Structure-activity relationships for a class of selective inhibitors of the major cysteine protease from Trypanosoma cruzi

Chagas` disease is a parasitic infection widely distributed throughout Latin America, with devastating consequences in terms of human morbidity and mortality. Cruzain, the major cysteine protease from Trypanosoma cruzi, is an attractive target for antitrypanosomal chemotherapy. In the present work, classical two-dimensional quantitative structure-activity relationships (2D QSAR) and hologram QSAR (HQSAR) studies were performed on a training set of 45 thiosemicarbazone and semicarbazone derivatives as inhibitors of T. cruzi cruzain. Significant statistical models (HQSAR, q2=0.75 and r2=0.96; classical QSAR, q2=0.72 and r2=0.83) were obtained, indicating their consistency for untested compounds. The models were then used to evaluate an external test set containing 10 compounds which were not included in the training set, and the predicted values were in good agreement with the experimental results (HQSAR, [image omitted]=0.95; classical QSAR, [image omitted]=0.91), indicating the existence of complementary between the two ligand-based drug design techniques.

MPO Inhibitors Selected by Virtual Screening

The hemeprotein myeloperoxidase (MPO) participates in innate immune defense through its ability to generate potent microbicidal oxidants. However, these oxidants are also key mediators of the tissue damage associated with many inflammatory diseases. Thus, there is considerable interest in developing therapeutically useful MPO inhibitors. Here, we used structure-based drug design (SBDD) and ligand-based drug design (LBDD) to select for potentially new and selective MPO inhibitors. A pharmacophore model was developed based on the crystal structure of human MPO in complex with salicylhydroxamic acid (SHA), a known inhibitor of the enzyme. The pharmacophore model was used to screen the ZINC database for potential ligands, which were further filtered on the basis of their physical-chemical properties and docking score. The filtered compounds were visually inspected, and nine were purchased for experimental studies. Surprisingly, almost all of the selected compounds belonged to the aromatic hydrazide class, which had been previously described as MPO inhibitors. The compounds selected by virtual screening were shown to inhibit the chlorinating activity of MPO; the top four compounds displayed IC(50) values ranging from 1.0 to 2.8 mM. MPO inactivation by the most effective compound was shown to be irreversible. Overall, our results show that SBDD and LBDD may be useful for the rational development of new MPO inhibitors.

Allergic asthma exhaled breath metabolome: a challenge for comprehensive two-dimensional gas chromatography

Allergic asthma represents an important public health issue, most common in the paediatric population, characterized by airway inflammation that may lead to changes in volatiles secreted via the lungs. Thus, exhaled breath has potential to be a matrix with relevant metabolomic information to characterize this disease. Progress in biochemistry, health sciences and related areas depends on instrumental advances, and a high throughput and sensitive equipment such as comprehensive two-dimensional gas chromatography–time of flight mass spectrometry (GC × GC–ToFMS) was considered. GC × GC–ToFMS application in the analysis of the exhaled breath of 32 children with allergic asthma, from which 10 had also allergic rhinitis, and 27 control children allowed the identification of several hundreds of compounds belonging to different chemical families. Multivariate analysis, using Partial Least Squares-Discriminant Analysis in tandem with Monte Carlo Cross Validation was performed to assess the predictive power and to help the interpretation of recovered compounds possibly linked to oxidative stress, inflammation processes or other cellular processes that may characterize asthma. The results suggest that the model is robust, considering the high classification rate, sensitivity, and specificity. A pattern of six compounds belonging to the alkanes characterized the asthmatic population: nonane, 2,2,4,6,6-pentamethylheptane, decane, 3,6-dimethyldecane, dodecane, and tetradecane. To explore future clinical applications, and considering the future role of molecular-based methodologies, a compound set was established to rapid access of information from exhaled breath, reducing the time of data processing, and thus, becoming more expedite method for the clinical purposes.

Tillage and phosphorus management effects on enzyme-labile bioactive phosphorus availability in Cerrado Oxisols

