PaDEL‐DDPredictor: Open‐source software for PD‐PK‐T prediction

ADMET (absorption, distribution, metabolism, excretion, and toxicity)‐related failure of drug candidates is a major issue for the pharmaceutical industry today. Prediction of PD‐PK‐T properties using in silico tools has become very important in pharmaceutical research to reduce cost and enhance efficiency. PaDEL‐DDPredictor is an in silico tool for rapid prediction of PD‐PK‐T properties of compounds from their chemical structures. It is free and open‐source software that, has both graphical user interface and command line interface, can work on all major platforms (Windows, Linux, and MacOS) and supports more than 90 different molecular file formats. The software can be downloaded from http://padel.nus.edu.sg/software/padelddpredictor . © 2012 Wiley Periodicals, Inc.     

DNA methylation-based age prediction with bloodstains using pyrosequencing and random forest regression

The use of DNA methylation to predict chronological age has shown promising potential for obtaining additional information in forensic investigations. To date, several studies have reported age prediction models based on DNA methylation in body fluids with high DNA content. However, it is often difficult to apply these existing methods in practice due to the low amount of DNA present in stains of body fluids that are part of a trace material. In this study, we present a sensitive and rapid test for age prediction with bloodstains based on pyrosequencing and random forest regression. This assay requires only 0.1 ng of genomic DNA and the entire procedure can be completed within 10 h, making it practical for forensic investigations that require a short turnaround time. We examined the methylation levels of 46 CpG sites from six genes using bloodstain samples from 128 males and 113 females aged 10–79 years. A random forest regression model was then used to construct an age prediction model for males and females separately. The final age prediction models were developed with seven CpG sites (three for males and four for females) based on the performance of the random forest regression. The mean absolute deviation was less than 3 years for each model. Our results demonstrate that DNA methylation-based age prediction using pyrosequencing and random forest regression has potential applications in forensics to accurately predict the biological age of a bloodstain donor.     

An alignment‐free methodology for modelling field‐based 3D‐structure activity relationships using inductive logic programming

Traditional 3D‐quantitative structure–activity relationship (QSAR)/structure–activity relationship (SAR) methodologies are sensitive to the quality of an alignment step which is required to make molecular structures comparable. Even though many methods have been proposed to solve this problem, they often result in a loss of model interpretability. The requirement of alignment is a restriction imposed by traditional regression methods due to their failure to represent relations between data objects directly. Inductive logic programming (ILP) is a class of machine‐learning methods able to describe relational data directly. We propose a new methodology which is aimed at using the richness in molecular interaction fields (MIFs) without being restricted by any alignment procedure. A set of MIFs is computed and further compressed by finding their minima corresponding to the sites of strongest interaction between a molecule and the applied test probe. ILP uses these minima to build easily interpretable rules about activity expressed as pharmacophore rules in the powerful language of first‐order logic. We use a set of previously published inhibitors of factor Xa of the benzamidine family to discuss the problems, requirements and advantages of the new methodology. Copyright © 2007 John Wiley & Sons, Ltd.     

Self‐organization of striped pattern of refractive indices in photopolymer film

We report on a self‐organized striped pattern of refractive indices in a photopolymer film. Silicon oxide (SiO₂) particles (1.3‐μm diameter) were dispersed on a cover glass above a monomer mixture (bifunctional methacrylate monomer, cyanoethylmethacrylate, and 2,4,6‐trimethylbenzoyldiphenylphosphine oxide), and the sample was uniformly irradiated from a tube light source. The self‐organized striped pattern was observed inside a 0.45‐mm thickness photopolymer film. In contrast, no pattern was observed in a 0.45‐mm thickness sample photopolymerized without particles on a cover glass. The results suggest that the SiO₂ particles acted as “lenses” and produced a light distribution reflecting the shape of the light source used during the irradiation. The photopolymerization extended in depth according to the light distribution, and then the striped pattern was generated inside a medium. The photopolymer film with the striped pattern has an angular dependence in the transmittance as a result of the microstructure and can be applied to a flexible optical transmission filter. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3351–3358, 2004     

Soluble high‐Tg polyetherimides with good flame retardancy based on an asymmetric phosphinated etherdiamine

