Structural Insights on the Role of Halogen Bonding in Protein MEK Kinase-Inhibitor Complexes.

Kinases are enzymes that play a critical role in governing essential biological processes. Due to their pivotal involvement in cancer cell signaling, they have become key targets in the development of anti-cancer drugs. Among these drugs, those containing the 2,4-dihalophenyl moiety demonstrated significant potential. Here we show how this moiety, particularly the 2-fluoro-4-iodophenyl one, is crucial for the structural stability of the formed drug-enzyme complexes. Crystallographic analysis of reported kinase-inhibitor complex structures highlights the role of the halogen bonding that this moiety forms with specific residues of the kinase binding site. This interaction is not limited to FDA-approved MEK inhibitors, but it is also relevant for other kinase inhibitors, indicating its broad relevance in the design of this class of drugs.

A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach.

The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.

Halogenation of the N-Terminus Tyrosine 10 Promotes Supramolecular Stabilization of the Amyloid-ß Sequence 7-12.

Here, we demonstrate that introduction of halogen atoms at the tyrosine 10 phenol ring of the DSGYEV sequence derived from the flexible amyloid-ß N-terminus, promotes its self-assembly in the solid state. In particular, we report the crystal structures of two halogen-modified sequences, which we found to be stabilized in the solid state by halogen-mediated interactions. The structural study is corroborated by Non-Covalent Interaction (NCI) analysis. Our results prove that selective halogenation of an amino acid enhances the supramolecular organization of otherwise unstructured biologically-relevant sequences. This method may develop as a general strategy for stabilizing highly polymorphic peptide regions.

Crystallographic insights into the self-assembly of KLVFF amyloid-beta peptides.

Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aß16-20 ), the core-sequence of the polypeptide Aß40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments. Detailed structural studies on the packing features of both monohalogenated derivatives reveal the role of the halogen atoms showing that when they are positioned on the Phe aromatic moiety at the C-terminus they do not form halogen bonds and thus do not produce any extra stabilization of the ß-sheet in the self-assembly process. The structural evidences gained from these studies corroborate the various polymorphic nanostructures of the halogenated variants of KLVFF and confirm the possibility to use halogenation as innovative strategy to tune the morphology of this pentapeptide.

The 1:1 co-crystal of triphen-yl(2,3,5,6-tetra-fluoro-benz-yl)phospho-nium bromide and 1,1,2,2-tetra-fluoro-1,2-di-iodo-ethane.

The title compound, C25H18F4P(+)·Br(-)·C2F4I2, is a 1:1 co-crystal of triphen-yl(2,3,5,6-tetra-fluoro-benz-yl)phospho-nium (TTPB) bromide and 1,1,2,2-tetra-fluoro-1,2-di-iodo-ethane (TFDIE). The crystal structure consists of a framework of TTPB cations held together by C-H⋯Br inter-actions. In this framework, infinite channels along [100] are filled by TFDIE mol-ecules held together in infinite ribbons by short F⋯F [2.863 (2)-2.901 (2)Å] inter-actions. The structure contains halogen bonds (XB) and hydrogen bonds (HB) in the bromide coordination sphere. TFDIE functions as a monodentate XB donor as only one I atom is linked to the Br(-) anion and forms a short and directional inter-action [I⋯Br(-) 3.1798 (7) Šand C-I⋯Br(-) 177.76 (5)°]. The coordination sphere of the bromide anion is completed by two short HBs of about 2.8 Š(for H⋯Br) with the acidic methyl-ene H atoms and two longer HBs of about 3.0 Šwith H atoms of the phenyl rings. Surprisingly neither the second iodine atom of TFDIE nor the H atom on the tetra-fluoro-phenyl group make any short contacts.

Tetra-phenyl-phospho-nium iodide-1,3,5-tri-fluoro-2,4,6-tri-iodo-benzene-methanol (3/4/1).

The crystallization of a 1:1 molar solution of 1,3,5-tri-fluoro-2,4,6-di-iodo-benzene (TFTIB) and tetra-phenyl-phosponium iodide (TPPI) from methanol produced tetra-gonal needles of pure TPPI and tabular pseudo-hexa-gonal truncated bipyramids of the title compound, 3C24H20P(+)·3I(-)·4C6F3I3·CH4O or (TPPI)3(TFTIB)4·MeOH. The asymmetric unit is composed of six TPPI mol-ecules, eight TFTIB mol-ecules and two methanol mol-ecules, overall 16 constituents. The formation of the architecture is essentially guided by a number of C-I⋯I(-) halogen bonds (XB), whose lengths are in the range 3.276 (1)-3.625 (1) Å. Layers of supra-molecular polyanions are formed parallel to (10-1) wherein iodide anions function as penta-, tetra- or bidentate XB acceptors. The structure is not far from being P21/n, but the centrosymmetry is lost due to a different conformation of a single couple of cations and the small asymmetry in the formed supra-molecular anion. One methanol mol-ecule is hydrogen bonded to an iodide anion, while the second is linked to the first one via an O-H⋯O contact. This second methanol mol-ecule is more loosely pinned in its position than the first and presents very high anisotropic displacement parameters and a seeming shortening of the C-O bond length. The crystal studied was refined as a perfect inversion twin.