Phosphorus (P) is an essential element in crop nutrition, which can be growth limiting or an environmental contaminant, if present in excess. Tillage practices have a direct effect on the behavior and availability of soil P. Sorption and availability of various P forms were evaluated in an incubation-fractionation study of three soils, a Typic Paleudults (CR soil) and two Cerrado Oxisols (Latossolo Vermelho-Amarelo [LVA] and Latossolo Vermelho [LV]) with distinct biogeochemical characteristics and tillage management history. Phosphate and myo-inositol hexakisphosphate (mIPH) were strongly sorbed by the soils. Maximum adsorption capacities (S(max)) were 2.2-6.9, 3.3-7.8, and 1.6-19.8 mmol kg(-1) for phosphate in the 0-40 cm depths of the CR, LV, and LVA soils, respectively. For mIPH, S. were 1.2-3.7, 3.7-5.5, and 4.6-5.2 mmol kg(-1). Saturation indices reflected the long-term effect of repeated manure applications on the Paleudults and the near saturation of its P holding capacity, in contrast to the recently cultivated Cerrado soils. Tillage method appeared to have altered P retention characteristics of the near-surface zone very slightly, while increases in ligand-exchangeable (EEP;) and enzyme-labile organic P (EDTA-PHP) forms were observed in no-till Oxisols. In the Paleudults, added manure P increased bioactive P fractions and P saturation of no-till near-surface soil zone. Estimates of all bioactive P fractions using the ligand-based enzymatic assay showed it to be an effective method for assessing P availability in soil and developing sustainable P management strategies, particularly in Cerrado Oxisols that were low in organic matter while having an extensive P-fixing capacity. Published by Elsevier B.V.

Discovery of novel Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase inhibitors

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A multi-agent architecture for intelligent data analysis

The present study introduces a multi-agent architecture designed for doing automation process of data integration and intelligent data analysis. Different from other approaches the multi-agent architecture was designed using a multi-agent based methodology. Tropos, an agent based methodology was used for design. Based on the proposed architecture, we describe a Web based application where the agents are responsible to analyse petroleum well drilling data to identify possible abnormalities occurrence. The intelligent data analysis methods used was the Neural Network.

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Perioperative fluid therapy: a statement from the international fluid optimization group

Perioperative fluid therapy remains a highly debated topic. Its purpose is to maintain or restore effective circulating blood volume during the immediate perioperative period. Maintaining effective circulating blood volume and pressure are key components of assuring adequate organ perfusion while avoiding the risks associated with either organ hypo- or hyperperfusion. Relative to perioperative fluid therapy, three inescapable conclusions exist: overhydration is bad, underhydration is bad, and what we assume about the fluid status of our patients may be incorrect. There is wide variability of practice, both between individuals and institutions. The aims of this paper are to clearly define the risks and benefits of fluid choices within the perioperative space, to describe current evidence-based methodologies for their administration, and ultimately to reduce the variability with which perioperative fluids are administered. Based on the abovementioned acknowledgements, a group of 72 researchers, well known within the field of fluid resuscitation, were invited, via email, to attend a meeting that was held in Chicago in 2011 to discuss perioperative fluid therapy. From the 72 invitees, 14 researchers representing 7 countries attended, and thus, the international Fluid Optimization Group (FOG) came into existence. These researches, working collaboratively, have reviewed the data from 162 different fluid resuscitation papers including both operative and intensive care unit populations. This manuscript is the result of 3 years of evidence-based, discussions, analysis, and synthesis of the currently known risks and benefits of individual fluids and the best methods for administering them. The results of this review paper provide an overview of the components of an effective perioperative fluid administration plan and address both the physiologic principles and outcomes of fluid administration. We recommend that both perioperative fluid choice and therapy be individualized. Patients should receive fluid therapy guided by predefined physiologic targets. Specifically, fluids should be administered when patients require augmentation of their perfusion and are also volume responsive. This paper provides a general approach to fluid therapy and practical recommendations.

Characterization of L-type Calcium Channel Binding-Site of a new class of Calcium modulators by a Multidisciplinary approach

