Stable Peptides Instead of Stapled Peptides: Highly Potent αvβ6‐Selective Integrin Ligands

The αvβ6 integrin binds the RGD‐containing peptide of the foot and mouth disease virus with high selectivity. In this study, the long binding helix of this ligand was downsized to an enzymatically stable cyclic peptide endowed with sub‐nanomolar binding affinity toward the αvβ6 receptor and remarkable selectivity against other integrins. Computational studies were performed to disclose the molecular bases underlying the high binding affinity and receptor subtype selectivity of this peptide. Finally, the utility of the ligand for use in biomedical studies was also demonstrated here.     

Novel inhibitor discovery through virtual screening against multiple protein conformations generated via ligand-directed modeling: a maternal embryonic leucine zipper kinase example

Kinase targets have been demonstrated to undergo major conformational reorganization upon ligand binding. Such protein conformational plasticity remains a significant challenge in structure-based virtual screening methodology and may be approximated by screening against an ensemble of diverse protein conformations. Maternal embryonic leucine zipper kinase (MELK), a member of serine-threonine kinase family, has been recently found to be involved in the tumerogenic state of glioblastoma, breast, ovarian, and colon cancers. We therefore modeled several conformers of MELK utilizing the available chemogenomic and crystallographic data of homologous kinases. We carried out docking pose prediction and virtual screening enrichment studies with these conformers. The performances of the ensembles were evaluated by their ability to reproduce known inhibitor bioactive conformations and to efficiently recover known active compounds early in the virtual screen when seeded with decoy sets. A few of the individual MELK conformers performed satisfactorily in reproducing the native protein-ligand pharmacophoric interactions up to 50% of the cases. By selecting an ensemble of a few representative conformational states, most of the known inhibitor binding poses could be rationalized. For example, a four conformer ensemble is able to recover 95% of the studied actives, especially with imperfect scoring function(s). The virtual screening enrichment varied considerably among different MELK conformers. Enrichment appears to improve by selection of a proper protein conformation. For example, several holo and unliganded active conformations are better to accommodate diverse chemotypes than ATP-bound conformer. These results prove that using an ensemble of diverse conformations could give a better performance. Applying this approach, we were able to screen a commercially available library of half a million compounds against three conformers to discover three novel inhibitors of MELK, one from each template. Among the three compounds validated via experimental enzyme inhibition assays, one is relatively potent (15; K(d) = 0.37 μM), one moderately active (12; K(d) = 3.2 μM), and one weak but very selective (9; K(d) = 18 μM). These novel hits may be utilized to assist in the development of small molecule therapeutic agents useful in diseases caused by deregulated MELK, and perhaps more importantly, the approach demonstrates the advantages of choosing an appropriate ensemble of a few conformers in pursuing compound potency, selectivity, and novel chemotypes over using single target conformation for structure-based drug design in general.     

Synthesis and Structural Characterization of New Divanada‐ and Diniobaboranes Containing Chalcogen Atoms

