Intramolecular Hydrogen-bonding Network Research Articles

The conformational behaviour of freed-glucose—at last

The conformational behaviour of isolated D-glucose has been revealed in this work using Fourier transform microwave spectroscopy coupled with laser ablation of crystalline α- and β-glucopyranose samples. Four conformers of α-D-glucopyranose and three of β-D-glucopyranose have been unequivocally identified on the basis of the spectroscopic rotational parameters in conjunction with ab initio predictions. Stereoelectronic hyperconjugative factors, like those associated with anomeric or gauche effects, as well as the cooperative OH⋯O chains extended along the entire molecule, are the main factors driving the conformational behaviour. The most abundant conformers exhibit a counter-clockwise arrangement (cc) of the network of intramolecular hydrogen bonds.

Molecular recognition: preparation and characterization of two tripodal anion receptors

Two new tripodal hydroxyl-based anion receptors (1 and 2) are reported and their 1:1 molecular complexes with Cl−, H2PO4−, and OAc− along with the (M − 1)− ion of 1 were characterized by negative ion photoelectron spectroscopy in the gas phase and by binding constant determinations in four solvents (i.e., CDCl3, CD2Cl2, CD3COCD3, and CD3CN). An intramolecular hydrogen bond network (HBN) in hexaol 1 was found to diminish its binding whereas the triol 2 is the strongest aliphatic hydroxyl-based receptor to date.

Abstract C212: Discovery of high affinity cyclic peptidomimetics binding Mcl-1 and Ras.

Abstract Many well-validated oncology targets regulate signaling pathways through interactions with other proteins. Addressing these targets, which often lack suitable small molecule binding sites, requires larger and more complex molecules that are capable of binding relatively large or flat surfaces. We are testing whether this target class can be addressed by using in vitro selection to screen extremely large cyclic peptidomimetic libraries with novel design features. Peptide-mRNA display libraries comprised of approximately 1 trillion cyclic peptidomimetics were created by in vitro translation using a mixture of natural, unnatural, and N-methylated amino acids. Pooled libraries were subjected to multiple rounds of selection and amplification to identify sequences that bound with high affinity to immobilized Mcl-1 or Ras. Selected Mcl-1 cyclic peptidomimetics were synthesized and their binding and specificity were studied by surface plasmon resonance (SPR) using immobilized Mcl-1 and Bcl-2. Fluorescence polarization (FP) was used to demonstrate that isolated peptidomimetics competed with Bim-derived peptides (IC50≈100-400 nM), a measure of their ability to block the interactions between Mcl-1 and binding partners. The co-crystal structure of one Mcl-1 inhibitor revealed that the cyclic peptidomimetic bound the BH3 helix-binding grove by forming a β-hairpin, an unprecedented type of interaction with Bcl-2 family members. The cell permeability of analogs of this compound was verified by fluorescence microscopy and by induction of apoptosis. In a second example, a cyclic peptidomimetic selected against mutant H-Ras was shown to bind both H-Ras and K-Ras with high affinity by SPR (KD=2.5 nM) and FP (Ki≈£10 nM). Despite its high affinity, this compound did not significantly impact Ras activity in several in vitro assays (GST-Raf-RBD binding, GTPase, and GDP/GTP exchange). A co-crystal structure with mutant K-Ras, however, revealed that this compound binds a novel site in the C-terminus of the Ras G-domain. Remarkably, this compound also forms a β-hairpin, and like the Mcl-1 compound, also appears to enter cells. Experiments to test how this compound may affect Ras signaling or localization, and the function of this novel site in cells or in vitro with full-length lipid modified Ras are in progress. The target-bound conformation of both inhibitors reveled a network of intramolecular hydrogen bonds that are predicted to reduce interactions with water and may help to explain the intrinsic cell permeability of these molecules. The use of extremely large peptidomimetic libraries built with novel chemical diversity appears to be an extremely efficient platform for isolating high affinity binders for hard-to-target intracellular targets, yielding novel binding modes and binding sites that are unlikely to be identified by typical small molecule approaches or rational design. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C212. Citation Format: Kristopher Josephson, Zhong Ma, Zhaolin Wang, Yili Sun, Sylvia Tobe, Sarah Perlmutter, Rohit Vyasamneni, Ping Ye, Nicolas Boyer, Micelle Arata, Kelli Pattavina, Kathleen Seyb, Hong Zheng, Imelda Sollomoni, Ezekiel Nims, Emily de Koning, Alonso Ricardo, Douglas Treco. Discovery of high affinity cyclic peptidomimetics binding Mcl-1 and Ras. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C212.