Many potential diltiazem related L-VDCC blockers were developed using a multidisciplinary approach. This current study was to investigate and compare diltiazem with to the newly developed compounds by mouse Langendorff-perfused heart, Ca2+-transient and on recombinant L-VDCC. Twenty particular compounds were selected by the ligand-based virtual screening procedure (LBVS). From these compounds, five of them (5b, M2, M7, M8 and P1) showed a potent and selective inotropic activity on guinea-pig left atria driven 1 Hz. Further assays displayed an interesting negative inotropic effect of M2, M8, P1 and M7 on guinea pig isolated left papillary muscle driven at 1 Hz, a relevant vasorelaxant activity of 5b, M2, M7, M8 and P1 on K+-depolarized guinea-pig ileum longitudinal smooth muscle and a significant inhibition of contraction of 5b, M2, M8 and P1 on carbachol stimulated ileum longitudinal smooth muscle. Wild-type human heart and rabbit lung α1 subunits were expressed (combined with the regulatory α2δ and β3 subunits) in Xenopus Leavis oocytes using a two-electrode voltage clamp technique. Diltiazem is a benzothiazepine Ca2+ channel blocker used clinically for its antihypertensive and antiarrhythmic effects. Previous radioligand binding assays revealed a complex interaction with the benzothiazepine binding site for M2, M7 and M8. (Carosati E. et al. J. Med Chem. 2006, 49; 5206). In agreement with this findings, the relative order of increased rates of contraction and relaxation at lower concentrations s(≤10-6M) in unpaced hearts was M7>M2>M8>P1. Similar increases in Ca2+ transient were observed in cardiomyocytes. Diltiazem showed negative inotropic effects whereas 5b had no significant effect. Diltiazem blocks Ca2+current in a use-dependent manner and facilitates the channel by accelerating the inactivation and decelerating the recovery from inactivation. In contrast to diltiazem, the new analogs had no pronounced use-dependence. Application of 100 μM M8, M2 showed ~ 10% tonic block; in addition, M8, M2 and P1 shifted the steady state inactivation in hyperpolarized direction and the current inactivation time was significantly decreased compared with control (219.6 ± 11.5 ms, 226 ± 14.5 vs. 269 ± 12.9 vs. 199.28 ± 8.19 ms). Contrary to diltiazem, the recovery from the block by M8 and M2 was comparable to control. Only P1 showed a significantly decrease of the time for the recovery from inactivation. All of the compounds displayed the same sensitivity on the Ca2+ channel rabbit lung α1 except P1. Taken together, these findings suggest that M8, M2 and P1 might directly decrease the binding affinity or allow rapid dissociation from the benzothiazepine binding site.

The discovery of new 11beta-hydroxysteroid dehydrogenase type 1 inhibitors by common feature pharmacophore modeling and virtual screening

11beta-Hydroxysteroid dehydrogenase (11beta-HSD) enzymes catalyze the conversion of biologically inactive 11-ketosteroids into their active 11beta-hydroxy derivatives and vice versa. Inhibition of 11beta-HSD1 has considerable therapeutic potential for glucocorticoid-associated diseases including obesity, diabetes, wound healing, and muscle atrophy. Because inhibition of related enzymes such as 11beta-HSD2 and 17beta-HSDs causes sodium retention and hypertension or interferes with sex steroid hormone metabolism, respectively, highly selective 11beta-HSD1 inhibitors are required for successful therapy. Here, we employed the software package Catalyst to develop ligand-based multifeature pharmacophore models for 11beta-HSD1 inhibitors. Virtual screening experiments and subsequent in vitro evaluation of promising hits revealed several selective inhibitors. Efficient inhibition of recombinant human 11beta-HSD1 in intact transfected cells as well as endogenous enzyme in mouse 3T3-L1 adipocytes and C2C12 myotubes was demonstrated for compound 27, which was able to block subsequent cortisol-dependent activation of glucocorticoid receptors with only minor direct effects on the receptor itself. Our results suggest that inhibitor-based pharmacophore models for 11beta-HSD1 in combination with suitable cell-based activity assays, including such for related enzymes, can be used for the identification of selective and potent inhibitors.

Applied Graph Theory in Computer Vision and Pattern Recognition

This book will serve as a foundation for a variety of useful applications of graph theory to computer vision, pattern recognition, and related areas. It covers a representative set of novel graph-theoretic methods for complex computer vision and pattern recognition tasks. The first part of the book presents the application of graph theory to low-level processing of digital images such as a new method for partitioning a given image into a hierarchy of homogeneous areas using graph pyramids, or a study of the relationship between graph theory and digital topology. Part II presents graph-theoretic learning algorithms for high-level computer vision and pattern recognition applications, including a survey of graph based methodologies for pattern recognition and computer vision, a presentation of a series of computationally efficient algorithms for testing graph isomorphism and related graph matching tasks in pattern recognition and a new graph distance measure to be used for solving graph matching problems. Finally, Part III provides detailed descriptions of several applications of graph-based methods to real-world pattern recognition tasks. It includes a critical review of the main graph-based and structural methods for fingerprint classification, a new method to visualize time series of graphs, and potential applications in computer network monitoring and abnormal event detection.

Discovery and characterization of a novel non-competitive inhibitor of the divalent metal transporter DMT1/SLC11A2

