Oxindole-Schiff base copper(II) complexes interactions with human serum albumin: Spectroscopic, oxidative damage, and computational studies

CD and EPR were used to characterize interactions of oxindole-Schiff base copper(II) complexes with human serum albumin (HSA). These imine ligands form very stable complexes with copper, and can efficiently compete for this metal ion towards the specific N-terminal binding site of the protein, consisting of the amino acid sequence Asp-Ala-His. Relative stability constants for the corresponding complexes were estimated from CD data, using the protein as competitive ligand, with values of log K(CuL) in the range 15.7-18.1, very close to that of [Cu(HSA)] itself, with log K(CuHSA) 16.2. Some of the complexes are also able to interfere in the a-helix structure of the protein, while others seem not to affect it. EPR spectra corroborate those results, indicating at least two different metal species in solution, depending on the imine ligand. Oxidative damage to the protein after incubation with these copper(II) complexes, particularly in the presence of hydrogen peroxide, was monitored by carbonyl groups formation, and was observed to be more severe when conformational features of the protein were modified. Complementary EPR spin-trapping data indicated significant formation of hydroxyl and carbon centered radicals, consistent with an oxidative mechanism. Theoretical calculations at density functional theory (DFT) level were employed to evaluate Cu(II)-L binding energies, L -> Cu(II) donation, and Cu(II) -> L back-donation, by considering the Schiff bases and the N-terminal site of HSA as ligands. These results complement previous studies on cytotoxicity, nuclease and pro-apoptotic properties of this kind of copper(II) complexes, providing additional information about their possibilities of transport and disposition in blood plasma. (C) 2009 Elsevier Inc. All rights reserved.

Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT i.s stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.

Computational study of the step size parameter of the subgradient optimization method

The subgradient optimization method is a simple and flexible linear programming iterative algorithm. It is much simpler than Newton's method and can be applied to a wider variety of problems. It also converges when the objective function is non-differentiable. Since an efficient algorithm will not only produce a good solution but also take less computing time, we always prefer a simpler algorithm with high quality. In this study a series of step size parameters in the subgradient equation is studied. The performance is compared for a general piecewise function and a specific p-median problem. We examine how the quality of solution changes by setting five forms of step size parameter.

Experimental and computational investigation of the roll forming process

One of the first questions to consider when designing a new roll forming line is the number of forming steps required to produce a profile. The number depends on material properties, the cross-section geometry and tolerance requirements, but the tool designer also wants to minimize the number of forming steps in order to reduce the investment costs for the customer. There are several computer aided engineering systems on the market that can assist the tool designing process. These include more or less simple formulas to predict deformation during forming as well as the number of forming steps. In recent years it has also become possible to use finite element analysis for the design of roll forming processes. The objective of the work presented in this thesis was to answer the following question: How should the roll forming process be designed for complex geometries and/or high strength steels? The work approach included both literature studies as well as experimental and modelling work. The experimental part gave direct insight into the process and was also used to develop and validate models of the process. Starting with simple geometries and standard steels the work progressed to more complex profiles of variable depth and width, made of high strength steels. The results obtained are published in seven papers appended to this thesis. In the first study (see paper 1) a finite element model for investigating the roll forming of a U-profile was built. It was used to investigate the effect on longitudinal peak membrane strain and deformation length when yield strength increases, see paper 2 and 3. The simulations showed that the peak strain decreases whereas the deformation length increases when the yield strength increases. The studies described in paper 4 and 5 measured roll load, roll torque, springback and strain history during the U-profile forming process. The measurement results were used to validate the finite element model in paper 1. The results presented in paper 6 shows that the formability of stainless steel (e.g. AISI 301), that in the cold rolled condition has a large martensite fraction, can be substantially increased by heating the bending zone. The heated area will then become austenitic and ductile before the roll forming. Thanks to the phenomenon of strain induced martensite formation, the steel will regain the martensite content and its strength during the subsequent plastic straining. Finally, a new tooling concept for profiles with variable cross-sections is presented in paper 7. The overall conclusions of the present work are that today, it is possible to successfully develop profiles of complex geometries (3D roll forming) in high strength steels and that finite element simulation can be a useful tool in the design of the roll forming process.

A computational comparison of different algorithms for very large p-median problems

In this paper, we propose a new method for solving large scale p-median problem instances based on real data. We compare different approaches in terms of runtime, memory footprint and quality of solutions obtained. In order to test the different methods on real data, we introduce a new benchmark for the p-median problem based on real Swedish data. Because of the size of the problem addressed, up to 1938 candidate nodes, a number of algorithms, both exact and heuristic, are considered. We also propose an improved hybrid version of a genetic algorithm called impGA. Experiments show that impGA behaves as well as other methods for the standard set of medium-size problems taken from Beasley’s benchmark, but produces comparatively good results in terms of quality, runtime and memory footprint on our specific benchmark based on real Swedish data.

Computational analysis and physico-chemical characterization of an inclusion compound between praziquantel and methyl-beta-cyclodextrin for use as an alternative in the treatment of schistosomiasis

Schistosomiasis is still an endemic disease in many regions, with 250 million people infected with Schistosoma and about 500,000 deaths per year. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment, however it is classified as Class II in the Biopharmaceutics Classification System, as its low solubility hinders its performance in biological systems. The use of cyclodextrins is a useful tool to increase the solubility and bioavailability of drugs. The aim of this work was to prepare an inclusion compound of PZQ and methyl-beta-cyclodextrin (MeCD), perform its physico-chemical characterization, and explore its in vitro cytotoxicity. SEM showed a change of the morphological characteristics of PZQ:MeCD crystals, and IR data supported this finding, with changes after interaction with MeCD including effects on the C-H of the aromatic ring, observed at 758 cm(-1). Differential scanning calorimetry measurements revealed that complexation occurred in a 1:1 molar ratio, as evidenced by the lack of a PZQ transition temperature after inclusion into the MeCD cavity. In solution, the PZQ UV spectrum profile in the presence of MeCD was comparable to the PZQ spectrum in a hydrophobic solvent. Phase solubility diagrams showed that there was a 5.5-fold increase in PZQ solubility, and were indicative of a type A(L) isotherm, that was used to determine an association constant (K(a)) of 140.8 M(-1). No cytotoxicity of the PZQ:MeCD inclusion compound was observed in tests using 3T3 cells. The results suggest that the association of PZQ with MeCD could be a good alternative for the treatment of schistosomiasis.