A Cyclochiral Conformational Motif Constructed Using a Robust Hydrogen-Bonding Network

A novel conformational motif constructed with a robust intramolecular hydrogen-bonding (H-bonding) network was discovered. A pyrrolidine derivative possessing four identical amide substituents at C(2) and C(5) formed a strong intramolecular H-bonding network consisting of all the amide groups. This conformation yielded a cyclochiral structure with a handedness that depended on the directionality of the H-bonding network. The most stable compound was isolated and applied to the acylative kinetic resolution of secondary alcohol. The handedness of the H-bonding network was biased by the presence of chiral substituents, and the preferred direction could be switched under an external stimulus. A structural analysis using NMR, X-ray crystallography, and theoretical calculation techniques indicated that the conformation of the substituents was highly ordered and depended on the directionality of the H-bonding network.

Structural Mimicry of A-Loop Tyrosine Phosphorylation by a Pathogenic FGF Receptor 3 Mutation

The K650E gain-of-function mutation in the tyrosine kinase domain of FGF receptor 3 (FGFR3) causes Thanatophoric Dysplasia type II, a neonatal lethal congenital dwarfism syndrome, and when acquired somatically, it contributes to carcinogenesis. In this report, we determine the crystal structure of the FGFR3 kinase domain harboring this pathogenic mutation and show that the mutation introduces a network of intramolecular hydrogen bonds to stabilize the active-state conformation. In the crystal, the mutant FGFR3 kinases are caught in the act of trans-phosphorylation on a kinase insert autophosphorylation site, emphasizing the fact that the K650E mutation circumvents the requirement for A-loop tyrosine phosphorylation in kinase activation. Analysis of this trans-phosphorylation complex sheds light onto the determinants of tyrosine trans-phosphorylation specificity. We propose that the targeted inhibition of this pathogenic FGFR3 kinase may be achievable by small molecule kinase inhibitors that selectively bind the active-state conformation of FGFR3 kinase.

DFT Study on the Conformational and Vibrational Properties of 3’-Deoxycytidine and Its Analogues

Impact of saturation of the sugar C(3’)=C(4’) bond of acytidine nucleoside derivative, 3’, 4’-didehydro-3’-deoxycytidine (I) is revealed usingsimulated vibrational spectra, with respect to 3’-deoxycytidine. The density functional theory based calculations found that the C(3’)=C(4’) double bondrestricts the sugar flexibility and affects the sugar-base intramolecular hydrogen bond network. For 3’-dC, two minimal energy conformers are identified on the potential energy surface. The first conformer (IIA) takes anO4’-endo and gauche-gauche (gg) orientation whereas the second (IIB) has a C3’-exo and gauche-trans (gt) orientation in gas phase. The two conformers which have been observed previously in the crystal structure are separated by a low energy barrier. The carbon double bond in the sugar moiety of I confines the pseudorotation of the pentagon ring to be significantly flatter than that of the sugar ring in IIA and IIB. The simulated vibrational spectra, both in gas phase and in solutions, report such structural caused spectral changes with red and blue vibrational frequency shifts.The firsthydration shell of 3’-dC has been also investigated applying hybrid QM/MM molecular dynamic simulation.