The reaction of [Cp_nMCl_4?x] (M=V: n=2, x=2; M=Nb: n=1, x=0; Cp=η⁵‐C₅H₅) with LiBH₄ ? THF followed by thermolysis in the presence of dichalcogenide ligands E₂R₂ (E=S, Te; R=2,6‐(tBu)₂‐C₆H₂OH, Ph) and 2‐mercaptobenzothiazole (C₇H₅NS₂) yielded dimetallaheteroboranes [{CpV(μ‐TePh)}₂(μ₃‐Te)BH ? thf] ( 1 ), [(CpV)₂(BH₃S)₂] ( 2 ), [(CpNb)₂B₄H₁₀S] ( 3 ), [(CpNb)₂B₄H₁₁S(tBu)₂C₆H₂OH] ( 4 ), and [(CpNb)₂B₄H₁₁TePh] ( 5 ). In cluster 1 , the V₂BTe atoms define a tetrahedral framework in which the boron atom is linked to a THF molecule. Compound 2 can be described as a dimetallathiaborane that is built from two edge‐fused V₂BS tetrahedron clusters. Cluster 3 can be considered as an edge‐fused cluster in which a trigonal‐bipyramidal unit (Nb₂B₂S) has been fused with a tetrahedral core (Nb₂B₂) by means of a common Nb₂ edge. In addition, thermolysis of an in‐situ‐generated intermediate that was produced from the reaction of [Cp₂VCl₂] and LiBH₄ ? THF with excess BH₃ ? THF yielded oxavanadaborane [(CpV)₂B₃H₈(μ₃‐OEt)] ( 6 ) and divanadaborane cluster [(CpV)₂B₅H₁₁] ( 7 ). Cluster 7 exhibits a nido geometry with C_2v symmetry and it is isostructural with [(Cp*M)₂B₅H_9+n] (M=Cr, Mo, and W, n=0; M=Ta, n=2; Cp*=η⁵‐C₅Me₅). All of these new compounds have been characterized by ¹H NMR, ¹¹B NMR, and ¹³C NMR spectroscopy and elemental analysis and the structural types were established unequivocally by crystallographic analysis of compounds  1 – 4 , 6 , and 7 .     

Enhanced light harvesting efficiencies of bis(ferrocenylmethyl)-based sulfur rich sensitizers used in dye sensitized TiO2 solar cells

In this work, the photosensitizing properties of ferrocene (Fc)-based compounds FcCH(2)CS(3)CH(2)Fc (1) and FcCH(2)SSCH(2)Fc (2) were investigated and significant enhancement in the light harvesting efficiency was observed compared to those achieved with previously reported compounds from our lab. The compounds were fully characterized by spectroscopy and X-ray crystallography, and their electrochemical properties studied. DSSCs based on these dyes display efficiencies comparable to those of a standard cell based on N719 under similar experimental conditions. These studies demonstrate that ferrocenyl-based sulfur rich compounds with proper orientation of the Fc groups assisted via suitable linkers, together with desired redox properties and visible region electronic absorption features could constitute a new class of photosensitizers targeting light driven reactions.     

Structural, dielectric relaxation and piezoelectric characterization of Sr substituted modified PMS-PZT ceramic

Pyrochlore phase free [Pb_0.94Sr_0.06] [(Mn_1/3Sb_2/3)_0.05(Zr_0.53Ti_0.47)_0.95] O₃ ceramics has been synthesized with pure Perovskite phase by semi-wet route using the columbite precursor method. The field dependences of the dielectric response and the conductivity have been measured in a frequency range from 50 Hz to 1 MHz and in a temperature range from 303 K to 773 K. An analysis of the real and imaginary parts of the dielectric permittivity with frequency has been performed, assuming a distribution of relaxation times. The scaling behavior of the dielectric loss spectra suggests that the distribution of the relaxation times is temperature independent. The SEM photographs of the sintered specimens present the homogenous structures and well-grown grains with a sharp grain boundary. The material exhibits tetragonal structure. When measured at frequency (100 Hz), the polarization shows a strong field dependence. Different piezoelectric figures of merit (k_p, d₃₃ and Q_m) of the material have also been measured obtaining their values as 0.53, 271 pC/N and 1115, respectively, which are even higher than those of pure PZT with morphotropic phase boundary (MPB) composition. Thus the present ceramics have the optimal overall performance and are promising candidates for the various high power piezoelectric applications.     

Estimation of shear wave velocity in gelatin phantoms utilizing PhS-SSOCT

We report a method for measuring shear wave velocity in soft materials using phase stabilized swept source optical coherence tomography (PhS-SSOCT). Wave velocity was measured in phantoms with various concentrations of gelatin and therefore different stiffness. Mechanical waves of small amplitudes (??10 ??m) were induced by applying local mechanical excitation at the surface of the phantom. Using the phase-resolved method for displacement measurement described here, the wave velocity was measured at various spatially distributed points on the surface of the tissue-mimicking gelatin-based phantom. The measurements confirmed an anticipated increase in the shear wave velocity with an increase in the gelatin concentrations. Therefore, by combining the velocity measurements with previously reported measurements of the wave amplitude, viscoelastic mechanical properties of the tissue such as cornea and lens could potentially be measured.     