[5,11,17,23-Tetra-tert-butyl-25,27-(3,6-dioxaoctan-1,8-di-oxy)-26,28-bis-(pyridin-2-ylmeth-oxy)calix[4]arene]sodium iodide-1,2,4,5-tetra-fluoro-3,6-diiodo-benzene-methanol (2/3/4).

The title compound, [Na(C62H76N2O6)]I·1.5C6F4I2·2CH3OH, is composed of five components: a calix[4]arene derivative (hereinafter C4), a sodium cation, an iodide anion, a 1,2,4,5-tetra-fluoro-3,6-diiodo-benzene (tFdIB) mol-ecule and a methanol mol-ecule in a 1:1:1:1.5:2 ratio. The complex shows several inter-esting features: (i) the polyoxygenated loop of C4 effectively chelates a sodium cation in the form of a distorted octahedron and separates it from the iodide counter-ion, the shortest Na(+)⋯I(-) distance being greater than 6.5 Å; (ii) the cavity of C4 is filled by a methanol mol-ecule; (iii) a second methanol mol-ecule is hydrogen-bonded to the N atom of a pyridinyl substituent pendant of C4 and halogen-bonded to the I atom of a tFdIB mol-ecule; (iv) the two I atoms of another tFdIB mol-ecule are halogen-bonded to two iodide anions, which act as monodentate halogen-bond acceptorss; (v) one of the two tFdIB molecules is located about a centre of inversion.

(Tris{2-[2-(2,3,5,6-tetra-fluoro-4-iodo-phen-oxy)eth-oxy]eth-yl}amine)-potassium iodide.

The title adduct, [K(C30H24F12I3NO6)]I, gives an extended tape of cations linked through I⋯I(-) halogen bonds (XBs), two of them being quite short and one quite long. In the structure, the cation is hosted in a cavity formed by the arms of the podand which presents a closed conformation wherein two tetra-fluoro-iodo-benzene rings are near parallel [dihedral angle = 15.8 (4)°; centroid-centroid distance = 3.908 (5) Å] and the third ring is closer to orthogonal [dihedral angles = 66.28 (14) and 75.20 (19)°] to the other two rings. The coordination sphere of the K(+) cation is composed of the six O atoms, the N atom and an F atom in the ortho position of one of the rings.

1,3-Bis(2,3,5,6-tetra-fluoro-4-iodo-phen-oxy)-2,2-bis-[(2,3,5,6-tetra-fluoro-4-iodo-phen-oxy)meth-yl]propane.

In the crystal structure of the title compound, C29H8F16I4O4, short I⋯I and I⋯F contacts, which can be understood as halogen bonds (XBs), represent the strongest inter-molecular inter-actions, consistent with the presence of I and F atoms, and the absence of H atoms, at the periphery of the mol-ecule. In addition, π-π stacking inter-actions between tetra-fluoro-iodo-phenyl (TFIP) groups and five short F⋯F inter-actions are present.

Multi-component synthesis of peptide-sugar conjugates.

Recent years have witnessed a growing interest in the development of new methods for linking sugars to peptides or proteins because natural glycopeptides or neoglycoconjugates with well defined chemical structures are very important tools to study diverse biological phenomena. Herein we report a novel, one-pot, three-component process for the synthesis of peptide-urea conjugates incorporating a hexafluorovaline or an aspartic acid alkyl ester residue under very mild conditions and high yields. The reaction has been exploited for the synthesis of a wide array of structurally diverse peptide-sugar conjugates through a regiospecific four-component, one-pot sequential domino process, by generating the reacting sugar-carbodiimides in situ from readily accessible starting materials.

2-Iodo-imidazolium receptor binds oxoanions via charge-assisted halogen bonding.

A detailed (1)H-NMR study of the anion binding properties of the 2-iodo-imidazolium receptor 1 in DMSO allows to fully attribute the observed affinities to strong charge-assisted C-I···X(-) halogen bonding (XB). Stronger binding was observed for oxoanions over halides. Phosphate, in particular, binds to 1 with an association constant of ca. 10(3) M(-1), which is particularly high for a single X-bond. A remarkably short C-I···O(-) contact is observed in the structure of the salt 1·H(2)PO(4)(-).