Docking of noncompetitive inhibitors into dengue virus type 2 protease: understanding the interactions with allosteric binding sites

A group of flavanones and their chalcones, isolated from Boesenbergia rotunda L., were previously reported to show varying degrees of noncompetitive inhibitory activities toward Dengue virus type 2 (Den2) protease. Results obtained from automated docking studies are in agreement with experimental data in which the ligands were shown to bind to sites other than the active site of the protease. The calculated K(i) values are very small, indicating that the ligands bind quite well to the allosteric binding site. Greater inhibition by pinostrobin, compared to the other compounds, can be explained by H-bonding interaction with the backbone carbonyl of Lys74, which is bonded to Asp75 (one of the catalytic triad residues). In addition, structure-activity relationship analysis yields structural information that may be useful for designing more effective therapeutic drugs against dengue virus infections.     

Probing the interactions between chlorpheniramine and 2:1 phyllosilicates

Interactions between chlorpheniramine (CP), an antihistamine drug used to treat allergy, and 2:1 phyllosilicates were studied under batch kinetic and different solution conditions to investigate the effect of charge density of the substrates on CP removal from solution. The CP removal by Na-montmorillonite was instantaneous, with a very large rate constant and a fast rate, reaching a capacity of 0.64 mmol/g, compared to its cation exchange capacity of 0.85 mmol_c/g. In contrast, CP removal by talc was 10 times lower at 0.06 mmol/g. Stoichiometric desorption of exchangeable cations accompanying CP removal by Na-montmorillonite confirmed cation exchange as the dominant interaction mechanism. Solution pH had a minimal effect on CP removal by Na-montmorillonite until pH 11. On the contrary, a slight increase in CP removal by talc was observed as the solution pH increased, due to increased negative charges on the pH-dependent surfaces of talc. Interactions between CP and Na-montmorillonite occurred on both external and interlayer sites, resulting in a d-spacing expansion from 12.5 Å to 15.2 Å. In contrast, interactions between CP and talc were only limited to the external surfaces. It was the charge density that ultimately controlled the amount of CP removal by 2:1 phyllosilicates. Thus, montmorillonite offers a superior option for the removal of cationic drugs from aqueous solution.     

Synthesis and DNA binding properties of iminodiacetic acid-linked polyamides: characterization of cooperative extended 2:1 side-by-side parallel binding

A series of iminodiacetic acid (IDA)-linked polyamides (DpPyPyPy-IDA-PyPyPyDp) were prepared and constitute polyamides joined head-to-head by a functionalizable five-atom linker. It was found that the IDA linker exerts a unique influence over the DNA binding conformation differing from both the beta-alanine (extended) or gamma-aminobutyric acid (hairpin) linkers, resulting in cooperative parallel side-by-side 2:1 binding in an extended conformation most likely with a staggered versus stacked alignment. A generalized variant of a fluorescent intercalator displacement (FID) assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding-site size was used to distinguish between the binding modes of the IDA-linked polyamides.     

Supramolecular interactions between ethylene-bridged oligoureas: nanorings and chains formed by cooperative positive allostery

Ethylene-bridged oligoureas are dynamic foldamers in which the polarity of a coherent chain of intramolecular hydrogen bonds may be controlled by intra- or intermolecular interactions with hydrogen-bond donors or acceptors. In this paper, we describe the way that supramolecular interactions between ethylene-bridged oligoureas bearing a 3,5-bis(trifluoromethyl)phenylurea (BTMP) terminus leads to higher-order structures both in the crystalline state and in solution. The oligoureas self-assemble by head-to-tail hydrogen bonding interactions to form either supramolecular ‘nanorings’ with cyclic hydrogen bond chain directionality, or supramolecular helical chains of hydrogen bonds. The self-assembly process features a cascade of cooperative positive allostery, in which each intermolecular hydrogen bond formation at the BTMP terminus switches the native hydrogen bond chain directionality of monomers, favouring further assembly. Monomers with a benzyl urea terminus self-assemble into nanorings, whereas monomers with a N-ethyl urea terminus form helical chains. In the crystal state, parallel helices have identical handedness and polarity, whereas antiparallel helices have opposite handedness. The overall dipole moment of crystals is zero due to the antiparallel arrangements of local dipoles in the crystal packing. Supramolecular interactions in solution were also examined by VT and DOSY NMR spectroscopy, up to the point of crystal formation. The size of higher aggregates in dichloromethane was estimated by their hydrodynamic radius. The relative orientation of the monomers within the aggregates, determined by 2D ROESY NMR, was the same as in the crystals, where syn-orientations lead to the formation of rings and anti-orientations result in chains. Overall, the switch of hydrogen bond polarity propagates intermolecularly in crystal and solution states, constituting an example of intermolecular communication within supramolecular polymers.

