Ligand-Based Pharmacophore Screening Strategy: a Pragmatic Approach for Targeting HER Proteins

Targeting ErbB family of receptors is an important therapeutic option, because of its essential role in the broad spectrum of human cancers, including non-small cell lung cancer (NSCLC). Therefore, in the present work, considerable effort has been made to develop an inhibitor against HER family proteins, by combining the use of pharmacophore modelling, docking scoring functions, and ADME property analysis. Initially, a five-point pharmacophore model was developed using known HER family inhibitors. The generated model was then used as a query to screen a total of 468,880 compounds of three databases namely ZINC, ASINEX, and DrugBank. Subsequently, docking analysis was carried out to obtain hit molecules that could inhibit the HER receptors. Further, analysis of GLIDE scores and ADME properties resulted in one hit namely BAS01025917 with higher glide scores, increased CNS involvement, and good pharmaceutically relevant properties than reference ligand, afatinib. Furthermore, the inhibitory activity of the lead compounds was validated by performing molecular dynamic simulations. Of note, BAS01025917 was found to possess scaffolds with a broad spectrum of antitumor activity. We believe that this novel hit molecule can be further exploited for the development of a pan-HER inhibitor with low toxicity and greater potential.     

Gradient echo single scan inversion recovery: application to proton and fluorine relaxation studies

Single scan longitudinal relaxation measurement experiments enable rapid estimation of the spin‐lattice relaxation time (T₁) as the time series of spin relaxation is encoded spatially in the sample at different slices resulting in an order of magnitude saving in time. We consider here a single scan inversion recovery pulse sequence that incorporates a gradient echo sequence. The proposed pulse sequence provides spectra with significantly enhanced signal to noise ratio leading to an accurate estimation of T₁ values. The method is applicable for measuring a range of T₁ values, thus indicating the possibility of routine use of the method for several systems. A comparative study of different single scan methods currently available is presented, and the advantage of the proposed sequence is highlighted. The possibility of the use of the method for the study of cross‐correlation effects for the case of fluorine in a single shot is also demonstrated. Copyright © 2015 John Wiley & Sons, Ltd.     

Electrochemical impedance spectroscopic studies on niobium anodic dissolution in HF

Journal of Solid State Electrochemistry - The dissolution of niobium electrode in anodic regime in hydrofluoric acid was studied using electrochemical techniques. In the active region, complex...     

Structure and conformational stability of CH2CHCH2X (X=F, Cl and Br) molecules—post Hartree–Fock and density functional theory methods

The molecular structure and conformational stability of CH₂CHCH₂X (X=F, Cl and Br) molecules were studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 3-fluoropropene were optimized employing BLYP and B3LYP levels of theory of DFT method implementing 6-311+G(d,p) basis set. The MP2/6-31G^*, BLYP and B3LYP levels of theory of ab initio and DFT methods were used to optimize the 3-chloropropene and 3-bromopropene molecules. The structural and physical parameters of the molecules are discussed with the available experimental values. The rotational potential energy surface of the above molecules were obtained at MP2/6-31G^* and B3LYP/6-311+G(d,p) levels of theory. The Fourier decomposition of the rotational potentials were analyzed. The HF/6-31G^* and MP2/6-31G^* levels of theory have predicted the cis conformer as the minimum energy structure for 3-fluoropropene, which is in agreement with the experimental values, whereas the BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory reverses the order of conformation. The ΔE values calculated for 3-chloropropene at MP2/6-31G^*, BLYP/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory show that the gauche form is more stable than the cis form, which is in agreement with the experimental value. The same levels of theory have also predicted that the gauche form is stable than cis for 3-bromopropene molecule. The maximum hardness principle has been able to predict the stable conformer of 3-fluoropropene at HF/6-31G^* level of theory, but the same level of theory reverses the conformational stability of 3-chloropropene and 3-bromopropene molecules and MP2/6-31G^* level of theory predicted the stable conformer correctly.     

A DFT study of substrate effect on the magnetism of V(001) surface

The effect of isoelectric transition metals (TM) Nb and Ta on the magnetism of the V(001) surface is investigated from first principles using Density functional theory (DFT), with the generalized gradient approximation (GGA). Ferromagnetic (FM) moments of 2.5 μ_B and 2.2 μ_B are obtained for the relaxed surface V monolayer (ML) in the V/Nb(001) and the V/Ta(001) systems respectively, at T = 0 K. The values are almost twice of those obtained with Mo and W of group VIB and can be attributed to the comparatively smaller bandwidths of the substrates Nb and Ta. Small induced magnetic moments are present on the Nb and Ta interfacial layers, which are coupled anti-ferromagnetically with the V ML.     

��Gold standard�� coupled-cluster study of acetylene pentamers and hexamers via molecular tailoring approach

Due to high scaling order of MP2 and CCSD(T) methods, it is either difficult or at times even impossible to treat even moderately sized molecular systems with elaborate basis sets such as aug-cc-pVXZ (X?=?D, T, Q). In the present work, several structures of acetylene pentamers and hexamers are explored at MP2 and CCSD(T) levels of theory as?prototypical examples of clusters bound by CH···?? interactions. To enable this investigation, fragment-based method Molecular Tailoring Approach (MTA) is employed. It is shown that these acetylene assemblies can be treated with substantial reduction in computational resources and time, yet retaining a sub-millihartree accuracy in the energy. Further, using standard extrapolation methodologies, stabilization energies at the complete basis set limit of the acetylene clusters under consideration are determined at MP2 and CCSD(T) levels of theory. To test out the feasibility of treating a large cluster at MP2 level, a demonstrative calculation on a dodecamer of acetylene is reported.     

A 2‐Tyr‐1‐carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

N,N‐dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α₂β₂ or (α₂β₂)₂ type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side‐chain phenolates and one carboxylate from Glu. The Fe³⁺ ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.     

Evolution and characterization of dynamically recrystallized microstructure in a titanium-modified austenitic stainless steel using ultrasonic and EBSD techniques

A C-scan ultrasonic imaging system was used to investigate the microstructural evolution during dynamic recrystallization (DRX) of a 15Cr–15Ni–2.2Mo–Ti modified austenitic stainless steel (alloy D9). Four specimens were forged at 1273 K to different strains in the range 0.1–0.5. Specimens with true strains of 0.2 or lower did not show any variation in the amplitude of the first back-wall echo. However, a visible variation in the C-scan image was observed at and above the 0.3 strain level. This variation was attributed to the evolution of fine grains. The formation of fine grains was related to DRX, as indicated by electron backscattered diffraction. This study also revealed the characteristics of the DRX or ‘necklace grains’, as opposed to the so-called parent grains or rest of the microstructure.