Vibrational Spectroscopy and Intramolecular Hydrogen Bond Network of (Didehydro)Deoxycytidine Nucleosides

Sugar puckering and hydrogen bond networks are the most important properties of nucleosides as either DNA functional moieties or antibiotics. This article studies such the relationship quantum mechanically for two cytidine nucleoside derivatives, 1’, 2’-didehydro-3’, 4’-deoxycytidine (I) and 2’-deoxycytidine (II) with respect to cytidine (III) in isolation. Vibrational infrared (IR) spectroscopy studied using density functional theory (DFT) models in addition to other properties such as potential energy surfaces (PES), geometries, molecular electrostatic potentials (MEP) and Fukui functions. The atomic site related Fukui function indicates that the sugar carbons are less chemically active in III but can be activated when losing the hydroxyl group at C(2’) as in II and can be significantly activated by forming a C=C double bond as in I. The simulated IR spectra indicate that the compounds are related structurally. Intramolecular hydrogen bond networks (as “spider webs”) of the biomolecules are revealed with IR red-shift and blue-shift. A detailed study in the region of C-H stretch in 2800-3300 cm-1 indicates that intramolecular H-bond networks cause IR spectral blue-shift.

Unveiling the Sweet Conformations of D‐Fructopyranose

Two conformers of D-fructopyranose are characterized using laser ablation and broadband Fourier-transform microwave spectroscopy. Both species are stabilized by complicated intramolecular hydrogen-bonding networks. Structural motifs related to the sweetness of D-fructopyranose are revealed for the most stable conformer.

Conformations of d-xylose: the pivotal role of the intramolecular hydrogen-bonding

Crystalline samples of D-xylose have been vaporized by laser ablation and probed in the gas phase using Fourier transform microwave spectroscopy. The rotational spectrum revealed the existence of two α-D-xylopyranose conformers stabilized by the anomeric effect and cooperative hydrogen bond networks. The experiment spectroscopically tracked fine structural changes upon clockwise and counterclockwise arrangements of the OH groups in the observed conformers. The five monosubstituted (13)C species of the most abundant conformer cc-α-(4)C1 have also been observed in their natural abundance, and its structure has been derived. This work demonstrates the pivotal role that the intramolecular hydrogen-bonding network plays in the conformational behavior of free monosaccharides.

Reactivity-Based Detection of Copper(II) Ion in Water: Oxidative Cyclization of Azoaromatics as Fluorescence Turn-On Signaling Mechanism

An oxidative cyclization reaction transforms nonemissive azoanilines into highly fluorescent benzotriazoles. We have found that introduction of multiple electron-donating amino groups onto a simple o-(phenylazo)aniline platform dramatically accelerates its conversion to the emissive polycyclic product. Notably, this chemistry can be effected by μM-level concentrations of copper(II) ion in water (pH = 6-8) at room temperature to elicit >80-fold enhancement in the green emission at λ(em) = 530 nm. Comparative kinetic and electrochemical studies on a series of structural analogues have established that the accelerated reaction rates correlate directly with a systematic cathodic shift in the oxidation onset potential of the azo precursors. In addition, single-crystal X-ray crystallographic analysis on the most reactive derivative revealed the presence of a five-membered ring intramolecular hydrogen-bonding network. An enhanced contribution of the quinoid-type resonance in such conformation apparently facilitates the mechanistically required proton transfer step, which, in conjunction with electron transfer at lower oxidation potential, contributes to a rapid cyclization reaction triggered by copper(II) ion in water.

Optically Active, Amphiphilic Poly(meta-phenylene ethynylene)s: Synthesis, Hydrogen-Bonding Enforced Helix Stability, and Direct AFM Observation of Their Helical Structures

Optically active, amphiphilic poly(meta-phenylene ethynylene)s (PPEa) bearing L- or D-alanine-derived oligo(ethylene glycol) side chains connected to the backbone via amide linkages were prepared by microwave-assisted polycondensation. PPEa's exhibited an intense Cotton effect in the π-conjugated main-chain chromophore regions in various polar and nonpolar organic solvents due to a predominantly one-handed helical conformation stabilized by an intramolecular hydrogen-bonding network between the amide groups of the pendants. The stable helical structure was retained in the bulk and led to supramolecular column formation from stacked helices in oriented polymer films as evidenced by X-ray diffraction. Atomic force microscopy was used to directly visualize the helical structures of the polymers in two-dimensional crystalline layers with molecular resolution, and, for the first time, their absolute helical senses could unambiguously be determined.

