β-Phenylproline: the high β-turn forming propensity of proline combined with an aromatic side chain

The conformational propensities of the proline analogue bearing a phenyl substituent attached to the β carbon, in either a cis or a trans configuration relative to the carbonyl group, have been investigated. The behaviour of cis- and trans(βPh)Pro has been compared with that of proline in homochiral and heterochiral dipeptide sequences. NMR and IR studies as well as X-ray diffraction analysis provide evidence that the β-phenyl substituent does not disrupt the tendency of proline to occupy the i+1 position of a β-turn. The puckering of the pyrrolidine ring is significantly affected by the presence of the aromatic substituent, which tends to occupy positions that minimize steric repulsions. As a consequence, this substituent adopts specific well-defined orientations, which are more restricted for the cis derivative. Interactions between this aromatic group and that in the adjacent phenylalanine residue may be responsible for some of the conformational differences observed among the different peptides studied.     

Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity

Mitomycin C (MMC) is a potent antitumour agent that forms a covalent bond with the 2-amino group of selected guanines in the minor groove of double-stranded DNA following intracellular reduction of its quinone ring and opening of its aziridine moiety. At some 5'-CG-3' (CpG) steps the resulting monofunctional adduct can evolve towards a more deleterious bifunctional lesion, which is known as an interstrand crosslink (ICL). MMC reactivity is enhanced when the cytosine bases are methylated (5 MC) and decreased when they are replaced with 5-F-cytosine (5FC) whereas the stereochemical preference of alkylation changes upon decarbamoylation. We have studied three duplex oligonucleotides of general formula d(CGATAAXGCTAACG) in which X stands for C, 5MC or 5FC. Using a combination of molecular dynamics simulations in aqueous solution, quantum mechanics and continuum electrostatics, we have been able to (i) obtain a large series of snapshots that facilitate an understanding in atomic detail of the distinct stereochemistry of monoadduct and ICL formation by MMC and its decarbamoylated analogue, (ii) provide an explanation for the altered reactivity of MMC towards DNA molecules containing 5MC or 5FC, and (iii) show the distinct accommodation in the DNA minor groove of the different covalent modifications, particularly the most cytotoxic C1α and C1β ICLs.     

Analysis of a unilateral contact problem taking into account adhesion and friction

In this paper, we investigate a contact problem between a viscoelastic body and a rigid foundation, when both the effects of the (irreversible) adhesion and of the friction are taken into account. We describe the adhesion phenomenon in terms of a damage surface parameter according to Frémond?s theory, and we model unilateral contact by Signorini conditions, and friction by a nonlocal Coulomb law. All the constraints on the internal variables as well as the contact and the friction conditions are rendered by means of subdifferential operators, whence the highly nonlinear character of the resulting PDE system. Our main result states the existence of a global-in-time solution (to a suitable variational formulation) of the related Cauchy problem. It is proved by an approximation procedure combined with time discretization.     

Social influence, agent heterogeneity and the emergence of the urban informal sector

We develop an agent-based computational model in which the urban informal sector acts as a buffer where rural migrants can earn some income while queuing for higher paying modern-sector jobs. In the model, the informal sector emerges as a result of rural-urban migration decisions of heterogeneous agents subject to social influence in the form of neighboring effects of varying strengths. Besides using a multinomial logit choice model that allows for agent idiosyncrasy, explicit agent heterogeneity is introduced in the form of socio-demographic characteristics preferred by modern-sector employers. We find that different combinations of the strength of social influence and the socio-economic composition of the workforce lead to very different urbanization and urban informal sector shares. In particular, moderate levels of social influence and a large proportion of rural inhabitants with preferred socio-demographic characteristics are conducive to a higher urbanization rate and a larger informal sector.     

Integration of gold nanoparticles in optical resonators

The optical absorption of one-dimensional photonic crystal based resonators containing different types of gold nanoparticles is controllably modified by means of the interplay between planar optical cavity modes and localized surface plasmons. Spin-casting of metal oxide nanoparticle suspensions was used to build multilayered photonic structures that host (silica-coated) gold nanorods and spheres. Strong reinforcement and depletion of the absorptance was observed at designed wavelength ranges, thus proving that our method provides a reliable means to modify the optical absorption originated at plasmonic resonances of particles of arbitrary shape and within a wide range of sizes. These observations are discussed on the basis of calculations of the spatial and spectral dependence of the optical field intensity within the multilayers.     

