QSAR modeling of in vitro inhibition of cytochrome P450 3A4

We report the QSAR modeling of cytochrome P450 3A4 (CYP3A4) enzyme inhibition using four large data sets of in vitro data. These data sets consist of marketed drugs and drug-like compounds all tested in four assays measuring the inhibition of the metabolism of four different substrates by the CYP3A4 enzyme. The four probe substrates are benzyloxycoumarin, testosterone, benzyloxyresorufin, and midazolam. We first show that using state-of-the-art QSAR modeling approaches applied to only one of these four data sets does not lead to predictive models that would be useful for in silico filtering of chemical libraries. We then present the development and the testing of a multiple pharmacophore hypothesis (MPH) that is formulated as a conceptual extension of the traditional QSAR approach to modeling the promiscuous binding of a large variety of drugs to CYP3A4. In the simplest form, the MPH approach takes advantage of the multiple substrate data sets and identifies the binding of test compounds as either proximal or distal relative to that of a given substrate. Application of the approach to the in silico filtering of test compounds for potential inhibitors of CYP3A4 is also presented. In addition to an improvement in the QSAR modeling for the inhibition of CYP3A4, the results from this modeling approach provide structural insights into the drug-enzyme interactions. The existence of multiple inhibition data sets in the BioPrint database motivates the original development of the concept of a multiple pharmacophore hypothesis and provides a unique opportunity for formulating alternative strategies of QSAR modeling of the inhibition of the in vitro metabolism of CYP3A4.     

Coplanarity in the backbones of ladder-type oligo(p-phenylene) homologues and derivatives

p-Tolyl-substituted ladder-type oligo(p-phenylene)s containing three, four, and five phenylene rings were readily synthesized. The uniform aryl substitution of these systems allowed us to determine the coplanarity of the pi-conjugated backbones crystallographically. The intramolecular annulations eliminate almost all of the conformational disorder and enhance the degree of pi-conjugation of the backbones, resulting in significant red shifts in the absorption and emission maxima and lower oxidation potentials in the higher homologues. [structure: see text]     

Synthesis of new amphiphilic dendrons bearing aliphatic hydrocarbon surface sectors and a monocarboxylic or dicarboxylic acid focal point

[structure: see text]. A new series of amphiphilic G1-G3 dendrons containing purely aliphatic hydrocarbon dendritic surface sectors and one or two carboxylic acid group(s) at the focal point was synthesized in good yields. The key branching steps involve diallylation reactions of diethyl malonate or Meldrum's acid. These dendrons are highly soluble in hexane despite having highly polar carboxylic acid groups at the focal point.     

Theoretical investigation on the replacement of CH groups by N atoms in caged structure (CH)8

A molecular design was performed for the caged molecule (CH)8: the replacement of CH groups by N atoms to increase the content of N as well as reduce the content of H. A series of caged molecules were obtained: (CH)xN(8-x) (0 < or = n < or = 8). The studied aspects are as follows: (i) molecular geometries and electronic structures, (ii) the analysis of the electronic structure using natural bond orbital (NBO) and atoms in molecules (AIM), and (iii) some physicochemical properties of studied molecules, such as the dipole moments, IR vibrational spectra, NMR chemical shifts, heats of formation, and relative specific impulses, were provided. Our studies show that these molecules should be a kind of potential and novel energetic material. Our work provides some useful information for the experimental study of these molecules. The effect of the substitution of N atoms for CH groups on the properties of this kind of caged molecule is presented.     

Lysophosphatidylcholine suppresses apoptosis and induces neurite outgrowth in PC12 cells through activation of phospholipase D2

Lysophosphatidylcholine (LPC) is a bioactive lipid generated by phospholipase A2-mediated hydrolysis of phosphatidylcholine. In the present study, we demonstrate that LPC stimulates phospholipase D2 (PLD2) activity in rat pheochromocytoma PC12 cells. Serum deprivation induced cell death of PC12 cells, as demonstrated by decreased viability, DNA fragmentation, and increased sub-G1 fraction of cell cycle. LPC treatment protected PC12 cells partially from the cell death and induced neurite outgrowth of the cells. Overexpression of PLD2 drastically enhanced the LPC-induced inhibition of apoptosis and neuritogenesis. Pretreatment of the cells with 1-butanol, a PLD inhibitor, completely abrogated the LPC-induced inhibition of apoptosis and neurite outgrowth in PC12 cells overexpressing PLD2. These results indicate that LPC possesses the neurotrophic effects, such as anti-apoptosis and neurite outgrowth, through activation of PLD2.     

