local inhomogeneity. Two simplifying concepts are presented as a framework for basing molecular design strategies. The first generalization is that association of two binding partners in a biomembrane will be dominated by one type of non-covalent interaction which is referred to as the keystone interaction. Structural mutations in membrane proteins that alter the strength of this keystone interaction will likely have a major effect on biological activity and often will be associated with disease. The second generalization is to view the structure of a cell membrane as three spatial regions, that is, the polar membrane surface, the midpolar interfacial region and the non-polar membrane interior. Each region has a distinct dielectric, and the dominating keystone interaction between binding partners will be different. At the highly polar membrane surface, the keystone interactions between charged binding partners are ion-ion and ion-dipole interactions; whereas, ion-dipole and ionic hydrogen bonding are very influential at the mid-polar interfacial region. In the non-polar membrane interior, van der Waals forces and neutral hydrogen bonding are the keystone interactions that often drive molecular association. Selected examples of lipid and transmembrane protein association systems are described to illustrate how the association thermodynamics and kinetics are dominated by these keystone noncovalent interactions.     

Structural diversity of lanthanide–amino acid complexes under near physiological pH conditions and their recognition of single-stranded DNA

We reported here four structures of lanthanide–amino acid complexes obtained under near physiological pH conditions and their individual formula can be described as [Tb₂(dl-Cys)₄(H₂O)₈]Cl₂ (1), [Eu₄(μ₃-OH)₄(l-Asp)₂(l-HAsp)₃(H₂O)₇] Cl · 11.5H₂O (2), [Eu₈(l-HVal)₁₆(H₂O)₃₂]Cl₂₄ · 12.5H₂O (3), and [Tb₂(dl-HVal)₄(H₂O)₈]Cl₆ · 2H₂O (4). These complexes showed diverse structures and have shown potential application in DNA detection. We studied the interactions of the complexes with five single-stranded DNA and found different fluorescence enhancement, binding affinity and binding stoichiometry when the complexes are bound to DNA.     

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

We have developed an iterative knowledge-based scoring function (ITScore) to describe protein-ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein-ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 2287), and compared with 14 other scoring functions. The results show that ITScore yielded a high success rate of 82% on identifying native-like binding modes under the criterion of rmsd < or = 2 A for each top-ranked ligand conformation. The success rate increased to 98% if the top five conformations were considered for each ligand. In the case of binding affinity prediction, ITScore also obtained a good correlation for this test set (R = 0.65). Next, ITScore was used to predict binding affinities of a second diverse test set of 77 protein-ligand complexes prepared by Muegge and Martin (J Med Chem 1999, 42, 791), and compared with four other widely used knowledge-based scoring functions. ITScore yielded a high correlation of R2 = 0.65 (or R = 0.81) in the affinity prediction. Finally, enrichment tests were performed with ITScore against four target proteins using the compound databases constructed by Jacobsson et al. (J Med Chem 2003, 46, 5781). The results were compared with those of eight other scoring functions. ITScore yielded high enrichments in all four database screening tests. ITScore can be easily combined with the existing docking programs for the use of structure-based drug design.     

Strong magnetic interactions through weak bonding interactions in organometallic radicals: combined experimental and theoretical study

The magnetic properties of a series of three neutral radical organometallic complexes of general formula [CpNi(dithiolene)]. have been investigated by a combination of X-ray crystal structure analysis and magnetic susceptibility measurements, while the assignment of the exchange coupling constants to the possible exchange pathways has been accomplished with the help of calculations based on density functional theory (DFT). The syntheses and X-ray structures of [CpNi(adt)] (adt=acrylonitrile-2,3-dithiolate) and [CpNi(tfd)] (tfd=1,2-bis(trifluoromethyl)ethene-1,2-dithiolate) complexes are described, while [CpNi(mnt)] (mnt=maleonitriledithiolate) was reported earlier. In the three complexes, we observed strong antiferromagnetic coupling that could not be explained solely by short SS intermolecular contacts. Our calculations indicated that spin density in these complexes is strongly delocalized on the NiS2 moiety, with up to 20% on the Cp ring. As a consequence, CpCp and Cpdithiolene overlap interactions have been identified as responsible for antiferromagnetic couplings. The [CpNi(adt)] complex thus has a value J=-369.5 cm(-1) for an exchange interaction through a pi stacking due to the CpCp overlap.     

Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B

Ligand-based NMR techniques to study protein–ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.     