Hydrogen-bonded urea oligomers form supramolecular aggregates in the crystalline state. Intermolecular hydrogen bonding generates nano-rings or chains, according to the length and substitution pattern of the oligomers.     

A dinuclear iron complex based on parallel malonate binding sites: cooperative activation of dioxygen and biomimetic ligand oxidation

A ligand that offers two parallel malonate binding sites linked by a xanthene backbone, namely, Xanthmal2-, has been utilised to synthesise dinuclear FeII complex [Fe2(Xanthmal)2] (1). The reactivity of 1 in contact with O2 was investigated at -40 degrees C and room temperature. After activation of O2 through interaction with both iron centres the ligand is oxidised: at the Calpha position monooxygenation and peroxide formation occur, partially accompanied by C-C bond cleavage to yield alpha-keto ester groups. To reveal mechanistic details investigations concerning 1) peroxide decomposition, 2) the reactivity of a corresponding mononuclear complex, 3) the influence of monooxygenation of the ligand on the reactivity and 4) product formation in dependence on time were carried out. The results can be explained by postulating formation of high-valent Fe intermediates and ligand-to-metal electron transfer, and the mechanistic scheme derived includes several steps that mimic the (suggested) functioning of non-heme iron enzymes. In agreement with this proposal, ligand oxidation can also be performed catalytically. Furthermore, we show that via a competitive route [(Xanthmal)2Fe2O] (2) is formed, which is unreactive towards O2 and thus is a dead end with respect to ligand oxidation. Both compounds 1 and 2 were fully characterised, and their properties are discussed.     

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3′- and 5′-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3′-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

Using small molecule microarray TDP1 inhibitors have been identified that bind in a trivalent mode.     

Chemical shifts as a novel measure of interactions between two binding sites of symmetric dialkyldimethylammonium bromides to α-cyclodextrin

Complex formation of α-cyclodextrin (α-CD) with decyltrimethylammonium (DeTAB), N,N-dioctyldimethylammonium (DOAB), and N,N-didecyldimethylammonium bromides (DDeAB) was investigated by proton NMR spectroscopy. Analysis of chemical shifts yielded macroscopic 1:1 and 1:2 binding constants (K₁ and K₂) and chemical shift differences (Δδ_SD and Δδ_SD2) for the 1:1 and 1:2 complexes of DeTAB, DOAB, and DDeAB with α-CD. The K₁ and K₂ values of DDeAB were quantitatively explained on the basis of the assumption that the microscopic 1:1 binding constant of DDeAB is identical to the observed K₁ value of DeTAB. The K₂ value of DDeAB was also explained in terms of its observed K₁ value and the independent binding of two alkyl chains. Furthermore, the Δδ_SD and Δδ_SD2 values for protons of DDeAB and α-CD were quantitatively explained on the basis of the assumption that the geometry of the decyl group of DDeAB in an α-CD cavity is identical to that of DeTAB. The Δδ_SD value was also explicable on the basis of the same geometric assumption and the observed Δδ_SD2 value for this system. Similar results were obtained for the 1:1 and 1:2 DOAB-α-CD complexes.     

