Structure-based design of potent non-peptide MDM2 inhibitors

A successful structure-based design of a class of non-peptide small-molecule MDM2 inhibitors targeting the p53-MDM2 protein-protein interaction is reported. The most potent compound 1d binds to MDM2 protein with a Ki value of 86 nM and is 18 times more potent than a natural p53 peptide (residues 16-27). Compound 1d is potent in inhibition of cell growth in LNCaP prostate cancer cells with wild-type p53 and shows only a weak activity in PC-3 prostate cancer cells with a deleted p53. Importantly, 1d has a minimal toxicity to normal prostate epithelial cells. Our studies provide a convincing example that structure-based strategy can be employed to design highly potent, non-peptide, cell-permeable, small-molecule inhibitors to target protein-protein interaction, which remains a very challenging area in chemical biology and drug design.     

Multi-state Systems with Graduate Failure and Equal Transition Intensities

We consider unrecoverable homogeneous multi-state systems with graduate failures, where each component can work at M + 1 linearly ordered levels of performance. The underlying process of failure for each component is a homogeneous Markov process such that the level of performance of one component can change only for one level lower than the observed one, and the failures are independent for different components. We derive the probability distribution of the random vector X, representing the state of the system at the moment of failure and use it for testing the hypothesis of equal transition intensities. Under the assumption that these intensities are equal, we derive the method of moments estimators for probabilities of failure in a given state vector and the intensity of failure. At the end we calculate the reliability function for such systems. Received: May 18, 2007., Revised: July 8, 2008., Accepted: September 29, 2008.     

The post-SCF quantum chemistry characteristics of the guanine-guanine stacking B-DNA

The stacking interactions of two guanine molecules were analyzed detail at the DF-MP2/aug-cc-pVDZ level of theory for conformations appearing B-DNA. The dependence of intermolecular interaction energies on the pairs of step parameters (shift, slide, rise, tilt, roll and twist) was determined. The values of these parameters were chosen to cover the whole range of variability appearing crystallographic data. The scanning procedure was performed by subsequent changes of two variables with fixed values of the remaining base-pair and base-step BDNA parameters. Additionally, the hybrid variational-perturbational scheme was applied for the decomposition of the interaction energy into physically meaningful contributions at the MP2 level of theory. The significant impact of the mutual orientations of guanine bases was observed not only on the total intermolecular energy but also on its components. The second-order dispersion interaction is the most significant contribution to stabilization energy and is about eight times larger compared to the first-order electrostatic term with relaxation effects, which is also of stabilizing character. The dispersion interactions may vary up to 9.6 kcal mol(-1) between different guanine-guanine conformations. The parameters defining the mutual orientation of stacked guanine molecules have a different impact on the stabilization of the investigated complex. The following base-step parameters have only a minor impact on the stabilization energies: shift-slide, shift-roll, shift-twist, slide-twist and roll-twist. On the other hand, parameters such as rise and tilt significantly influence intermolecular interactions, i.e. strong attraction occurs only for a limited range of their values.     

Experimental study on predicting skin flap necrosis by fluorescence in the FAD and NADH bands during surgery

The objective of the present study was to assess the feasibility of using endogenous fluorescence in intraoperative prediction of skin flap necrosis. The investigation was carried out in 10 Sprague-Dawley rats in which proximally based over-dimensioned random pattern skin flaps were dissected on the back and thereafter fixed into position. Immediately after surgery on each rat, synchronous fluorescence spectra (Deltalambda=90 nm) from five parts of the skin flap surface were measured. The presence of necrosis was evaluated on postoperative day 7. In flap parts designated as necrotic (n=18), a significantly lower (P<0.001) fluorescent signal from the nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) bands (360-380 and 440-460 nm, respectively) was detected in comparison with the vital parts (n=32) (for FAD:1767+/-39 versus 2579+/-65 auxiliary units [A.U]. and for NADH:11724+/-340 versus 16810+/-473 A.U.). The results suggested a close relationship between the fluorescent signals from the FAD and NADH bands on one side and flap necrosis or survival on the other side. Thus, the use of fluorescence spectroscopy may be considered as a valuable noninvasive tool for the prediction of skin flap necrosis.     

Synthesis of Au-based porous magnetic spheres by selective laser heating in liquid

We report the synthesis of Au-based submicrometer-sized spherical particles with uniform morphology/size and integrated porosity-magnetic property in a single particles. The particles are synthesized by a two-step process: (a) selective pulsed laser heating of colloidal nanoparticles to form particles with Au-rich core and Fe-rich shell and (b) acid treatment which leads to formation of porous architecture on particle surface. The simple, fast, inexpensive technique that is proposed demonstrates very promising perspectives for synthesis of composite particles.     