A Disulfide Bridge Allows for Site‐Selective Binding in Liver Bile Acid Binding Protein Thereby Stabilising the Orientation of Key Amino Acid Side Chains

The presence of a disulfide bridge in liver bile acid binding protein (L-BABP/S-S) allows for site-selective binding of two bile acids, glycochenodeoxycholic (GCDA) and glycocholic acid (GCA), differing only in the presence of a hydroxyl group. The protein form devoid of the disulfide bridge (L-BABP) binds both bile salts without discriminating ability. We investigate the determinants of the molecular recognition process in the formation of the heterotypic L-BABP/S-S complex with GCDA [corrected] and GCA [corrected] located in the superficial and inner protein sites, respectively. The comparison of the NMR spectroscopy structure of heterotypic holo L-BABP/S-S, the first reported for this protein family, with that of the homotypic L-BABP complex demonstrates that the introduction of a S-S link between adjacent strands changes the conformation of three key residues, which function as hot-spot mediators of molecular discrimination. The favoured χ(1) rotameric states (t, g(+) and g(-) for E99, Q100 and E109 residues, respectively) allow the onset of an extended intramolecular hydrogen-bond network and the consequent stabilisation of the side-chain orientation of a buried histidine, which is capable of anchoring a specific ligand.

Synthesis, structure, and physical properties for a series of trigonal bipyramidal M(II)-Cl complexes with intramolecular hydrogen bonds.

A series of transition metal chloro complexes with the tetradentate tripodal tris(2-amino-oxazoline)amine ligand (TAO) have been synthesized and characterized. X-Ray structural analyses of these compounds demonstrate the formation of the mononuclear complexes [M(II)(TAO)(Cl)](+), where M(II) = Cr, Mn, Fe, Co, Ni, Cu and Zn. These complexes exhibit distorted trigonal-bipyramidal geometry, coordinating the metal through an apical tertiary amine, three equatorial imino nitrogen atoms, and an axial chloride anion. All the complexes possess an intramolecular hydrogen-bonding (H-bonding) network within the cavity occupied by the metal-bound chloride ion. The metal-chloride bond distances are atypically long, which is attributed to the effects of the H-bonding network. Nuclear magnetic resonance (NMR) spectroscopy of the Zn complex suggests that the solid-state structures are representative of that observed in solution, and that the H-bonding interactions persist as well. Additionally, density functional theory (DFT) calculations were carried out to probe the electronic structures of the complexes.

Thermal Properties of Rhodopsin: INSIGHT INTO THE MOLECULAR MECHANISM OF DIM-LIGHT VISION

Rhodopsin has developed mechanisms to optimize its sensitivity to light by suppressing dark noise and enhancing quantum yield. We propose that an intramolecular hydrogen-bonding network formed by ∼20 water molecules, the hydrophilic residues, and peptide backbones in the transmembrane region is essential to restrain thermal isomerization, the source of dark noise. We studied the thermal stability of rhodopsin at 55 °C with single point mutations (E181Q and S186A) that perturb the hydrogen-bonding network at the active site. We found that the rate of thermal isomerization increased by 1-2 orders of magnitude in the mutants. Our results illustrate the importance of the intact hydrogen-bonding network for dim-light detection, revealing the functional roles of water molecules in rhodopsin. We also show that thermal isomerization of 11-cis-retinal in solution can be catalyzed by wild-type opsin and that this catalytic property is not affected by the mutations. We characterize the catalytic effect and propose that it is due to steric interactions in the retinal-binding site and increases quantum yield by predetermining the trajectory of photoisomerization. Thus, our studies reveal a balancing act between dark noise and quantum yield, which have opposite effects on the thermal isomerization rate. The acquisition of the hydrogen-bonding network and the tuning of the steric interactions at the retinal-binding site are two important factors in the development of dim-light vision.

