Rational Design of an Organometallic Glutathione Transferase Inhibitor

Double trouble : A hybrid organic–inorganic (organometallic) inhibitor was designed to target glutathione transferases. The metal center is used to direct protein binding, while the organic moiety acts as the active‐site inhibitor (see picture). The mechanism of inhibition was studied using a range of biophysical and biochemical methods.

     

Effect of linker and spacer on the design of a fibronectin-mimetic peptide evaluated via cell studies and AFM adhesion forces

The design of a fibronectin-mimetic peptide that specifically binds to the alpha 5beta 1 integrin has been widely studied because of this integrin's participation in many physiological and pathological processes. A promising design for such a peptide includes both the primary binding site RGD and the synergy site PHSRN connected by a linker and extended off of a surface by a spacer. Our original hypothesis was that the degree of hydrophobicity/hydrophilicity between the two sequences (RGD and PHSRN) in fibronectin is an important parameter in designing a fibronectin-mimetic peptide (Mardilovich, A.; Kokkoli, E. Biomacromolecules 2004, 5, 950-957). A peptide-amphiphile, PR_b, that was previously designed in our laboratory employed a hydrophobic tail connected to the N terminus of a peptide headgroup that was composed of a spacer, the synergy site sequence, a linker mimicking both the distance and hydrophobicity/hydrophilicity present in the native protein fibronectin (thus presenting an overall "neutral" linker), and finally the primary binding sequence. Even though our previous work (Mardilovich, A.; Craig, J. A.; McCammon, M. Q.; Garg, A.; Kokkoli, E. Langmuir 2006, 22, 3259-3264) demonstrated that PR_b is a promising sequence compared to fibronectin, this is the first study that tests our hypothesis by comparing PR_b to other peptides with hydrophobic or hydrophilic linkers. Furthermore, different peptide-amphiphiles were designed that could be used to study the effect of building blocks systematically, such as the peptide headgroup linker length and hydrophobicity/hydrophilicity as well as the headgroup spacer length on integrin adhesion. Circular dichroism spectroscopy was first employed, and the collected spectra demonstrated that only one peptide-amphiphile exhibited a secondary structure. Their surface topography was evaluated by taking atomic force microscopy (AFM) images of Langmuir-Blodgett peptide-amphiphile membranes supported on mica. Their adhesion was first evaluated with AFM force measurements between the different sequences and an AFM tip functionalized with purified integrins. The amphiphiles were further characterized via 1-12 h cell studies that examined human umbilical vein endothelial cell adhesion and extracellular matrix fibronectin production. The AFM studies were in good agreement with the cell studies. Overall, the adhesion studies validated our hypothesis and demonstrated for the first time that a "neutral" linker, which more closely mimics the cell adhesion domain of fibronectin, supports higher levels of adhesion compared to other peptide designs with a hydrophobic or hydrophilic linker or even fibronectin. Neutral linker lengths that were within the distance found between PHSRN and RGD in fibronectin performed equally well. However, the 10 amino acid neutral linker gave slightly better cell adhesion than did the control fibronectin at all times. Also, a short spacer was shown to give higher adhesion than other sequences with no spacer or a longer spacer, suggesting that a short spacer is necessary to extend the sequence further away from the interface. In conclusion, this work outlines a logical approach that can be applied for the rational design of any protein-mimetic peptide with two binding sites.     

Identification of pyrrolo-pyridine derivatives as novel class of antibacterials

Molecular Diversity - A series of 5-oxo-4H-pyrrolo[3,2-b]pyridine derivatives was identified as novel class of highly potent antibacterial agents during an extensive large-scale high-throughput...     

New indoline spiropyrans with highly stable merocyanine forms

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Exact parametric analytic solutions of the elastica ODEs for bars including effects of the transverse deformation

We succeed in constructing exact parametric analytic solutions for the non-linear ordinary differential equations governing the elastica response of a cantilever due to a generalized end loading by taking into account the effects of transverse deformation. Application to the case of the eccentric buckling of a cantilever by taking into account the above influences is developed.     

The exterior magnetic field for the multilayer ellipsoidal model of the brain

The magnetic induction field in the exterior of an ellipsoidallyinhomogeneous, four-conducting-layer model of the human headis obtained analytically up to its quadrupole approximation.The interior ellipsoidal core represents the homogeneous brainwhile each one of the shells represents the cerebrospinal fluid,the skull and the scalp, all characterized by different conductivities.The inhomogeneities of these four domains, together with theanisotropy imposed by the use of the ellipsoidal geometry, providethe most realistic physical and geometrical model of the brainfor which an analytic solution of the biomagnetic forward problemis possible. It is shown that in contrast to the spherical model,where shells of different conductivity are magnetically invisible,the magnetic induction field in ellipsoidal geometry is stronglydependent on the conductivity supports. The fact that sphericalshells of different conductivity are invisible has enhancedthe common belief that the biomagnetic forward solution doesnot depend on the conductivity profiles. As we demonstrate inthe present work, this is not true. Hence, the proposed multilayeredellipsoidal model provides a qualitative improvement of therealistic interpretation of magnetoencephalography (MEG) measurements.We show that the presence of the shells of different conductivitycan be incorporated in the form of the dipole vector for thehomogeneous model. Numerical investigations show that the effectsof shell inhomogeneities are almost as sound as the level ofMEG measurements themselves. The degenerate cases, where eitherthe differences of the conductivities within the shells disappear,or the ellipsoidal geometry is reduced to the spherical one,are also considered.     

Quantum Hamiltonians with Weak Random Abstract Perturbation. I. Initial Length Scale Estimate

We study random Hamiltonians on finite-size cubes and waveguide segments of increasing diameter. The number of random parameters determining the operator is proportional to the volume of the cube. In the asymptotic regime where the cube size, and consequently the number of parameters as well, tends to infinity, we derive deterministic and probabilistic variational bounds on the lowest eigenvalue, i.e., the spectral minimum, as well as exponential off-diagonal decay of the Green function at energies above, but close to the overall spectral bottom.     

TiF4-mediated biomimetic alkylation-cyclization cascade reaction of 2-trimethylsilylmethyl-1,5-dienes with aldehydes

TiF₄ has proven to be the Lewis acid of choice for promoting the biomimetic addition of 2-trimethylsilylmethyl-1,5-dienes to aliphatic aldehydes with concomitant cyclization. 1,3-cis-Disubstituted methylenecyclohexanes are thus produced in good yields and high diastereoselectivity. The reaction appears to proceed via a highly concerted mechanism involving a chair-like transition state.