Unveiling the Noncovalent Interaction of Thiazol-2-ylidene and Its Derivatives as N-heterocyclic Carbene with Different Proton Donor Molecules

The importance of noncovalent interaction has gained attention in various domains covering drug and novel catalyst design. The present study mainly characterizes the role of hydrogen bond (H-bond) and other intermolecular interactions in different (1 : 1) complex analogues formed between the N-aryl-thiazol-2-ylidene (YR) and five proton donor (HX) molecules. The analysis of the singlet-triplet energy gap ( ) confirmed the stability of the singlet state for this class of N-aryl-thiazol-2-ylidenes than the triplet state. The interaction energy values of the YR-HX complexes follow the order: YR-NH₃<YR-HCN<YR-H₂O<YR-MeOH<YR-HF. In addition, substituting the H-atom of the N−H bond with bulky groups (−R) leads to an increase in the interaction energy of the YR-HX complexes. Hence, it was found that the replacement of N-atom in N-heterocyclic carbene (NHC) by S-atom forming N-aryl-thiazol-2-ylidene results in comparable intermolecular interactions with proton donor molecules similar to imidazole-2-ylidene (NHC). The current study enlightened the role of noncovalent interactions in carbene complexes with proton donor molecules. We hope that our work on carbene chemistry will pave the way for its application in the designing and synthesis of efficient catalysts.     

Molecular mechanics on bonding and non-bonding interactions in (atom@C_(60))

The interactions between the embedded atom X (X=Li,Na,K,Rb,Cs; F,Cl,Br,I) and C60cage in the endohedral-form complexes (X@C60) are calculated and discussed according to molecular mechanics from the point of view of the bonding and non-bonding.It is found from the computational results that for atoms with radii larger than Li's,their locations with the minimum interaction in (X@C60) are at the cage center,while atom Li has an off-center location with the minimum interaction deviation of-0.05 nm,and the cage-environment in C60 can be regarded as sphero-symmetry in the region with radius r of ~0.2 nm.It is shown that the interaction between X and C60 cage is of non-bonding characteristic,and this non-bonding interaction is not purely electrostatic.The repulsion and dispersion in non-bonding interactions should not be neglected,which make important contribution to the location with minimum interaction of X,at center or off center.Some rules about the variations of interactions with atomic radii have been ob     

Nature of the water/aromatic parallel alignment interactions

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O? H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE_{CCSD(T)(limit)} = ?2.45 kcal mol^?1 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry‐adapted perturbation theory, and extended transition state‐natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV‐based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O? H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.     

Exploring the (Very Flat) Potential Energy Landscape of R−Br⋅⋅⋅π Interactions with Accurate CCSD(T) and SAPT Techniques

Halogen bonds involving an aromatic moiety as an acceptor, otherwise known as R?X???π interactions, have increasingly been recognized as being important in materials and in protein–ligand complexes. These types of interactions have been the subject of many recent investigations, but little is known about the ways in which the strengths of R?X???π interactions vary as a function of the relative geometries of the interacting pairs. Here we use the accurate CCSD(T) and SAPT2+3δMP2 methods to investigate the potential energy landscapes for systems of HBr, HCCBr, and NCBr complexed with benzene. It is found that only the separation between the complexed molecules have a strong effect on interaction strength while other geometric parameters, such as tilting and shifting R?Br???π donor relative to the benzene plane, affect these interactions only mildly. Importantly, it is found that the C_6v (T‐shaped) configuration is not the global minimum for any of the dimers investigated.     

Weak interactions and molecular recognition in systems involving electron transfer proteins

Electrostatic interactions and other weak interactions between amino acid side chains on protein surfaces play important roles in molecular recognition, and the mechanism of their intermolecular interactions has gained much interest. We established that charged peptides are useful for investigating the molecular recognition character of proteins and their molecular interaction induced structural changes. Positively charged lysine peptides competitively inhibited electron transfer from reduced cytochrome f (cyt f or cytochrome c (cyt c) to oxidized plastocyanin (PC), due to neutralization of the negatively charged site of PC by formation of PC-lysine peptide complexes. Lysine peptides also inhibited electron transfer from cyt c to cytochrome c peroxidase. Likewise, negatively charged aspartic acid peptides interacted with the positively charged sites of cytfand cyt c, and competitively inhibited electron transfer from reduced cytfor cyt c to oxidized PC and from [Fe(CN)6]4- to oxidized cyt c. Changes in the geometry and a shift to a higher redox potential of the active site Cu of PC on oligolysine binding were detected by spectroscopic and electrochemical measurements, owing to the absence of absorption in the visible region for lysine peptides. Structural and redox potential changes were also observed for cyt f and cyt c by interaction with aspartic acid peptides.     