General bottom-up construction of spherical particles by pulsed laser irradiation of colloidal nanoparticles: a case study on CuO

The development of a general method to fabricate spherical semiconductor and metal particles advances their promising electrical, optical, magnetic, plasmonic, thermoelectric, and optoelectric applications. Herein, by using CuO as an example, we systematically demonstrate a general bottom-up laser processing technique for the synthesis of submicrometer semiconductor and metal colloidal spheres, in which the unique selective pulsed heating assures the formation of spherical particles. Importantly, we can easily control the size and phase of resultant colloidal spheres by simply tuning the input laser fluence. The heating-melting-fusion mechanism is proposed to be responsible for the size evolution of the spherical particles. We have systematically investigated the influence of experimental parameters, including laser fluence, laser wavelength, laser irradiation time, dispersing liquid, and starting material concentration on the formation of colloidal spheres. We believe that this facile laser irradiation approach represents a major step not only for the fabrication of colloidal spheres but also in the practical application of laser processing for micro- and nanomaterial synthesis.     

Preconcentration and Fractionation of Cd, Co, Cu, Ni, Pb and Zn in Natural Water Samples Prior to Analysis by Inductively Coupled Plasma Atomic Emission Spectrometry

The strong cation exchanger Dowex 50W-x4 was used for the enrichment of traces of Cd, Co, Cu, Fe, Ni, Pb and Zn in mineral and mine waters as an alternative to the commonly applied procedures based on the application of chelating resins. The resin used was found suitable for complete retention of these metals both from the solutions of very low pH as well as those close to neutral, thus eliminating the need to buffer the samples. An analytical scheme based on filtration and solid phase extraction with Dowex 50W-x4 was proposed for partitioning Cd, Co, Cu, Fe, Ni and Pb in the examined waters. The fraction of metals associated with the suspended particles was determined after filtration through a 0.45 µm pore size filter and decomposition of the deposited matter. For the evaluation of fractions of the labile metal species and the total dissolved metals, the untreated filtrates and the solutions resulting from their digestion, respectively, were passed through Dowex 50W-x4 cation exchange columns. The retrieval of the metals was completed using a 4.0 mol L⁻¹ solution of HCl. The described metal preconcentration and fractionation protocol offered the enrichment factor of 25 with detection limits equal to 22, 30, 92, 41, 70, 36 and 340 ng L⁻¹, respectively for Cd, Co, Cu, Fe, Ni and Pb. Reasonably good precision and accuracy were attained.     

(alpha/beta+alpha)-peptide antagonists of BH3 domain/Bcl-x(L) recognition: toward general strategies for foldamer-based inhibition of protein-protein interactions

The development of molecules that bind to specific protein surface sites and inhibit protein-protein interactions is a fundamental challenge in molecular recognition. New strategies for approaching this challenge could have important long-term ramifications in biology and medicine. We are exploring the concept that unnatural oligomers with well-defined conformations ("foldamers") can mimic protein secondary structural elements and thereby block specific protein-protein interactions. Here, we describe the identification and analysis of helical peptide-based foldamers that bind to a specific cleft on the anti-apoptotic protein Bcl-xL by mimicking an alpha-helical BH3 domain. Initial studies, employing a fluorescence polarization (FP) competition assay, revealed that among several alpha/beta- and beta-peptide foldamer backbones only alpha/beta-peptides intended to adopt 14/15-helical secondary structure display significant binding to Bcl-xL. The most tightly binding Bcl-xL ligands are chimeric oligomers in which an N-terminal alpha/beta-peptide segment is fused to a C-terminal alpha-peptide segment ((alpha/beta + alpha)-peptides)). Sequence-affinity relationships were probed via standard and nonstandard techniques (alanine scanning and hydrophile scanning, respectively), and the results allowed us to construct a computational model of the ligand/Bcl-xL complex. Analytical ultracentrifugation with a high-affinity (alpha/beta + alpha)-peptide established 1:1 ligand:Bcl-xL stoichiometry under FP assay conditions. Binding selectivity studies with the most potent (alpha/beta + alpha)-peptide, conducted via surface plasmon resonance measurements, revealed that this ligand binds tightly to Bcl-w as well as to Bcl-xL, while binding to Bcl-2 is somewhat weaker. No binding could be detected with Mcl-1. We show that our most potent (alpha/beta + alpha)-peptide can induce cytochrome C release from mitochondria, an early step in apoptosis, in cell lysates, and that this activity is dependent upon inhibition of protein-protein interactions involving Bcl-xL.