Thermodynamic characterization of 3-[(3-cholamidopropyl)-dimethylammonium]-1-propanesulfonate (CHAPS) micellization using isothermal titration calorimetry: temperature, salt, and pH dependence

A systematic investigation of the micellization process of a biocompatible zwitterionic surfactant 3-[(3-cholamidopropyl)-dimethylammonium]-1-propanesulfonate (CHAPS) has been carried out by isothermal titration calorimetry (ITC) at temperatures between 278.15 K and 328.15 K in water, aqueous NaCl (0.1, 0.5, and 1 M), and buffer solutions (pH = 3.0, 6.8, and 7.8). The effect of different cations and anions on the micellization of CHAPS surfactant has been also examined in LiCl, CsCl, NaBr, and NaI solutions at 308.15 K. It turned out that the critical micelle concentration, cmc, is only slightly shifted toward lower values in salt solutions, whereas in buffer media it remains similar to its value in water. From the results obtained, it could be assumed that CHAPS behaves as a weakly charged cationic surfactant in salt solutions and as a nonionic surfactant in water and buffer medium. Conventional surfactants alike, CHAPS micellization is endothermic at low and exothermic at high temperatures, but the estimated enthalpy of micellization, ΔHM0, is considerably lower in comparison with that obtained for ionic surfactants in water and NaCl solutions. The standard Gibbs free energy, ΔGM0, and entropy, ΔSM0, of micellization were estimated by fitting the model equation based on the mass action model to the experimental data. The aggregation numbers of CHAPS surfactant around cmc, obtained by the fitting procedure also, are considerably low (nagg ≈ 5 ± 1). Furthermore, some predictions about the hydration of the micelle interior based on the correlation between heat capacity change, Δcp,M0, and changes in solvent-accessible surface upon micelle formation were made. CHAPS molecules are believed to stay in contact with water upon aggregation, which is somehow similar to the micellization process of short alkyl chain cationic surfactants.     

Plants as sources of new antimicrobials and resistance-modifying agents

Covering: up to November 2011Infections caused by multidrug-resistant bacteria are an increasing problem due to the emergence and propagation of microbial drug resistance and the lack of development of new antimicrobials. Traditional methods of antibiotic discovery have failed to keep pace with the evolution of resistance. Therefore, new strategies to control bacterial infections are highly desirable. Plant secondary metabolites (phytochemicals) have already demonstrated their potential as antibacterials when used alone and as synergists or potentiators of other antibacterial agents. The use of phytochemical products and plant extracts as resistance-modifying agents (RMAs) represents an increasingly active research topic. Phytochemicals frequently act through different mechanisms than conventional antibiotics and could, therefore be of use in the treatment of resistant bacteria. The therapeutic utility of these products, however, remains to be clinically proven. The aim of this article is to review the advances in in vitro and in vivo studies on the potential chemotherapeutic value of phytochemical products and plant extracts as RMAs to restore the efficacy of antibiotics against resistant pathogenic bacteria. The mode of action of RMAs on the potentiation of antibiotics is also described.     

Biosynthesis of mycobacterial methylglucose lipopolysaccharides

Mycobacterial pathogenesis is closely associated with a unique cell envelope rich in complex carbohydrates and unique lipids, among which are the mycolic acids. Mycobacteria also synthesize unique intracellular polymethylated polysaccharides (PMPSs), namely methylglucose lipopolysaccharides (MGLPs), which are acylated with short-chain fatty acids, and methylmannose polysaccharides (MMPs). Since PMPSs modulate the synthesis of long-chain fatty acids in vitro, the possibility of a similar role in vivo and the regulation of mycolic acids assembly have been anticipated. Unlike MGLPs, MMPs have been identified in M. smegmatis and other fast-growing mycobacteria but not in M. tuberculosis, implying an essential role for MGLPs in this pathogen and turning the biosynthetic enzymes into attractive drug targets. The genome of M. tuberculosis was decoded 14 years ago but only recently has the identity of the genes involved in MGLPs biosynthesis been investigated. Two gene clusters (Rv1208-Rv1213 and Rv3030-Rv3037c) containing a few genes considered to be essential for M. tuberculosis growth, have initially been proposed to coordinate MGLPs biosynthesis. Among these genes, only the product of Rv1208 for the first step in the MGLPs pathway has, so far, been crystallized and its three-dimensional structure been determined. However, recent results indicate that at least three additional clusters may be involved in this pathway. The functional assignment of authentic roles to some of these M. tuberculosis H37Rv genes sheds new light on the intricacy of MGLPs biogenesis and renewed interest on their biological role.     

Simultaneous analysis of mitotane and its main metabolites in human blood and urine samples by SPE-HPLC technique

Adrenocortical carcinoma (ACC) is a rare malignancy with an incompletely understood pathogenesis and a poor prognosis. The adrenalytic activity of mitotane has made it the most important single drug in the treatment of ACC. Unfortunately, the exact mechanism of mitotane action is still unknown. It is believed that mitotane belongs to the class of drugs that require metabolic transformation by cytochrome P450 for therapeutic action; therefore determination of plasma levels of not only mitotane but also its metabolites would help in carrying out the treatment. The objective of this work was to develop and validate an SPE‐HPLC method for simultaneous determination of mitotane and its metabolites in different biological fluids. The sample preparation consisted of a solid‐phase extraction on a Discovery DSC₁₈ cartridge, while analysis of extracts was performed on a Symmetry C₁₈ column. The usefulness of the proposed method was confirmed by analysis of plasma, red cell and urine samples from patient chronically treated with 1.5 g of mitotane. The patient involved in this study had a high plasma concentration of mitotane and none of the investigated metabolites were found. In order to investigate whether the polymorphism of CYP2C9 and CYP2C19 enzymes could be related to the metabolism of mitotane, RT‐PCR analysis was performed. Copyright © 2012 John Wiley & Sons, Ltd.