Helical structures induced by laterally-connected chiral twin molecules

A novel chiral twin material, (R)-bis[5-octyloxy-2-(4-octyloxyphenoxycarbonyl)phenyl] 3-methyladipate, has been prepared, where two mesogenic parts are connected laterally by a spacer possessing a chiral centre. A weaker helical structure, in particular in the chiral smectic C (S*_c) phase, was found to be induced by the laterally-connected twin material than by the analogous terminally-connected twin material. If laterally-connected chiral twin molecules prefer to stay in the smectic layer structure so that the two mesogenic parts exist in the same smectic layer, the twist interaction between adjacent layers cannot be produced by direct correlation of motion and directions of two mesogenic parts. Thus, the helical structure in the S*_c phase induced by laterally-connected chiral twin molecules becomes weak. An analogous laterally-branched 'monomeric' compound, (S)-5-octyloxy-2-(4-octyloxyphenoxycarbonyl)phenyl 3-methyl-pentanoate, has also been prepared, and the induced helical structures compared.     

Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site

Aminoglycoside antibiotics target the decoding aminoacyl site (A site) on the 16S ribosomal RNA and induce miscoding during translation. Here, we present the crystal structure, at 2.54 A resolution, of an RNA oligonucleotide containing the A site sequence complexed to the 4,6-disubstituted 2-deoxystreptamine aminoglycoside tobramycin. The three aminosugar rings making up tobramycin interact with the deep-groove atoms directly or via water molecules and stabilize a fully bulged-out conformation of adenines A(1492) and A(1493). The comparison between this structure and the one previously solved in the presence of paromomycin confirms the importance of the functional groups on the common neamine part of these two antibiotics for binding to RNA. Furthermore, the analysis of the present structure provides a molecular explanation to some of the resistance mechanisms that have spread among bacteria and rendered aminoglycoside antibiotics inefficient.     

Stable supramolecular helical structure of C6-symmetric hydrogen-bonded hexakis(phenylethynyl)benzene derivatives with amino acid pendant groups and their unique fluorescence properties

A highly stable supramolecular helical structure was formed by the self-assembly of novel C6-symmetric hydrogen-bonded discotic molecules, hexakis(phenylethynyl)benzene derivatives with chiral alanine parts, and exhibited orange excimer emission with a large Stokes shift.     

Sequence, structure, and active site analyses of p38 MAP kinase: exploiting DFG-out conformation as a strategy to design new type II leads

A new knowledge, structure, and sequence based strategy involving the effective exploitation of the DFG-out conformation is delineated. A comprehensive analysis of the structure, sequence, cocrystals, and active sites of p38 MAP kinase crystal structures present in Protein Data Bank (PDB) and the FDA approved MAP kinase drugs has been done, and the information is used for the design of type II leads. The 98 crystal structures, 138 cocrystals, and 31 FDA drugs comprise of 7 different sequences of 2 organisms viz., Homo sapiens and Mus musculus differing in sequence length, constituting both homo- and heterochains. Multiple sequence alignment with ClustalW showed >95% sequence similarity with highly conserved domains and a high propensity for mutations in the activation loop. The bound ligands were extracted, and their interactions with DFG in and out conformations were studied. These cocrystals and FDA drugs were fragmented on the basis of their binding interactions and their affinity to ATP and allosteric sites. The fragment library thus generated contains 106 fragments with overlapping drug fragments. A blue print constituting three main parts viz., head (ATP region), linker (DFG region), and tail (allosteric region) has thus been formulated and used to design 64 type II p38 MAP kinase inhibitors. The above strategy has been employed to design potent type II p38 MAP kinase inhibitors, which are shown to be very promising.     

First carbohydrate liquid crystals of columnar structure

S, S-Dialkylacetals of aldoses, tripodal in structure and recently synthesized in large numbers by three groups, do not exhibit thermotropically a smectic, but a columnar hexagonal mesophase (Hx) as we have proved by X-ray diffraction. The molecular organization in this mesophase is comparable with a similar one known for phasmidic molecules. These various multiols, although different in stereo-chemistry, form only one type of hydrogen-bonded disc-shaped multimer. Its mesophase structure is made up of about five molecules placed in columns with a skeleton of hydrogen-bridged sugar parts surrounded by thioalkyl groups in the periphery. Since three 6-deoxy sugar dithioacetals were shown to be non-thermomesomorphic the terminal hydroxyl function is essential for this molecular arrangement which seems not to be true for missing ones in the inner part of a sugar chain, as we have found in one case.     