Guanidiniocarbonyl-pyrrole-aryl conjugates as nucleic acid sensors: switch of binding mode and spectroscopic responses by introducing additional binding sites into the linker

Two novel guanidiniocarbonyl pyrrole-pyrene conjugates 3 and 4 as spectroscopic probes for ds-polynucleotides were synthesized and their interaction with different ds-DNAs/RNAs studied. Compared to a previously reported first set of conjugates (1 and 2) the significant extension and increased rigidity of the central part of the structure resulted in a switch of DNA binding mode from intercalative (previously studied derivatives 1 and 2 with a nonbinding and flexible linker) to minor groove binding of the two novel guanidiniocarbonyl-pyrrole-pyrene conjugates 3 and 4. These two compounds interact strongly with ds-DNAs, but only weakly with ds-RNA. The newly incorporated heterocyclic moieties within the central part of the structure of 3 and 4 were able to control by steric and hydrogen-bonding effects the alignment of the molecules within various, structurally different forms of DNA minor grooves, whereby even small differences in the position of the attached pyrene within the groove were reflected in different fluorimetric responses. In addition, 3 and 4 revealed intriguing in vitro selectivity among various human tumour cell lines.     

Ni(II).Arg-Gly-His-DNA interactions: investigation into the basis for minor-groove binding and recognition

A study of the minor-groove recognition of A/T-rich DNA sites by Ni(II).L-Arg-Gly-His and Ni(II).D-Arg-Gly-His was carried out with a fluorescence-based binding assay, one- and two-dimensional (1D and 2D) NMR methodologies, and molecular simulations. Fluorescence displacement titrations revealed that Ni(II).L-Arg-Gly-His binds to A/T-rich sequences better than the D-Arg diastereomer, while NMR investigations revealed that both metallopeptides bind to the minor groove of an AATT core region as evidenced by an intermolecular nuclear Overhauser effect (NOE) between each metallopeptide His imidazole C4 proton and the C2 proton of adenine. Results from molecular dynamics simulations of these systems were consistent with the experimental data and indicated that the His imidazole N-H, the N-terminal peptide amine, and Arg side chains of each metallopeptide are major determinants of minor-groove recognition by functioning as H-bond donors to the O2 of thymine residues or N3 of adenine residues.     

Insights into the N-terminal Cu(II) and Cu(I) binding sites of the human copper transporter CTR1

Abstract

Copper transporter 1 (CTR1) is the main copper transporter in the eukaryotic system. CTR1 has several important roles: It binds Cu(II) ions that are present in the blood; it reduces those Cu(II) ions to Cu(I); and it subsequently transfers Cu(I) to the cytoplasmic domain, where the ion is delivered to various cellular pathways. Here, we seek to identify CTR1 binding sites for Cu(II) and Cu(I) and to shed light on the Cu(II)-to-Cu(I) reduction process. We focus on the first 14 amino acids of CTR1. This N-terminal segment is rich with histidine and methionine residues, which are known to bind Cu(II) and Cu(I), respectively; thus, this region has been suggested to have an important function in recruiting Cu(II) and reducing it to Cu(I). We utilize electron paramagnetic resonance (EPR) spectroscopy together with nuclear magnetic resonance (NMR) and UV-VIS spectroscopy and alanine substitution to reveal Cu(II) and Cu(I) binding sites in the focal 14-amino-acid segment. We show that H5 and H6 directly coordinate to Cu(II), whereas M7, M9, and M12 are involved in Cu(I) binding. This research is another step on the way to a complete understanding of the cellular copper regulation mechanism in humans.     

Enhancing binding affinity by the cooperativity between host conformation and host-guest interactions

Glutamate-functionalized oligocholate foldamers bound Zn(OAc)(2), guanidine, and even amine compounds with surprisingly high affinities. The conformational change of the hosts during binding was crucial to the enhanced binding affinity. The strongest cooperativity between the conformation and guest-binding occurred when the hosts were unfolded but near the folding-unfolding transition. These results suggest that high binding affinity in molecular recognition may be more easily obtained from large hosts capable of strong cooperative conformational changes instead of those with rigid, preorganized structures.     