Tripodal oxazoline-based homochiral coordination cages with internal binding sites

Homochiral coordination cages, which have two well-defined internal binding sites for ammonium and organoammonium ions, have been constructed by Pd(II)-mediated self-assembly of preorganized tripodal oxazolines containing pyridine pendant groups.     

Structural and spectroscopic properties of trans-difluoro(1,4,8,12-tetraazacyclopentadecane)chromium(III) perchlorate hydrate

The structure of [CrF(2)([15]aneN(4))]ClO(4).H(2)O ([15]aneN(4)=1,4,8,12-tetraazacyclopentadecane) has been determined by a single-crystal X-ray diffraction study at 173 K. The complex crystallizes in the space group P1- of the triclinic system with two mononuclear formula units in a cell of dimensions a=9.6117(7) A, b=10.2882(7) A, c=11.0001(7) A and alpha=99.7570(10) degrees, beta=105.6080(10) degrees and gamma=113.7130(10) degrees. The complex cation unit has its central Cr atom in an octahedral coordination with four nitrogen atoms and two fluorine atoms in a trans position. Three six-membered and one five-membered chelate rings of the [15]aneN(4) ligand are in a chair-twist(skew)-chair-gauche conformation sequence. The gauche five-membered ring is disordered with the twist six-membered ring opposite. The four H atoms in the chiral N atoms have the trans-II (CTCg) type configuration. The mean Cr-N and Cr-F bonds are 2.095(2) and 1.8752(13) A, respectively. The IR and visible spectral properties are consistent with the result of X-ray crystallography. The resolved band maxima of the electronic d-d spectrum are fitted with secular determinant for quartet state energy of d(3) configuration in tetragonal field including configurational but neglecting spin-orbit coupling. It is confirmed that the fluoride has strong sigma- and pi-donor properties toward the chromium(III) ion and the nitrogen atoms of the [15]aneN(4) ligand also have a strong sigma-donor character.     

Theoretical study on "multilayer" nitrogen cages

The relative stabilities of nonisomers are investigated. Twenty-two species of nitrogen cage molecules N(2n) (N6 (D(3h)), N8 (Oh), N10 (D(5h)), N12 (D(6h)), N12 (D(3d)), N16 (D(4d)), N18 (D(3h)), N20 (Ih), N24 (D(3d)), N24 (D(4h)), N24 (D(6d)), N30 (D(3h)), N30 (D(5h)), N32 (D(4d)), N36 (D(3d)), N40 (D(4h)), N42 (D(3h)), N48 (D(4d)), N48 (D(3d)), N54 (D(3h)), N56 (D(4h)), and N60 (D(3d))), which are divided into four sets, have been studied in detail. The geometries and varieties of energies are examined extensively, and NBO analysis and AIM analysis are applied to investigate the bonding properties of the cage molecules. The introducing of the concept of "layer" can well assist in explaining why one nonisomer molecule is more stable than another one. The results show that the lengths of bonds, on both sides of which are five-membered rings (referred to as pentagons), are the shortest and the orbital energies are the lowest. The nonlocalized electron numbers of orbitals, on at least one side of which is a triangle, are the greatest. Pentagons play a major role in the stability of a cage molecule, and the three-membered rings (referred to as triangles) play the second one. The layers in nitrogen cage molecules also contribute to the relative stabilities.     

Molecular dynamics simulation of laser desorption of a fragment of protein kinase A from two MALDI matrices

We have carried out molecular dynamics simulations to study the desorption of a dephosphorylated fragment of protein kinase A from two matrices, sinapic acid (SA) and 2,5-dihydroxybenzoic acid (DHB), after laser excitation. We have examined the results as a function of the laser fluence and of the burial depth of the guest peptide in the matrices. In most cases, we found that the energy transferred from the matrix to the guest peptide was not sufficiently large to fragment the peptide. Exceptions occurred when the peptide was more buried. This finding suggested that protein analytes might be less likely to break into smaller fragments if they were placed closer to the surface of the matrix. We have also examined how likely the guest peptide could form small clusters with the matrix molecules and found that the results depended on the degree of burial of the peptide, on the laser fluence, and on which matrix was used. Generally, stable clusters were more likely to be formed for guest peptides that were more buried, at a lower laser fluence, and in the SA rather than the DHB matrix. In addition, we found that the DHB matrix was broken down more easily by the laser than the SA matrix.