This study focuses on preparing soluble, high‐T_g polyetherimides (PEIs) with good flame retardancy. To achieve this goal, a phosphinated aminophenol, 1‐(4‐hydroxyphenyl)‐1‐(4‐aminophenyl)‐1‐(6‐oxido‐6H‐dibenz〈c,e〉〈1,2〉oxaphosphorin‐6‐yl)ethane ( 1 ), was prepared. Then, an asymmetric etherdiamine, 1‐(4‐(4‐aminophenoxy)phenyl)‐1‐(4‐aminophenyl)‐1‐(6‐oxido‐6H‐dibenz〈c,e〉〈1,2〉oxaphosphorin‐6‐yl)ethane ( 3 ), was prepared from the nucleophilic substitution of ( 1 ) with 4‐chloronitrobenzene, followed by catalytic hydrogenation. Light colored, tough, and foldable PEIs ( 5 ) with good thermal stability, organo‐solubility, and good flame retardancy were synthesized from the condensation of ( 3 ) with various aromatic dianhydrides in N,N‐dimethylacetamide, followed by thermal imidization. Properties of the resulting PEIs were evaluated and compared with those of symmetric PEIs ( 5 ′) and polyimides ( 5 ″). The structure–property relationships were discussed. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Observation of a CuII2(μ‐1,2‐peroxo)/CuIII2(μ‐oxo)2 Equilibrium and its Implications for Copper–Dioxygen Reactivity

Synthesis of small‐molecule Cu₂O₂ adducts has provided insight into the related biological systems and their reactivity patterns including the interconversion of the Cu^II₂(μ‐η²:η²‐peroxo) and Cu^III₂(μ‐oxo)₂ isomers. In this study, absorption spectroscopy, kinetics, and resonance Raman data show that the oxygenated product of [(BQPA)Cu^I]⁺ initially yields an “end‐on peroxo” species, that subsequently converts to the thermodynamically more stable “bis‐μ‐oxo” isomer (K_eq=3.2 at ?90 °C). Calibration of density functional theory calculations to these experimental data suggest that the electrophilic reactivity previously ascribed to end‐on peroxo species is in fact a result of an accessible bis‐μ‐oxo isomer, an electrophilic Cu₂O₂ isomer in contrast to the nucleophilic reactivity of binuclear Cu^II end‐on peroxo species. This study is the first report of the interconversion of an end‐on peroxo to bis‐μ‐oxo species in transition metal‐dioxygen chemistry.     

Energetic N‐Nitramino/N‐Oxyl‐Functionalized Pyrazoles with Versatile π–π Stacking: Structure–Property Relationships of High‐Performance Energetic Materials

N‐Nitramino/N‐oxyl functionalization strategies were employed to investigate structure–property relationships of energetic materials. Based on single‐crystal diffraction data, π–π stacking of pyrazole backbones can be tailored effectively by energetic functionalities, thereby resulting in diversified energetic compounds. Among them, hydroxylammonium 4‐amino‐3,5‐dinitro‐1H‐pyrazol‐1‐olate and dipotassium N,N′‐(3,5‐dinitro‐1H‐pyrazol‐1,4‐diyl)dinitramidate, with unique face‐to‐face π–π stacking, can be potentially used as a high‐performance explosive and an energetic oxidizer, respectively.     

Symmetry Breaking in Pyrrolo[3,2‐b]pyrroles: Synthesis,Solvatofluorochromism and Two‐photon Absorption

Five centrosymmetric and one dipolar pyrrolo[3,2‐b ]pyrroles, possessing either two or one strongly electron‐withdrawing nitro group have been synthesized in a straightforward manner from simple building blocks. For the symmetric compounds, the nitroaryl groups induced spontaneous breaking of inversion symmetry in the excited state, thereby leading to large solvatofluorochromism. To study the origin of this effect, the series employed peripheral structural motifs that control the degree of conjugation via altering of dihedral angle between the 4‐nitrophenyl moiety and the electron‐rich core. We observed that for compounds with a larger dihedral angle, the fluorescence quantum yield decreased quickly when exposed to even moderately polar solvents. Reducing the dihedral angle (i.e., placing the nitrobenzene moiety in the same plane as the rest of the molecule) moderated the dependence on solvent polarity so that the dye exhibited significant emission, even in THF. To investigate at what stage the symmetry breaking occurs, we measured two‐photon absorption (2PA) spectra and 2PA cross‐sections (σ_2PA) for all six compounds. The 2PA transition profile of the dipolar pyrrolo[3,2‐b ]pyrrole, followed the corresponding one‐photon absorption (1PA) spectrum, which provided an estimate of the change of the permanent electric dipole upon transition, ≈18 D. The nominally symmetric compounds displayed an allowed 2PA transition in the wavelength range of 700–900 nm. The expansion via a triple bond resulted in the largest peak value, σ_2PA=770 GM, whereas altering the dihedral angle had no effect other than reducing the peak value two‐ or even three‐fold. In the S ₀→S ₁ transition region, the symmetric structures also showed a partial overlap between 2PA and 1PA transitions in the long‐wavelength wing of the band, from which a tentative, relatively small dipole moment change, 2–7 D, was deduced, thus suggesting that some small symmetry breaking may be possible in the ground state, even before major symmetry breaking occurs in the excited state.     

