Modeling and predicting binding affinity of phencyclidine‐like compounds using machine learning methods

Machine learning methods have always been promising in the science and engineering fields, and the use of these methods in chemistry and drug design has advanced especially since the 1990s. In this study, molecular electrostatic potential (MEP) surfaces of phencyclidine‐like (PCP‐like) compounds are modeled and visualized in order to extract features that are useful in predicting binding affinities. In modeling, the Cartesian coordinates of MEP surface points are mapped onto a spherical self‐organizing map (SSOM). The resulting maps are visualized using electrostatic potential (ESP) values. These values also provide features for a prediction system. Support vector machines and partial least‐squares method are used for predicting binding affinities of compounds. Copyright © 2009 John Wiley & Sons, Ltd.     

Diabetes induces compositional, structural and functional alterations on rat skeletal soleus muscle revealed by FTIR spectroscopy: a comparative study with EDL muscle

Diabetes Mellitus (DM) is a metabolic disorder, characterized by abnormally high blood glucose levels due to decreased secretion or effectiveness in function of insulin. Having a role in carbohydrate and lipid metabolism, skeletal muscle is affected by the absence of insulin in diabetic conditions. This current study reports the application of Fourier transform infrared (FTIR) spectroscopy in the determination of macromolecular alterations in streptozotocin (STZ)-induced diabetic rat skeletal Soleus (SOL) muscles, which highlight the promise of this technique in medical research. The results revealed that DM induced several alterations in macromolecular content and structure of slow-contracting SOL muscles. In diabetic SOL muscles, a decrease in the content of lipids, proteins and nucleic acids together with an increase in lipid order was observed. The decrease in the level of unsaturation and acyl chain length of lipids demonstrated the increased lipid peroxidation in DM. There were alterations in protein secondary structure in DM with a decrease in α-helix and β-sheet content of proteins, whereas the content of aggregated β-strands increased, which is generally seen when proteins denature. Besides, the integrity of collagen molecules was found to be decreased, demonstrating the alterations in its triple helical structure in diabetic muscles. Furthermore, the same alterations mentioned above were also observed in diabetic fast-contracting Extensor Digitorum Longus (EDL) muscles. However, having a high content of mitochondria and relying on an oxidative pathway, SOL muscle was found to be more affected by DM.     

Scattering from a PT symmetric standing wave

We study the Kapitza–Dirac diffraction of a free beam particle in the presence of a PT symmetric standing wave. We discuss that the momentum and total probability are not conserved in the non-Hermitian scattering process. We show that the average momentum gain/loss does not vanish over a period even if the non-Hermitian optical potential changes periodically in time. We give the resonance conditions at which large momentum transfer is produced.     

Domain compression via anisotropic metamaterials designed by coordinate transformations

We introduce a spatial coordinate transformation technique to compress the excessive white space (i.e. free-space) in the computational domain of finite methods. This approach is based on the form-invariance property of Maxwell’s equations under coordinate transformations. Clearly, Maxwell’s equations are still satisfied inside the transformed space, but the medium turns into an anisotropic medium whose constitutive parameters are determined by the coordinate transformation. The proposed technique can be employed to reduce the number of unknowns especially in high-frequency applications wherein a finite method requires an electrically-large computational domain. After developing the analytical background of this technique, we report some numerical results for finite element simulations of electromagnetic scattering problems.     

A phenanthrene-based calix[4]arene as a fluorescent sensor for Cu and F

A new phenanthrene-based fluorescent calix[4]arene (4) has been synthesized in cone conformation. This compound was examined for its fluorescent properties towards different metal ions (Na⁺, Li⁺, Mg²⁺, Ni²⁺, Ba²⁺, Ca²⁺, Cu²⁺, Pb²⁺) and anions (F⁻, Cl⁻, Br⁻, H₂₄PO⁻,${{\text{H}}_2{\text{PO}}_4}^{-}\text{,}$₃NO⁻,${{\text{NO}}_3}^{-}\text{,}$₄HSO⁻,${{\text{HSO}}_4}^{-}\text{,}$ CH₃COO⁻) by fluorescence spectroscopy. The properties of the compound were evaluated and show that it is a fluorescence sensor for Cu²⁺ and F⁻. With the addition of Cu²⁺ and F⁻, the fluorescence was severely quenched.     

