Publications

Abstract Today, emerging and increasing resistance to antibiotics has become a threat to public health worldwide. Antimicrobial peptides have unique action mechanisms making them an attractive therapeutic prospect to be applied against resistant bacteria. However, the major drawback is related with their high hemolytic activity which cancels out the safety requirements for a human antibiotic. Therefore, additional efforts are needed to develop new antimicrobial peptides that possess a greater potency for bacterial cells and less or no toxicity over erythrocytes. In this paper, we introduce a practical approach to simultaneously deal with these two conflicting properties. The convergence of machine learning techniques and desirability theory allowed us to derive a simple, predictive, and interpretable multicriteria classification rule for simultaneously handling the antibacterial and hemolytic properties of a set of cyclic beta-hairpin cationic peptidomimetics (C beta-HCPs). The multicriteria classification rule exhibited a prediction accuracy of about 80% on training and external validation sets. Results from an additional concordance test have shown an excellent agreement between the multicriteria classification rule predictions and the predictions from independent classifiers for complementary antibacterial and hemolytic activities, respectively, evidencing the reliability of the multicriteria classification rule. The rule was also consistent with the general mode of action of cationic peptides pointing out its biophysical relevance. We also propose a multicriteria virtual screening strategy based on the joint use of the multicriteria classification rule, desirability, similarity, and chemometrics concepts. The ability of such a virtual screening strategy to prioritize selective (nonhemolytic) antibacterial C beta-HCPs was assessed and challenged for their predictivity regarding the training, validation, and overall data. In doing so, we were able to rank a selective antibacterial C beta-HCP earlier than a biologically inactive or nonselective antibacterial C beta-HCP with a probability of ca. 0.9. Our results thus indicate that promising chemoinformatics tools were obtained by considering both the multicriteria classification rule and the virtual screening strategy, which could, for instance, be used to aid the discovery and development of potent and nontoxic antimicrobial peptides.

Abstract We present molecular dynamics simulations of solvated cocaine and its metabolites in water, using both the Optimized Potentials for Liquid Simulations (OPLS) force field and the same force field but with Quantum Theory of Atoms In Molecules (QTAIM) atomic charges. We focus on the microscopic aspects of solvation, e.g. hydrogen bonds, and investigate influence of partial charges applied. Hydrophobicity or hydrophicility of these molecules were analyzed in terms of solute-solvent radial distribution functions and, for their most hydrophilic atoms, by spatial density functions. These hydration studies allowed us to classify these molecules according to their total coordination numbers, from the most hydrated metabolite to least hydrated, and this trend matches the degree of each metabolite is excreted in urine of patients with a high consumption of cocaine. Finally, we observed that QTAIM charges provide a more physically reasonable description of electrostatic environment of these solvated molecules than those of OPLS charges.

Abstract Amino acid-derived surfactants have increasingly become a viable biofriendly alternative to petrochemically based amphiphiles as speciality surfactants. Herein, the Krafft temperatures and critical micelle concentrations (cmc) of three series of novel amino acid-derived surfactants have been determined by differential scanning microcalorimetry and surface tension measurements, respectively. The compounds comprise cationic molecules based on serine and tyrosine headgroups and anionic ones based on 4-hydroxyproline headgroups, with varying chain lengths. A linear dependence of the logarithm of cmc on chain length is found for all series, and in comparison to conventional ionic surfactants of equal chain length, the new amphiphiles present lower cmc and lower surface tension at the cmc. These observations highlight their enhanced interfacial performance. For the 18-carbon serine-derived surfactant the effects of counterion change and of the presence of a cis-double bond in the alkyl chain have also been investigated. The overall results are discussed in terms of headgroup and alkyl chain effects on micellization, in the light of available data for conventional surfactants and other types of amino acid-based amphiphiles reported in the literature.

Abstract Carbon dots (CDs) comprise a recently discovered class of strongly fluorescent, emission-color-tuning and non-blinking nanoparticles with great analytical and bioanalytical potential. Raw CDs can be obtained by laser ablation or electrochemical exfoliation of graphite, from soot, or thermal carbonization, acid dehydration or ultrasonic treatment of molecular precursors. Passivation of raw CDs makes them fluorescent and their functionalization confers reactivity towards selected targets. CDs can be excited by single-photon (ultraviolet or near-ultraviolet) and multi-photon (red or near-infrared) excitation, and their luminescence properties are due to surface defects. CDs are being proposed as bioimaging probes because they comprise non-toxic elements and are biocompatible. Passivated and functionalized CDs can be made to sense pH, metal ions and molecular substances.

