Use of 19F NMR spectroscopy to screen chemical libraries for ligands that bind to proteins

Identification of compounds from chemical libraries that bind to macromolecules by use of NMR spectroscopy has gained increasing importance during recent years. A simple methodology based on (19)F NMR spectroscopy for the screening of ligands that bind to proteins, which also provides qualitative information about relative binding strengths and the presence of multiple binding sites, is presented here. A library of fluorinated compounds was assembled and investigated for binding to the two bacterial chaperones PapD and FimC, and also to human serum albumin (HSA). It was found that library members which are bound to a target protein could be identified directly from line broadening and/or induced chemical shifts in a single, one-dimensional (19)F NMR spectrum. The results obtained for binding to PapD using (19)F NMR spectroscopy agreed well with independent studies based on surface plasmon resonance, providing support for the versatility and accuracy of the technique. When the library was titrated to a solution of PapD chemical shift and linewidth changes were observed with increasing ligand concentration, which indicated the presence of several binding sites on PapD and enabled the assessment of relative binding strengths for the different ligands. Screening by (19)F NMR spectroscopy should thus be a valuable addition to existing NMR techniques for evaluation of chemical libraries in bioorganic and medicinal chemistry.     

Polymer‐Bound,Amphiphilic Hoveyda‐Grubbs‐Type Catalyst for Ring‐Closing Metathesis in Water

Summary: We report on the synthesis of a new amphiphilic, polymer‐bound variant of the Hoveyda‐Grubbs catalyst via the coupling reaction of a carboxylic acid‐functionalized poly(2‐oxazoline) block copolymer with 2‐isopropoxy‐5‐hydroxystyrene and subsequent reaction of the resulting macroligand with a second generation Grubbs catalyst. For the benchmark, the substrate diethyl diallylmalonate was studied in the ring‐closing metathesis (RCM) reaction and a turn‐over number (TON) of up to 390 in water was achieved. To the best of our knowledge, this is the highest value for any aqueous RCM reaction to date. For the first time, recycling of a ruthenium initiator in an aqueous RCM reaction has been successful to some extent. In addition, the micellar conditions accelerate the conversion of the hydrophobic diene and at the same time stabilize the active alkylidene species, although competing decomposition of the catalyst in water still impairs the catalyst performance. Residual ruthenium content was determined to be below 1 ppm in the product suggesting a very low leaching of the polymeric catalyst system.

Simplified chemical structure of the amphiphilic, polymer‐bound Grubbs‐Hoveyda catalyst.     

Toward understanding the ionization of biomarkers from micrometer particles by bio-aerosol mass spectrometry

The appearance of informative signals in the mass spectra of laser-ablated bio-aerosol particles depends on the effective ionization probabilities (EIP) of individual components during the laser ionization process. This study investigates how bio-aerosol chemical composition governs the EIP values of specific components and the overall features of the spectra from the bio-aerosol mass spectrometry (BAMS). EIP values were determined for a series of amino acid, dipicolinic acid, and peptide aerosol particles to determine what chemical features aid in ionization. The spectra of individual amino acids and dipicolinic acid, as well as mixtures, were examined for extent of fragmentation and the presence of molecular ion dimers, which are indicative of ionization conditions. Standard mixtures yielded information with respect to the significance of secondary ion plume reactions on observed spectra. A greater understanding of how these parameters affect EIP and spectra characteristics of bio-aerosols will aid in the intelligent selection of viable future biomarkers for the identification of bio-terrorism agents.     

X-ray magnetic circular dichroism of Pseudomonas aeruginosa nickel(II) azurin

We show that X-ray magnetic circular dichroism (XMCD) can be employed to probe the oxidation states and other electronic structural features of nickel active sites in proteins. As a calibration standard, we have measured XMCD and X-ray absorption (XAS) spectra for the nickel(II) derivative of Pseudomonas aeruginosa azurin (NiAz). Our analysis of these spectra confirms that the electronic ground state of NiAz is high-spin (S = 1); we also find that the L(3)-centroid energy is 853.1(1) eV, the branching ratio is 0.722(4), and the magnetic moment is 1.9(4) mu(B). Density functional theory (DFT) calculations on model NiAz structures establish that orbitals 3d(x2-y2) and 3d(z2) are the two valence holes in the high-spin Ni(II) ground state, and in accord with the experimentally determined orbital magnetic moment, the DFT results also demonstrate that both holes are highly delocalized, with 3d(x2-y2) having much greater ligand character.     