Helical structures induced by laterally-connected chiral twin molecules

Abstract

A novel chiral twin material, (R)-bis[5-octyloxy-2-(4-octyloxyphenoxycarbonyl)phenyl] 3-methyladipate, has been prepared, where two mesogenic parts are connected laterally by a spacer possessing a chiral centre. A weaker helical structure, in particular in the chiral smectic C (S?_c) phase, was found to be induced by the laterally-connected twin material than by the analogous terminally-connected twin material. If laterally-connected chiral twin molecules prefer to stay in the smectic layer structure so that the two mesogenic parts exist in the same smectic layer, the twist interaction between adjacent layers cannot be produced by direct correlation of motion and directions of two mesogenic parts. Thus, the helical structure in the S?_c phase induced by laterally-connected chiral twin molecules becomes weak. An analogous laterally-branched ‘monomeric’ compound, (S)-5-octyloxy-2-(4-octyloxyphenoxycarbonyl)phenyl 3-methyl-pentanoate, has also been prepared, and the induced helical structures compared.     

Planar or nonplanar: what is the structure of urea in aqueous solution?

A combined quantum chemical statistical mechanical method has been used to study the solvation of urea in water, with emphasis on the structure of urea. The model system consists of three parts: a Hartree-Fock quantum chemical core, 99 water molecules described with a polarizable force-field, and a dielectric continuum. A free-energy profile along the transition of urea from planar to a nonplanar structure is calculated. This mode in aqueous solution is found to be floppy. That is, the structure of urea in water is not well-defined because the planar to nonplanar transition requires an energy of the order of the thermal energy at room temperature. We discuss the implications of this finding for simulation studies of urea in polar environments like water and proteins.     

Thermotropic liquid crystals from N-alkylpyridinium halides ω-substituted with a mesogenic group

A series of N-alkylpyridinium halides ω-substituted with a 4-methoxybiphen-ylyloxy mesogenic group were synthesized and characterized. The molecules of these compounds contain three distinct parts: a flexible aliphatic chain, a rigid polarizable aromatic core, and a positively charged pyridinium ring associated with a negatively charged counterion. Their thermotropic liquid-crystalline behaviour was studied by differential scanning calorimetry and optical microscopy. Three types of smectic mesophase, namely A, B, and E, were identified by X-ray diffraction. Their structure consists of single layers of upright molecules laterally arranged head to tail. Segregated from the non-ionic parts of the molecules, the ionic end groups are set in double layers with the oppositely charged species facing each other and equally distributed between the two sub-layers. For the ordered smectic E phases, the anions are arranged in rows along the rectangular two dimensional unit cell diagonals with the pyridinium rings sandwiched between them in a chevron-type structure. As for smectic mesophases obtained with soaps, the smectic ordering described in the present work relies primarily on the electrical interactions of the ionic endgroups. Although present, the van der Waals repulsions of the aliphatic and aromatic moieties turn out to be ineffectual.     

Development of a microcapillary column for detecting targeted messenger RNA molecules

A capillary column in a rapid-flow system has been developed for detecting targeted messenger RNA (mRNA) molecules. The column has a structure made of two beds-one bed of porous microbeads and one bed of microbeads with a polythymidine base sequence. The targeted eukaryotic mRNA molecules are detected by two-step hybridization (sandwich hybridization) composed of polyadenosine selection of mRNA molecules and formation of a probe-target (targeted mRNA) hybrid. The sandwich hybridization, which is accomplished within 1 h, was tested using synthetic polydeoxynucleotides. Ten picomoles of the targeted polydeoxynucleotide were detected.     

Uranyl selenates with organic templates: Principles of structure and characteristics of self-organization

Basic structural principles of uranyl selenates with organic templates are outlined as follows. In compounds with short chain amine molecules (C:N < 8) the primary role plays the correspondence between topology of inorganic complex (isomerism) and structure and shape of a template. In the structures with long chain molecules (C:N ≤ 8), the molecules are associated to form 2- or 1-dimensional supramolecular templates that are connected with inorganic structure according to the charge density matching principle. Compounds with electro neutral molecules (crown ethers) have composite structure, where bonding between organic and inorganic parts is achieved through hydrogen bonding via intermediate oxonium clusters.     