Abstract Thin films composed of oleylamine (OLA) and double-stranded deoxyribonucleic acid (dsDNA from Salmon testes) have been successfully constructed on polycrystalline Au surfaces using the electrostatic adsorption and self-assembly (SA) technique. The formation of the Au/OLA/dsDNA films was followed step-by-step by Quartz Crystal Microbalance with energy dissipation (QCM-D), Atomic Force Microscopy (AFM), and electrochemical techniques such as Cyclic Voltammetry (CV) and Electrochemical Impedance Spectroscopy (EIS). The use of these techniques allowed the characterization and the follow up of the successful construction of the OLA/dsDNA composite film. The main advantages of the proposed methodology are the simplicity of the modification procedure, the stability of the dsDNA self-assembled film, and the potential employment of the dsDNA modified gold electrodes to study the interactions of DNA with target molecules. Copyright

Abstract The electrodeposition of metals using ionic liquids has received considerable attention during the last ten years. Recent developments have taken these novel electrolytes from laboratory to commercial scale. One of the factors limiting the development into practical plating systems is the understanding of how brighteners function. In this study we describe the addition of three polar additives and their effect upon the nucleation mechanism of zinc and the resultant morphology. It is shown that the structure of the zinc deposits is controlled by double layer properties and it is proposed that the brightening effect of ethylene diamine and ammonia are caused by their ability to inhibit the adsorption of chloride at the electrode surface. The deposition of most metals using ionic liquids results in apparently amorphous deposits, which tend to be actually nano-crystalline. The additives used in this study produce macro-crystalline deposits, which resemble those obtained from aqueous solutions.

Abstract The electrodeposition of zinc has been studied in two deep eutectic solvents. Unlike the metals studied to date in these liquids, zinc electrodeposition is not mass transport limited and the morphology of the deposit differs in the two liquids. This study shows that changing the concentration of solute affects the physical properties of the liquid to different extents although this is found to not effect the morphology of the metal deposited. EXAFS was used to show that the speciation of zinc was the same in both liquids. Double layer capacitance studies showed differences between the two liquids and these are proposed to be due to the adsorption of a species on the electrode which is thought to be chloride. The differences in zinc morphology is attributed to blocking of certain crystal faces leading to deposition of small platelet shaped crystals in the glycol based liquid.

Abstract Firefly luciferase is the most studied bioluminescence system, and its catalyzed reactions have been relatively well characterized. However, the color tuning mechanism that leads to firefly multicolor bioluminescence is still unknown, nor is consensual which is the yellow-green and red emitters. Computational studies have been essential in the study of oxyluciferin (OxyLH(2)) chemi- and bioluminescence and are responsible for most of our knowledge of this natural phenomenon. The objective of this manuscript is the analysis of the benefits and the conclusions derived from the theoretical studies of the light emitter, OxyLH(2), and its applications on bioluminescence research.

Abstract In the present work, lipophilic caffeic and ferulic acid derivatives were synthesized, and their cytotoxicity on cultured breast cancer cells was compared. A total of six compounds were initially evaluated: caffeic acid (CA), hexyl caffeate (HC), caffeoylhexylamide (HCA), ferulic acid (FA), hexyl ferulate (HF), and feruloylhexylamide (HFA). Cell proliferation, cell cycle progression, and apoptotic signaling were investigated in three human breast cancer cell lines, including estrogen-sensitive (MCF-7) and insensitive (MDA-MB-231 and HS578T). Furthermore, direct mitochondrial effects of parent and modified compounds were investigated by using isolated liver mitochondria. The results indicated that although the parent compounds presented no cytotoxicity, the new compounds inhibited cell proliferation and induced cell cycle alterations and cell death, with a predominant effect on MCF-7 cells. Interestingly, cell cyle data indicates that effects on nontumor BJ fibroblasts were predominantly cytostatic and not cytotoxic. The parent compounds and derivatives also promoted direct alterations on hepatic mitochondrial bioenergetics, although the most unexpected and never before reported one was that FA induces the mitochondrial permeability transition. The results show that the new caffeic and ferulic acid lipophilic derivatives show increased cytotoxicity toward human breast cancer cell lines, although the magnitude and type of effects appear to be dependent on the cell type. Mitochondrial data had no direct correspondence with effects on intact cells suggesting that this organelle may not be a critical component of the cellular effects observed. The data provide a rational approach to the design of effective cytotoxic lipophilic hydroxycinnamic derivatives that in the future could be profitably applied for chemopreventive and/or chemotherapeutic purposes.