Direct observation of phenylalanine orientations in statherin bound to hydroxyapatite surfaces

Extracellular biomineralization proteins such as salivary statherin control the growth of hydroxyapatite (HAP), the principal component of teeth and bones. Despite the important role that statherin plays in the regulation of hard tissue formation in humans, the surface recognition mechanisms involved are poorly understood. The protein-surface interaction likely involves very specific contacts between the surface atoms and the key protein side chains. This study demonstrates for the first time the power of combining near-edge X-ray absorption fine structure (NEXAFS) spectroscopy with element labeling to quantify the orientation of individual side chains. In this work, the 15 amino acid N-terminal binding domain of statherin has been adsorbed onto HAP surfaces, and the orientations of phenylalanine rings F7 and F14 have been determined using NEXAFS analysis and fluorine labels at individual phenylalanine sites. The NEXAFS-derived phenylalanine tilt angles have been verified with sum frequency generation spectroscopy.     

Exploring the trifluoromenadione core as a template to design antimalarial redox-active agents interacting with glutathione reductase

Menadione is the 2-methyl-1,4-naphthoquinone core used to design potent antimalarial redox-cyclers to affect the redox equilibrium of Plasmodium-infected red blood cells. Exploring the reactivity of fluoromethyl-1,4-naphthoquinones, in particular trifluoromenadione, under quasi-physiological conditions in NADPH-dependent glutathione reductase reactions, is discussed in terms of chemical synthesis, electrochemistry, enzyme kinetics, and antimalarial activities. Multitarget-directed drug discovery is an emerging approach to the design of new antimalarial drugs. Combining in one single 1,4-naphthoquinone molecule, the trifluoromenadione core with the alkyl chain at C-3 of the known antimalarial drug atovaquone, revealed a mechanism for CF(3) as a leaving group. The resulting trifluoromethyl derivative 5 showed a potent antimalarial activity per se against malarial parasites in culture.     

Structural characterization of the voltage-sensor domain and voltage-gated K+-channel proteins vectorially oriented within a single bilayer membrane at the solid/vapor and solid/liquid interfaces via neutron interferometry

The voltage-sensor domain (VSD) is a modular four-helix bundle component that confers voltage sensitivity to voltage-gated cation channels in biological membranes. Despite extensive biophysical studies and the recent availability of X-ray crystal structures for a few voltage-gated potassium (Kv) channels and a voltage-gate sodium (Nav) channel, a complete understanding of the cooperative mechanism of electromechanical coupling, interconverting the closed-to-open states (i.e., nonconducting to cation conducting) remains undetermined. Moreover, the function of these domains is highly dependent on the physical-chemical properties of the surrounding lipid membrane environment. The basis for this work was provided by a recent structural study of the VSD from a prokaryotic Kv-channel vectorially oriented within a single phospholipid (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)) membrane investigated by X-ray interferometry at the solid/moist He (or solid/vapor) and solid/liquid interfaces, thus achieving partial to full hydration, respectively (Gupta et al. Phys. Rev. E2011, 84, 031911-1-15). Here, we utilize neutron interferometry to characterize this system in substantially greater structural detail at the submolecular level, due to its inherent advantages arising from solvent contrast variation coupled with the deuteration of selected submolecular membrane components, especially important for the membrane at the solid/liquid interface. We demonstrate the unique vectorial orientation of the VSD and the retention of its molecular conformation manifest in the asymmetric profile structure of the protein within the profile structure of this single bilayer membrane system. We definitively characterize the asymmetric phospholipid bilayer solvating the lateral surfaces of the VSD protein within the membrane. The profile structures of both the VSD protein and phospholipid bilayer depend upon the hydration state of the membrane. We also determine the distribution of water and exchangeable hydrogen throughout the profile structure of both the VSD itself and the VSD:POPC membrane. These two experimentally determined water and exchangeable hydrogen distribution profiles are in good agreement with molecular dynamics simulations of the VSD protein vectorially oriented within a fully hydrated POPC bilayer membrane, supporting the existence of the VSD's water pore. This approach was extended to the full-length Kv-channel (KvAP) at a solid/liquid interface, providing the separate profile structures of the KvAP protein and the POPC bilayer within the reconstituted KvAP:POPC membrane.     