The effect of molecular structure on the chiral random grain boundary phase

A chiral random grain boundary (RGB) phase was recently observed in a hockey-stick biphenyl-substituted 1,3,4-oxadiazole derivative. In the RGB phase, achiral molecules self-assemble into randomly oriented blocks of chiral smectic layers and the motif of the unique microstructure is attributed to the similarity of hockey-stick molecules both to bent-core and to rod-like molecules. In order to explore the effect of molecular structure on the RGB phase in detail, we systematically change the molecular design. When the flexible tail decreases, the high-temperature Smectic A (SmA) phase is replaced by a nematic phase, showing a phase sequence of Iso-N-SmA-RGB-Cryst in 2-(4-dodecyloxyphenyl)-5-biphenyl-1,3,4-oxadiazole. However, when we replace the 1,3,4-oxadiazole group by the 1,3,4-thiadiazole group, the bending angle increases in the 1,3,4-thiadiazole derivatives and the RGB phase disappears. Or when the length of the arm becomes short in naphthalene-substituted 1,3,4-oxadiazole, these molecules exhibited only normal rod-like molecules’ mesomorphism. These results will provide deep insights on the relationship of molecular structure and mesophase structural property.     

Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex

The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA sequence d(G(4)T(3)G(4)) has been determined at 1.5 A resolution, together with that of the brominated analogue d(G(4)(Br)UTTG(4)) at 2.4 A resolution. Both sequences form bimolecular intermolecular G-quadruplexes with lateral loops. d(G(4)(Br)UTTG(4)) crystallized in the monoclinic space group P2(1) with three quadruplex molecules in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and form an eight-G-quartet stack, with a linear array of seven K(+) ions between the quartets. d(G(4)T(3)G(4)) crystallized in the orthorhombic space group C222 and has a structure very similar to the head-to-tail dimer in the P2(1) unit cell. The sequence studied here is able to form several different folds; however, all four quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the analogous quadruplex with T(4) loops. A total of seven independent T(3) loops were observed in the two structures. These can be classified into two discrete conformational classes, suggesting that these represent preferred loop conformations that are independent of crystal-packing forces.     

Selectivity over coverage in de novo sequencing of IgGs

Although incredibly diverse in specificity, millions of unique Immunoglobulin G (IgG) molecules in the human antibody repertoire share most of their amino acid sequence. These constant parts of IgG do not yield any useful information in attempts to sequence antibodies de novo. Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous. We report a mass spectrometry-based method that uses electron capture dissociation (ECD) to provide straightforward-to-read sequence ladders for the variable parts of both the light and heavy chains, with a preference for the functionally important CDR3. We optimized this method on the therapeutic antibody Trastuzumab and demonstrate its applicability on two monoclonal quartets of the four IgG subclasses, IgG1, IgG2, IgG3 and IgG4. The method is based on proteolytically separating the variable F(ab′)₂ part from the conserved Fc part, whereafter the F(ab′)₂ portions are mass-analyzed and fragmented by ECD. Pure ECD, without additional collisional activation, leads to straightforward-to-read sequence tags covering the CDR3 of both the light and heavy chains. Using molecular modelling and structural analysis, we discuss and explain this selective fragmentation behavior and describe how structural features of the different IgG subclasses lead to distinct fragmentation patterns. Overall, we foresee that pure ECD on F(ab′)₂ or Fab molecules can become a valuable tool for the de novo sequencing of serum antibodies.     

部分同谱分子

本文在HMO近似内讨论部分同谱分子。认为在一个没有对称面的分子中, 可能隐含着一个对称面。对称面将分子分成两部分。这两部分所表示的共轭体系是部分同谱分子。它们与整个分子也是部分同谱分子。文中讨论了三顶点链图, 这种链图表示了无数个部分同谱分子进行收缩的总结果, 同时用少数例子加以说明。     