Relationship between Molecular Stacking and Optical Properties of 9,10‐Bis((4‐N,N‐dialkylamino)styryl) Anthracene Crystals: The Cooperation of Excitonic and Dipolar Coupling

Five 9,10‐bis((4‐N,N‐dialkylamino)styryl) anthracene derivatives (DSA‐C1–DSA‐C7) with different length alkyl chains were synthesized. They showed the same color in dilute solutions but different colors in crystals. The absorption, photoluminescence, and fluorescence decay indicate that there exist both excitonic and dipolar coupling in crystals of DSA‐C1–DSA‐C7. X‐ray crystallographic analysis revealed that all the crystals belong to the triclinic space group P$\bar 1$ with one molecule per unit cell and that the molecules in every crystal have the identical orientation. This offers ideal samples to investigate the impact of the molecular stacking on the optical properties of the crystals. For the first time, the cooperation of excitonic and dipolar coupling has been comprehensively studied, and the contribution to the spectral shift from the excitonic and dipolar couplings quantitatively obtained. The experiments of amplified spontaneous emission (ASE) together with measurements of the quantum efficiency further confirmed this interpretation. The results suggest that the excitonic and dipolar couplings between the adjacent molecules are both important and jointly induce the spectral shifts of the crystals.     

Cationic Poly([R]‐3‐hydroxybutyrate) Copolymers as Antimicrobial Agents

Poly([R]‐3‐hydroxybutyrate) (PHB), a natural biodegradable polyester, has attracted much attention as a new biomaterial because of its sustainability and good biocompatibility. In this study, it is discovered that PHB can be conveniently functionalized to obtain a number of platform chain architectures that may provide a wide range of functional copolymers. In a transesterification reaction, linear (di‐hydroxylated) and star shaped (tri‐ and tetra‐hydroxylated) PHB oligomers are synthesized, followed by copolymerization with 2‐(dimethylamino)ethyl methacrylate and quaternization with benzyl bromide to afford antimicrobial properties. The antimicrobial activities of the quaternary salts against clinically relevant pathogens on the interactions with outer and cytoplasmic membranes, lethal mechanisms, multipassage resistance, and synergy effect with antibiotics are investigated. Cationic PHB copolymers show effectiveness as antimicrobial agents, with minimum inhibitory concentration values 0.24–0.65 µm (or µmol dm^?3) (or 32–128 µg mL^?1) against Gram‐positive and Gram‐negative bacteria. Modifying the copolymer architectures into star shapes results in enhanced effectiveness to disrupt the membrane integrity. Synergistic effects are attained for all the quaternized PHB derivatives when they are used together with tobramycin. Multipassage resistance does not occur in both the linear and star derivatives against Gram‐negative bacteria after 20 passages.     

Structure–activity relationship of N‐heterocyclic carbene–Pd(II)–imidazole complexes in Suzuki–Miyaura coupling between 4‐methoxyphenyl chloride and phenylboronic acid

A series of N‐heterocyclic carbene–PdCl₂–imidazole [NHC–Pd(II)–Im] complexes were synthesized and the structure of most of them was unambiguously determined by X‐ray single‐crystal diffraction. The structure–activity relationship of these complexes was investigated for the Suzuki–Miyaura coupling between 4‐methoxyphenyl chloride and phenylboronic acid, and the effect of the NHCs and Im moieties were fully discussed. The sterically hindered IPr‐based complex showed the highest catalytic activity. Copyright © 2013 John Wiley & Sons, Ltd.     