Soft- and reactive-landing of Cr(aniline)2 sandwich complexes onto self-assembled monolayers: separation between functional and binding sites

Soft- and reactive-landing of gas-phase synthesized cationic Cr(aniline)(2) complexes onto self-assembled monolayers of methyl-terminated (CH(3)-SAM) and carboxyl-terminated (COOH-SAM) organothiolates coated on gold were performed at hyperthermal collision energy (5-20 eV). The properties of the Cr(aniline)(2) complexes on the SAM surfaces were characterized using infrared reflection absorption spectroscopy (IRAS) and temperature-programmed desorption (TPD), together with theoretical calculations based on density functional theory (DFT). For the CH(3)-SAM, the Cr(aniline)(2) complexes were embedded inside the SAM matrix in a neutral charge state, keeping a sandwich structure. For the COOH-SAM, the IRAS and TPD study revealed that the amine-containing Cr(aniline)(2) complexes were bound to the SAM surface in two forms of physisorption and chemical linking through an amide bond. In the desorption, the latter form appeared as the reaction product between organothiolates and Cr(aniline)(2) above 400 K, where the organothiolate molecules, forming the SAM, were desorbed from the gold surface. The results show that the hyperthermal depositions onto a COOH-SAM bring about reactive-landing followed by covalent linking of an amide bond between the amine-containing Cr(aniline)(2) complexes to the carboxyl-terminated SAM surface, in which the binding sites can be separated from the functional sites of the d-π interaction.     

Dipolar interactions and hydrogen bonding in supramolecular aggregates: understanding cooperative phenomena for 1st hyperpolarizability

Weak intermolecular forces like dipolar interactions and hydrogen-bonding lead to a variety of different packing arrangements of molecules in crystals and self-assemblies. Such differences in the arrangements change the extent of excitonic splitting and excitation spectra in the multichromophore aggregates. In this tutorial review, the role of such interactions in fine tuning the linear and 1st non-linear optical (NLO) responses in molecular aggregates are discussed. The non-additivity of these optical properties arise specifically due to such cooperative interactions. Calculations performed on dimers, trimers and higher aggregates for model systems provide insights into the interaction mechanisms and strategies to enhance the 1st hyperpolarizabilities of pi-conjugated molecular assemblies. Flexible dipole orientations in the alkane bridged chromophores show odd-even variations in their second-harmonic responses that are explained through their dipolar interactions in different conformations. Parameters for the optical applications of molecules arranged in constrained geometry, like in Calix[n]arene, have been elucidated. We also highlight the recent developments in this field of research together with their future prospects.     

Nanofibers resulting from cooperative electrostatic and hydrophobic interactions between peptides and polyelectrolytes of opposite charge

We investigated whether cationic peptides that contain hydrophobic side chains were able to stabilize themselves via hydrophobic interactions between neighboring peptide molecules upon electrostatic binding to oppositely charged polyelectrolytes. The interaction mechanism was examined through a model system consisting of the anionic polyelectrolyte alginate and the cationic decapeptide ozarelix. The interaction resulted in the formation of highly ordered complexes that were noticeable upon visual inspection. These complexes were then investigated by microscopic techniques and shown to exhibit a branched network structure. Cryogenic-temperature transmission electron microscopy (cryo-TEM) and negative staining TEM revealed that the molecular interactions between alginate and ozarelix led to the formation of nanofibers. The rodlike nanofibers had a diameter distribution of 4-8 nm. Isothermal titration calorimetry was used to determine the thermodynamic parameters of the alginate-ozarelix interaction. The binding constant was found to be on the order of 10(6) M(-1), indicating a high binding affinity. The interaction of the peptide with the polyelectrolyte triggered profound changes in the conformation of ozarelix, which was confirmed by UV spectroscopy and circular dichroism. On the basis of these experimental results, a theoretical modeling study of the alginate-ozarelix interaction was conducted to gain a better molecular-level understanding of the complex structure. It revealed that, upon binding of ozarelix to alginate, new intermolecular and intramolecular aromatic interactions between the ozarelix molecules occurred. These interactions changed the conformation of the peptide, a modification in which the aromatic side chains played a major role. Our results indicate that the cationic peptides interact with the polyanions via electrostatic interactions, but are additionally stabilized via hydrophobic interactions. This binding mode may serve as a powerful tool to extend the duration of drug release in hydrogel drug delivery systems.     

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.