QXP: Powerful, rapid computer algorithms for structure-based drug design

New methods for docking, template fitting and building pseudo-receptors are described. Full conformational searches are carried out for flexible cyclic and acyclic molecules. QXP (quick explore) search algorithms are derived from the method of Monte Carlo perturbation with energy minimization in Cartesian space. An additional fast search step is introduced between the initial perturbation and energy minimization. The fast search produces approximate low-energy structures, which are likely to minimize to a low energy. For template fitting, QXP uses a superposition force field which automatically assigns short-range attractive forces to similar atoms in different molecules. The docking algorithms were evaluated using X-ray data for 12 protein–ligand complexes. The ligands had up to 24 rotatable bonds and ranged from highly polar to mostly nonpolar. Docking searches of the randomly disordered ligands gave rms differences between the lowest energy docked structure and the energy-minimized X-ray structure, of less than 0.76 Å for 10 of the ligands. For all the ligands, the rms difference between the energy-minimized X-ray structure and the closest docked structure was less than 0.4 Å, when parts of one of the molecules which are in the solvent were excluded from the rms calculation. Template fitting was tested using four ACE inhibitors. Three ACE templates have been previously published. A single run using QXP generated a series of templates which contained examples of each of the three. A pseudo-receptor, complementary to an ACE template, was built out of small molecules, such as pyrrole, cyclopentanone and propane. When individually energy minimized in the pseudo-receptor, each of the four ACE inhibitors moved with an rms of less than 0.25 Å. After random perturbation, the inhibitors were docked into the pseudo-receptor. Each lowest energy docked structure matched the energy-minimized geometry with an rms of less than 0.08 Å. Thus, the pseudo-receptor shows steric and chemical complementarity to all four molecules. The QXP program is reliable, easy to use and sufficiently rapid for routine application in structure-based drug design.     

DFT study on singlet diradical character of zethrenes

The diradical character of zethrenes was investigated using a symmetry-broken UB3LYP/6-311G(d,p) method. The number of hexagons in the investigated molecules ranges from 6 to 12. It was found that all zethrenes are singlet diradicals, whose diradical character increases with the increasing size of the molecules. A singlet diradical structure provides a possibility for an electron pair to occupy different parts of space, and allows for achieving aromatic stabilization. It can be predicted, on the basis of the singlet-triplet values, that even higher zethrenes will be singlet, but not triplet molecules.     

Evolutionary chemistry approach toward finding novel inhibitors of the type 2 diabetes target glucose-6-phosphate translocase

A genetic algorithm (GA), driven by experimentally determined biological activities as a feedback fitness function, was used to propose novel small molecules as inhibitors of glucose-6-phosphate translocase (G6PT) in iterative rounds of evolutionary optimization. A straightforward polymer-supported synthetic sequence was implemented to synthesize molecules proposed by the GA, and the biological activities of the compounds were determined by a microsomal assay. Additional compound design strategies were integrated, such as Tanimoto similarity-based selection of starting materials and transfer of favored structure elements into a new chemical scaffold to identify more active and selective inhibitors.     

Microstructuring of a polymer globule in solution in the presence of an amphiphilic substance

Microstructuring in the bulk of a polymer globule in a solution that contains dimeric amphiphilic molecules, in particular, surfactants, is studied in terms of the weak-segregation theory. An inhomogeneous structure can result from a decrease in free energy with the orientation of amphiphilic molecules in the region of inhomogeneity owing to the interaction of hydrophobic and polar parts of the molecules with the solvent. For the sake of simplicity, we discuss the case of identical second virial coefficients of the interaction of monomer units and amphiphilic molecules with different energies of interaction of the hydrophobic and polar parts of the molecule with the solvent. By comparing the free energy for different types of microstructures, we predict that, with deterioration in the quality of the solvent, there is an initial formation of a homogeneous globule followed by formation of a body-centered cubic structure; a hexagonal cylindrical structure; and, finally, a lamellar structure. For a low degree of amphiphilicity, the transition from a homogeneous globule to only a lamellar structure occurs. An increase in the concentration of the amphiphilic substance in the surrounding solution hinders the formation of a globule but facilitates its microstructuring, which is also promoted by an increase in the volume of the amphiphilic molecule and the difference in the interaction energies of its hydrophobic and polar parts with the solvent. Phase diagrams of a globule??s state at different values of model parameters are plotted.     

Synthesis and Structural Determination of Binuclear Nine-Coordinate K_4[Y_2(Httha)_2]·14H_2O

IntroductionThe compounds of the radioactive metal90 Yare often used for the treatment of all kinds ofcancer[1] because90 Y has an appropriate half- life( t1/2 =64.0 h) and moderate energy( Emax=2 .2 7Me V) .However,the compounds of the radioactivemetals usually result in the strong toxicities tohuman bodies because they can react with somebiological molecules in human bodies.In addition,the radioactive metal compounds can not only killtumor cells but also harm a large quantity ofnormal cell…