Optically Biaxial,Re‐entrant and Frustrated Mesophases in Chiral,Non‐symmetric Liquid Crystal Dimers and Binary Mixtures

Sixteen optically active, non‐symmetric dimers, in which cyanobiphenyl and salicylaldimine mesogens are interlinked by a flexible spacer, were synthesized and characterized. While the terminal chiral tail, in the form of either (R)‐2‐octyloxy or (S)‐2‐octyloxy chain attached to salicylaldimine core, was held constant, the number of methylene units in the spacer was varied from 3 to 10 affording eight pairs of (R & S) enantiomers. They were probed for their thermal properties with the aid of orthoscopy, conoscopy, differential scanning calorimetry and X‐ray powder diffraction. In addition, the binary mixture study was carried out using chiral and achiral dimers with the intensions of stabilizing optically biaxial phase/s, re‐entrant phases and important phase sequences. Notably, one of the chiral dimers as well as some mixtures exhibited a biaxial smectic A (SmA_b) phase appearing between a uniaxial SmA and a re‐entrant uniaxial SmA phases. The mesophases such as chiral nematic (N*) and frustrated phases viz., blue phases (BPs) and twist grain boundary (TGB) phases, were also found to occur in most of the dimers and mixtures. X‐ray diffraction studies revealed that the dimers possessing oxybutoxy and oxypentoxy spacers show interdigitated (SmA_d) phase where smectic periodicity is over 1.4 times the molecular length; whereas in the intercalated SmA (SmA_c) phase formed by a dimer having oxydecoxy spacer the periodicity was found to be approximately half the molecular length. The handedness of the helical structure of the N* phases formed by two enantiomers was examined with the aid of CD measurements; as expected, these enantiomers showed optical activities of equal magnitudes but with opposite signs. Overall, it appears that the chiral dimers and mixtures presented herein may serve as model systems in design and developing novel materials exhibiting the apolar SmA_b phase possessing D_2h symmetry and nematic‐type biaxiality.     

Imine‐N‐Heterocyclic Carbenes as Versatile Ligands in Ruthenium(II) p‐Cymene Anticancer Complexes: A Structure–Activity Relationship Study

A family of novel imine‐N‐heterocyclic carbene ruthenium(II) complexes of the general formula [(η⁶‐p‐cymene)Ru(C^N)Cl]PF₆⁻ (where C^N is an imine‐N‐heterocyclic carbene chelating ligand with varying substituents) have been prepared and characterized. In this imine‐N‐heterocyclic carbene chelating ligand framework, there are three potential sites that can be modified, which distinguishes this class of ligand and provides a body of flexibilities and opportunities to tune the cytotoxicity of these ruthenium(II) complexes. The influence of substituent effects of three tunable domains on the anticancer activity and catalytic ability in converting coenzyme NADH to NAD⁺ is investigated. This family of complexes displays an exceedingly distinct anticancer activity against A549 cancer cells, despite their close structural similarity. Complex 9 shows the highest anticancer activity in this series against A549 cancer cells (IC₅₀=14.36 μm ), with an approximately 1.5‐fold better activity than the clinical platinum drug cisplatin (IC₅₀=21.30 μm ) in A549 cancer cells. Mechanistic studies reveal that complex 9 mediates cell death mainly through cell stress, including cell cycle arrest, inducing apoptosis, increasing intracellular reactive oxygen species (ROS) levels, and depolarization of the mitochondrial membrane potential (MMP). Furthermore, lysosomal damage is also detected by confocal microscopy.     

Carbohydrate Chain of Ganglioside GM1 as a Ligand: Identification of the Binding Strategies of Three 15 mer Peptides and Their Divergence from the Binding Modes of Growth‐Regulatory Galectin‐1 and Cholera Toxin

The branched pentasaccharide chain of ganglioside GM₁ is a prominent cell surface ligand, for example, for cholera toxin or tumor growth‐regulatory homodimeric galectins. This activity profile via protein recognition prompted us to examine the binding properties of peptides with this specificity. Our study provides insights into the mechanism of molecular interaction of this thus far unexplored size limit of the protein part. We used three pentadecapeptides in a combined approach of mass spectrometry, NMR spectroscopy and molecular modelling to analyze the ligand binding in solution. Availability of charged and hydrophobic functionalities affected the intramolecular flexibility of the peptides differently. Backfolding led to restrictions in two cases; the flexibility was not reduced significantly by association of the ligand in its energetically privileged conformations. Major contributions to the interaction energy arise from the sialic acid moiety contacting Arg/Lys residues and the N‐terminal charge. Considerable involvement of stacking between the monovalent ligand and aromatic rings could not be detected. This carbohydrate binding strategy is similar to how an adenoviral fiber knob targets sialylated glycans. Rational manipulation for an affinity enhancement can now be directed to reduce the flexibility, exploit the potential for stacking and acquire the cross‐linking capacity of the natural lectins by peptide attachment to a suitable scaffold.