Solution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin

The structure-based design of multivalent ligands offers an attractive strategy toward high affinity protein inhibitors. The spatial arrangement of the receptor-binding sites of cholera toxin, the causative agent of the severe diarrheal disease cholera and a member of the AB(5) bacterial toxin family, provides the opportunity of designing branched multivalent ligands with 5-fold symmetry. Our modular synthesis enabled the construction of a family of complex ligands with five flexible arms each ending with a bivalent ligand. The largest of these ligands has a molecular weight of 10.6 kDa. These ligands are capable of simultaneously binding to two toxin B pentamer molecules with high affinity, thus blocking the receptor-binding process of cholera toxin. A more than million-fold improvement over the monovalent ligand in inhibitory power was achieved with the best branched decavalent ligand. This is better than the improvement observed earlier for the corresponding nonbranched pentavalent ligand. Dynamic light scattering studies demonstrate the formation of concentration-dependent unique 1:1 and 1:2 ligand/toxin complexes in solution with no sign of nonspecific aggregation. This is in complete agreement with a crystal structure of the branched multivalent ligand/toxin B pentamer complex solved at 1.45 A resolution that shows the specific 1:2 ligand/toxin complex formation in the solid state. These results reiterate the power of the structure-based design of multivalent protein ligands as a general strategy for achieving high affinity and potent inhibition.     

Isolation of cholera toxin receptors from a mouse fibroblast and lymphoid cell line by immune precipitation

Cholera toxin receptors have been isolated from both a mouse fibroblast (Balbc/3T3) and mouse lymphoid cell line labeled by the galactose oxidase borotritiide technique. Tritiated receptor-toxin complexes solubilized in NP40 were isolated by addition of toxin antibody followed by a protein A-containing strain of Staphylococcus aureus. In both cell types by far the major species of toxin receptor isolated was ganglioside in nature, although galactoproteins were also present in the immune complexes. Whether the galactoproteins form part of a toxin-receptor complex or are artifacts of the isolation procedure is presently unclear. The relative specificity of cholera toxin for a carbohydrate sequence in a glycolipid suggests that the toxin might prove a useful tool in establishing the function and organization of glycolipids in membranes. For example, interaction of cholera toxin with the mouse lymphoid cell line was shown to result in patching and capping of bound toxin, raising the possibility that the glycolipid receptor interacts indirectly with cytoskeletal elements. Cholera toxin might also be used to select for mutant fibroblasts lacking the toxin receptor and therefore having an altered glycolipid profile. Such mutants might prove useful in establishing the relationship (if any) between modified glycolipid pattern and other aspects of the transformed phenotype. Attempts to isolate mutants, based on the expectation that growth of cells containing the toxin receptor would be inhibited by the increase in cAMP levels normally induced by cholera toxin, proved unsuccessful. Cholera toxin failed to inhibit significantly the growth of either Balbc or Swiss 3T3 mouse fibroblasts although it markedly elevated cAMP levels.     

Gas‐phase interactions of organotin compounds with cysteine

The gas‐phase interactions of cysteine with di‐organotin and tri‐organotin compounds have been studied by mass spectrometry experiments and quantum calculations. Positive‐ion electrospray spectra show that the interaction of di‐ and tri‐organotins with cysteine results in the formation of [(R)₂Sn(Cys‐H)]⁺ and [(R)₃Sn(Cys)]⁺ ions, respectively. MS/MS spectra of [(R)₂Sn(Cys‐H)]⁺ complexes are characterized by numerous fragmentation processes, notably associated with elimination of NH₃ and (C,H₂,O₂). Several dissociation routes are characteristic of each given organic species. Upon collision, both the [(R)₃Sn(Gly)]⁺ and [(R)₃Sn(Cys)]⁺ complexes are associated with elimination of the intact amino acid, leading to the formation of [(R)₃Sn]⁺ cation. But for the latter complex, two additional fragmentation processes are observed, associated with the elimination of NH₃ and C₃H₄O₂S. Calculations indicate that the interaction between organotins and cysteine is predominantly electrostatic but also exhibits a considerable covalent character, which is slightly more pronounced in tri‐organotin complexes. A preferred bidentate interaction of the type ‐η²‐S‐NH₂, with sulfur and the amino group, is observed. As for the [(R)₃Sn(Cys)]⁺ complexes, their stability is due to the combination of the hydrogen bond taking place between the amino group and the sulfur lone pair and the interaction between the carboxylic oxygen atom and the metal. Copyright © 2016 John Wiley & Sons, Ltd.