Effects of ELF Magnetic Field in Combination with Iron(III) Chloride (FeCl3) on Cellular Growth and Surface Morphology of Escherichia coli (E. coli)

This study investigated the effects of extremely low frequency (ELF) magnetic field with/without iron(III) chloride (FeCl₃) on bacterial growth and morphology. The ELF exposures were carried out using a pair of Helmholtz coil-based ELF exposure system which was designed to generate 50 Hz sinusoidal magnetic field. The field was approximately uniform throughout the axis of the coil pair. The samples which were treated or non-treated with different concentrations FeCl₃ were exposed to 50 Hz, 2 millitesla (mT) magnetic field for 24 h. ELF effect on viability was assessed in terms of viable colony counts (in colony-forming unit per milliliter) with the standard plate count technique. Scanning electron microscopy was used to investigate the magnetic field effect on surface morphology of Escherichia coli. No significant results were seen in terms of cell viability between ELF and sham-exposed bacterial strains. Similarly, FeCl₃ treatment did not change cell viability of E. coli samples. However, we observed some morphological changes on E. coli cell surfaces. Pore formations and membrane destruction were seen on the surface of 24 h ELF field-exposed cells. We concluded that ELF magnetic field exposure at 2 mT does not affect cell viability; however, it may affect bacterial surface morphology.     

Relationships between unfolded configurations of proteins and dynamics of folding to the native state

We compare folding trajectories of chymotrypsin inhibitor (CI2) using a dynamic Monte Carlo scheme with Go-type potentials. The model considers the four backbone atoms of each residue and a sphere centered around C^β the diameter of which is chosen according to the type of the side group. Bond lengths and bond angles are kept fixed. Folding trajectories are obtained by giving random increments to the φ and ψ torsion angles with some bias toward the native state. Excluded volume effects are considered. Two sets of 20 trajectories are obtained, with different initial configurations. The first set is generated from random initial configurations. The initial configurations of the second set are generated according to knowledge-based neighbor dependent torsion probabilities derived from triplets in the Protein Data Bank. Compared to chains with randomly generated initial configurations, those generated with neighbor-dependent probabilities (i) fold faster, (ii) have better defined secondary structure elements, and (iii) have less number of non-native contacts during folding. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3667–3678, 2006     

Aurones: Small Molecule Visible Range Fluorescent Probes Suitable for Biomacromolecules

Aurones, derivatives of 2-benylidenebenzofuran-3(2H)-one, are natural products that serve as plant pigments. There have been reports that some of these substances fluoresce, but little information about their optical properties is in the literature. In this report, series of aurone derivatives were synthesized as possible fluorescent probes that can be excited by visible light. We found that an amine substituent shifted the lowest energy absorption band from the near-UV to the visible region of the electromagnetic spectrum. Four amine-substituted aurone derivatives were synthesized to explore the effect of this substituent on the absorption and emission properties of the aurone chromophore. The emission maxima and intensities of the molecules are strongly dependent on the nature of the substituent and the solvent polarity. Overall, the emission intensity increases and the maximum wavelength decreases in less polar solvents; thus, the aurones may be useful probes for hydrophobic sites on biological molecules. A limited investigation with model protein, nucleic acid and fixed cells supports this idea. It is known that the sulfur analog of aurone can undergo photo-induced E/Z isomerization. This possibility was investigated for one of the aminoaurones, which was observed to reversible photoisomerize. The two isomers have similar absorption spectra, but the emission properties are distinct. We conclude that appropriately substituted aurones are potentially useful as biological probes and photoswitches.