Catalytic Reduction of Dioxygen to Water with a Monomeric Manganese Complex at Room Temperature

There have been numerous efforts to incorporate dioxygen into chemical processes because of its economic and environmental benefits. The conversion of dioxygen to water is one such example, having importance in both biology and fuel cell technology. Metals or metal complexes are usually necessary to promote this type of reaction and several systems have been reported. However, mechanistic insights into this conversion are still lacking, especially the detection of intermediates. Reported herein is the first example of a monomeric manganese(II) complex that can catalytically convert dioxygen to water. The complex contains a tripodal ligand with two urea groups and one carboxyamidopyridyl unit; this ligand creates an intramolecular hydrogen-bonding network within the secondary coordination sphere that aids in the observed chemistry. The manganese(II) complex is five-coordinate with an N(4)O primary coordination sphere; the oxygen donor comes from the deprotonated carboxyamido moiety. Two key intermediates were detected and characterized: a peroxo-manganese(III) species and a hybrid oxo/hydroxo-manganese(III) species (1). The formulation of 1 was based on spectroscopic and analytical data, including an X-ray diffraction analysis. Reactivity studies showed dioxygen was catalytically converted to water in the presence of reductants, such as diphenylhydrazine and hydrazine. Water was confirmed as a product in greater than 90% yield. A mechanism was proposed that is consistent with the spectroscopy and product distribution, in which the carboxyamido group switches between a coordinated ligand and a basic site to scavenge protons produced during the catalytic cycle. These results highlight the importance of incorporating intramolecular functional groups within the secondary coordination sphere of metal-containing catalysts.

Mechanism for the Alteration of the Substrate Specificities of Template-Independent RNA Polymerases

PolyA polymerase (PAP) adds a polyA tail onto the 3'-end of RNAs without a nucleic acid template, using adenosine-5'-triphosphate (ATP) as a substrate. The mechanism for the substrate selection by eubacterial PAP remains obscure. Structural and biochemical studies of Escherichia coli PAP (EcPAP) revealed that the shape and size of the nucleobase-interacting pocket of EcPAP are maintained by an intra-molecular hydrogen-network, making it suitable for the accommodation of only ATP, using a single amino acid, Arg(197). The pocket structure is sustained by interactions between the catalytic domain and the RNA-binding domain. EcPAP has a flexible basic C-terminal region that contributes to optimal RNA translocation for processive adenosine 5'-monophosphate (AMP) incorporations onto the 3'-end of RNAs. A comparison of the EcPAP structure with those of other template-independent RNA polymerases suggests that structural changes of domain(s) outside the conserved catalytic core domain altered the substrate specificities of the template-independent RNA polymerases.

Proximal and distal N,C-linked tetra-peptidocalix[4]arenes as bifunctional receptors: synthesis, conformation and preliminary binding studies

New 1,2-proximal N,N,C,C-linked and 1,3-distal N,C,N,C-linked tetra-peptidocalix[4]arenes have been synthesised by functionalisation of the corresponding calixarene bis-amino acids. Their conformational properties in solution, which have been studied by 1H NMR, are determined by the presence of an extensive network of intramolecular hydrogen bonds. Electrospray ionisation mass spectrometry studies show that the 1,2-proximal peptidocalix[4]arene 19 is a more efficient receptor than the 1,3-distal isomer 8 in the gas phase and that it is able to recognise aromatic amino acids both as methyl esters and N-acetyl derivatives. Interestingly, these observations indicate that 19 is a bifunctional receptor since it displays both the selectivity of N-linked peptidocalixarenes for ammonium groups and that of C-linked peptidocalixarenes for carboxylates.