Comparing the structural stability of PbS nanocrystals assembled in fcc and bcc superlattice allotropes

We investigated the structural stability of colloidal PbS nanocrystals (NCs) self-assembled into superlattice (SL) allotropes of either face-centered cubic (fcc) or body-centered cubic (bcc) symmetry. Small-angle X-ray scattering analysis showed that the NC packing density is higher in the bcc than in the fcc SL; this is a manifestation of the cuboctahedral shape of the NC building block. Using the high-pressure rock-salt/orthorhombic phase transition as a stability indicator, we discovered that the transition pressure for NCs in a bcc SL occurs at 8.5 GPa, which is 1.5 GPa higher than the transition pressure (7.0 GPa) observed for a fcc SL. The higher structural stability in the bcc SL is attributed primarily to the effective absorption of loading force in specific SL symmetry and to a lesser extent to the surface energy of the NCs. The experimental results provide new insights into the fundamental relationship between the symmetry of the self-assembled SL and the structural stability of the constituent NCs.     

The Ligand‐Based Quintuple Bond‐Shortening Concept and Some of Its Limitations

Herein, the ligand‐based concept of shortening quintuple bonds and some of its limitations are reported. In dichromium–diguanidinato complexes, the length of the quintuple bond can be influenced by the substituent at the central carbon atom of the used ligand. The guanidinato ligand with a 2,6‐dimethylpiperidine backbone was found to be the optimal ligand. The reduction of its chromium(II) chloride–ate complex gave a quintuply bonded bimetallic complex with a Cr? Cr distance of 1.7056 (12) Å. Its metal–metal distance, the shortest observed in any stable compound yet, is of essentially the same length as that of the longest alkane C? C bond (1.704 (4) Å). Both molecules, the alkane and the Cr complex, are of remarkable stability. Furthermore, an unsupported Cr^I dimer with an effective bond order (EBO) of 1.25 between the two metal atoms, indicated by CASSCF/CASPT2 calculations, was isolated as a by‐product. The formation of this by‐product indicates that with a certain bulk of the guanidinato ligand, other coordination isomers become relevant. Over‐reduction takes place, and a chromium–arene sandwich complex structurally related to the classic dibenzene chromium complex was observed, even when bulkier substituents are introduced at the central carbon atom of the used guanidinato ligand.     

Phase Formation Studies of Lead(II) Copper(II) Oxotellurates: The Crystal Structures of Dimorphic PbCuTeO5, PbCuTe2O6, and [Pb2Cu2(Te4O11)](NO3)2

Two modifications of the oxotellurate(VI) PbCuTeO₅ were isolated as single crystals from product mixtures obtained from solid state reactions, whereas single crystals of the oxotellurates(IV) PbCuTe₂O₆ and [Pb₂Cu₂(Te₄O₁₁)](NO₃)₂ were grown under hydrothermal conditions. The crystal structures of all compounds comprise of characteristic coordination polyhedra, viz. nearly square [CuO₄] plaquettes for divalent copper, octahedral [TeO₆] units for hexavalent tellurium, trigonal‐pyramidal [TeO₃] and bisphenoidal [TeO₄] groups for tetravalent tellurium, and distorted [PbO_x] polyhedra for divalent lead. PbCuTeO₅ is dimorphic and crystallizes in a monoclinic and a triclinic modification, related by a translationengleiche group‐subgroup relation of index 2. PbCuTe₂O₆ represents the ideal composition of the rare mineral choloalite. The characteristic feature of the crystal structure of [Pb₂Cu₂(Te₄O₁₁)](NO₃)₂ is its layered set‐up, comprised of cationic [Pb₂Cu₂(Te₄O₁₁)]²⁺ ribbons (width approximately 6.7 Å) sandwiched between nitrate anions that are only weakly bound to the cationic layers.