Bioactivity and mechanical properties of nickel‐incorporated hydrogenated carbon nanocomposite thin films

In this paper, the influence of nickel incorporation on the mechanical properties and the in vitro bioactivity of hydrogenated carbon thin films were investigated in detail. Amorphous hydrogenated carbon (a‐C:H) and nickel‐incorporated hydrogenated carbon (Ni/a‐C:H) thin films were deposited onto the Si substrates by using reactive biased target ion beam deposition technique. The films' chemical composition, surface roughness, microstructure and mechanical properties were investigated by using XPS, AFM, TEM, nanoindentation and nanoscratch test, respectively. XPS results have shown that the film surface is mainly composed of nickel, nickel oxide and nickel hydroxide, whereas at the core is nickel carbide (Ni₃C) only. The presence of Ni₃C has increased the sp² carbon content and as a result, the mechanical hardness of the film was decreased. However, Ni/a‐C:H films shows very low friction coefficient with higher scratch‐resistance behavior than that of pure a‐C:H film. In addition, in vitro bioactivity study has confirmed that it is possible to grow dense bone‐like apatite layer on Ni/a‐C:H films. Thus, the results have indicated the suitability of the films for bone‐related implant coating applications. Copyright © 2011 John Wiley & Sons, Ltd.     

Nonlinear optical study of palladium Schiff base complex using femtosecond differential optical Kerr gate and Z-scan techniques

A femtosecond differential optical Kerr gate (DOKG) and Z-scan techniques, have been applied to investigate the third-order optical nonlinearity of composite film of the coordination complex [PdLPPh₃] (L=N-(2-pyridyl)-N′-(salicylidene)hydrazine, PPh₃=triphenylphosphine). Film exhibits superior nonlinear optical properties in the near-infrared spectral region. The nonlinear response time and third-order nonlinear optical susceptibility of complex were found to be≤90 fs and 3.9×10^?10 esu, respectively. The Z-scan result shows that saturable absorption property of the film and its nonlinear absorption coefficient of the sample was found to be ?23 cm/GW.     

Implementation of the multireference Brillouin-Wigner and Mukherjee's coupled cluster methods with non-iterative triple excitations utilizing reference-level parallelism

In this paper we discuss the performance of the non-iterative state-specific multireference coupled cluster (SS-MRCC) methods accounting for the effect of triply excited cluster amplitudes. The corrections to the Brillouin-Wigner and Mukherjee's MRCC models based on the manifold of singly and doubly excited cluster amplitudes (BW-MRCCSD and Mk-MRCCSD, respectively) are tested and compared with exact full configuration interaction results for small systems (H(2)O, N(2), and Be(3)). For the larger systems (naphthyne isomers) the BW-MRCC and Mk-MRCC methods with iterative singles, doubles, and non-iterative triples (BW-MRCCSD(T) and Mk-MRCCSD(T)) are compared against the results obtained with single reference coupled cluster methods. We also report on the parallel performance of the non-iterative implementations based on the use of processor groups.     

Revisiting the properties of delafossite CuCrO2: A single crystal study

Platelet-like single-crystals of delafossite CuCrO₂ have been successfully grown and characterised by X-ray diffraction and pole figures, scanning electron and atomic force microscopy. Transport measurements reveal that the resistivity is highly anisotropic, with a ratio of about 35 at 300 K between the in- and out-of-plane directions, reflecting the layered crystal structure. The magnetization and specific heat data show that CuCrO₂ undergoes a unique antiferromagnetic transition at T_N=24.0 K, in contrast to a recent report on CuCrO₂ single-crystals [16] showing the existence of two magnetic transitions, T_N1=24.2 K and T_N2=23.6 K, depending on the orientation of the applied magnetic field along and perpendicular to c, respectively.