Torsionally Responsive C3-Symmetric Azo Dyes: Azo−Hydrazone Tautomerism, Conformational Switching, and Application for Chemical Sensing

An efficient triple azo coupling reaction between anilines and phloroglucinol furnished a series of C(3)-symmetric molecules 7-9 supporting multiple conjugation pathways that converge at the molecular core. A combination of (1)H/(13)C NMR spectroscopy, X-ray crystallography, and density functional theory computational studies provided a coherent picture of the [n,pi]-conjugated molecular core, which is best described as the tris(hydrazone) [rather than tris(azo)] tautomer stabilized by resonance-assisted hydrogen bonding. For a homologous series of compounds, an increase in the torsional angles between the planar molecular core and the peripheral aryl groups results in a systematic blue shift in the low-energy electronic transitions (7, 523 nm; 8, 505 nm; 9, 445 nm in CHCl(3)) that qualitatively correlates with the shrinkage of effective conjugation through structural distortion. Similar spectral shifts could also be induced by amine substrates that interact with the intramolecular hydrogen-bonding network to trigger bond-twisting motions. Specifically, a brief exposure of a thin film of 7 to vapor samples of butyl-, hexyl-, diethyl-, and diisopropylamine resulted in a rapid and reversible color change from pink to dark-orange. Under similar conditions, however, triethylamine did not elicit any detectable color change, despite the fact that it has a significantly higher vapor pressure than n-hexylamine. These findings implicate that the hydrogen-bonding donor ability is a key requirement for the binding-induced conformational switching, which allows for direct naked-eye detection of volatile amines under ambient conditions.

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations

In this study, interactions of selected monosaccharides with the Pseudomonas aeruginosa Lectin II (PA-IIL) are analyzed in detail. An interesting feature of the PA-IIL binding is that the monosaccharide is interacting via two calcium ions and the binding is unusually strong for protein–saccharide interaction. We have used Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) and normal mode analysis to calculate the free energy of binding. The impact of intramolecular hydrogen bond network for the lectin/monosaccharide interaction is also analyzed.

Synthesis and Characterization of Ruthenium(II)−Pyridylamine Complexes with Catechol Pendants as Metal Binding Sites

A novel tris(2-pyridylmethyl)amine (TPA) derivate having two catechol moieties linked by amide linkages at the 6-positions of two pyridyl groups was synthesized. The ligand, N,N-bis[6-{3,4-(dihydroxy)benzamide}-2-pyridyl-methyl]-N-(2-pyridylmethyl)amine (Cat(2)-TPA; L2), and its precursor, N,N-bis[6-{3,4-bis(benzyloxy)-benzamide}-2-pyridyl-methyl]-N-(2-pyridylmethyl)-amine ((Bn(2)Cat)(2)-TPA; L1), formed stable ruthenium(II) complexes, [RuCl(L2)]PF(6) (2) and [RuCl(L1)]PF(6) (1), respectively. The crystal structure of [RuCl(L2)]Cl (2') was determined by X-ray crystallography to show two isomers in terms of the orientation of one catechol moiety. In complex 2, the ligand bearing catechols acts as a pentadentate ligand involving coordination of one of the amide oxygen atoms in addition to that of the tetradentate TPA moiety and two metal-free catechol moieties as metal-binding sites. The coordination of L2 results in the preorganization of the two catechols to converge them to undergo intramolecular pi-pi interactions. The (1)H NMR spectrum of 2 in DMSO-d(6) revealed that only one isomer was present in the solution. This selective formation could be ascribed to the formation of an intramolecular hydrogen-bonding network among the hydroxyl groups of the catechol moieties, as suggested by X-ray analysis. This intramolecular hydrogen bonding could differentiate the pK(a) values of the hydroxy groups of the catechol moieties into three kinds, as indicated by spectroscopic titration with tetramethylammonium hydroxide (TMAOH) in DMF. The complexation of 2 with other metal ions was also examined. The reaction of 2 with [Cu(NO(3))(2)(TMEDA)] (TMEDA = N,N,N',N'-tetramethylethylenediamine) in methanol allowed us to observe the selective formation of a binuclear complex, [RuCl(L2(2-)){Cu(TMEDA)}]PF(6) (3), which was characterized by ESI-MS, UV-vis, and ESR spectroscopies. Its ESR spectrum in methanol suggested that the coordination of the Cu(II)-TMEDA unit to the converged catechol moieties would be different from conventional kappa(2)-O,O':eta(2)-coordination: it exhibits a novel bridging coordination mode, bis-kappa(1)-O:eta(1)-coordination, to form the binuclear Ru(II)-Cu(II) complex.