Divalent metal transporter-1 (SLC11A2/DMT1) uses the H+ electrochemical gradient as the driving force to transport divalent metal ions such as Fe2+, Mn2+ and others metals into mammalian cells. DMT1 is ubiquitously expressed, most notably in proximal duodenum, immature erythroid cells, brain and kidney. This transporter mediates H+-coupled transport of ferrous iron across the apical membrane of enterocytes. In addition, in cells such as to erythroid precursors, following transferrin receptor (TfR) mediated endocytosis; it mediates H+-coupled exit of ferrous iron from endocytic vesicles into the cytosol. Dysfunction of human DMT1 is associated with several pathologies such as iron deficiency anemia hemochromatosis, Parkinson's disease and Alzheimer's disease, as well as colorectal cancer and esophageal adenocarcinoma, making DMT1 an attractive target for drug discovery. In the present study, we performed a ligand-based virtual screening of the Princeton database (700,000 commercially available compounds) to search for pharmacophore shape analogs of recently reported DMT1 inhibitors. We discovered a new compound, named pyrimidinone 8, which mediates a reversible linear non-competitive inhibition of human DMT1 (hDMT1) transport activity with a Ki of ∼20 μM. This compound does not affect hDMT1 cell surface expression and shows no dependence on extracellular pH. To our knowledge, this is the first experimental evidence that hDMT1 can be allosterically modulated by pharmacological agents. Pyrimidinone 8 represents a novel versatile tool compound and it may serve as a lead structure for the development of therapeutic compounds for pre-clinical assessment.

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

CHARACTERIZATION OF SELECTIVE INHIBITION OF ADENYLYL CYCLASE ACTIVITY BY SMALL MOLECULE INHIBITOR NKY80

The nine membrane-bound isoforms of adenylyl cyclase (AC), via synthesis of the signaling molecule cyclic AMP (cAMP), are involved in many isoform specific physiological functions. Decreasing AC5 activity has been shown to have potential therapeutic benefit, including reduced stress on the heart, pain relief, and attenuation of morphine dependence and withdrawal behaviors. However, AC structure is well conserved, and there are currently no isoform selective AC inhibitors in clinical use. P-site inhibitors inhibit AC directly at the catalytic site, but with an uncompetitive or noncompetitive mechanism. Due to this mechanism and nanomolar potency in cell-free systems, attempts at ligand-based drug design of novel AC inhibitors frequently use P-site inhibitors as a starting template. One small molecule inhibitor designed through this process, NKY80, is described as an AC5 selective inhibitor with low micromolar potency in vitro. P-site inhibitors reveal important ligand binding “pockets” in the AC catalytic site, but specific interactions that give NKY80 selectivity are unclear. Identifying and characterizing unique interactions between NKY80 and AC isoforms would significantly aid the development of isoform selective AC inhibitors. I hypothesized that NKY80’s selective inhibition is conferred by AC isoform specific interactions with the compound within the catalytic site. A structure-based virtual screen of the AC catalytic site was used to identify novel small molecule AC inhibitors. Identified novel inhibitors are isoform selective, supporting the catalytic site as a region capable of more potent isoform selective inhibition. Although NKY80 is touted commercially as an AC5 selective inhibitor, its characterization suggests strong inhibition of both AC5 and the closely related AC6. NKY80 was also virtually docked to AC to determine how NKY80 binds to the catalytic site. My results show a difference between NKY80 binding and the conformation of classic P-site inhibitors. The selectivity and notable differences in NKY80 binding to the AC catalytic site suggest a catalytic subregion more flexible in AC5 and AC6 that can be targeted by selective small molecule inhibitors.

Cognitive risk perception system for obstacle avoidance in outdoor mUAV missions

La robótica ha evolucionado exponencialmente en las últimas décadas, permitiendo a los sistemas actuales realizar tareas sumamente complejas con gran precisión, fiabilidad y velocidad. Sin embargo, este desarrollo ha estado asociado a un mayor grado de especialización y particularización de las tecnologías implicadas, siendo estas muy eficientes en situaciones concretas y controladas, pero incapaces en entornos cambiantes, dinámicos y desestructurados. Por eso, el desarrollo de la robótica debe pasar por dotar a los sistemas de capacidad de adaptación a las circunstancias, de entendedimiento sobre los cambios observados y de flexibilidad a la hora de interactuar con el entorno. Estas son las caracteristicas propias de la interacción del ser humano con su entorno, las que le permiten sobrevivir y las que pueden proporcionar a un sistema inteligencia y capacidad suficientes para desenvolverse en un entorno real de forma autónoma e independiente. Esta adaptabilidad es especialmente importante en el manejo de riesgos e incetidumbres, puesto que es el mecanismo que permite contextualizar y evaluar las amenazas para proporcionar una respuesta adecuada. Así, por ejemplo, cuando una persona se mueve e interactua con su entorno, no evalúa los obstáculos en función de su posición, velocidad o dinámica (como hacen los sistemas robóticos tradicionales), sino mediante la estimación del riesgo potencial que estos elementos suponen para la persona. Esta evaluación se consigue combinando dos procesos psicofísicos del ser humano: por un lado, la percepción humana analiza los elementos relevantes del entorno, tratando de entender su naturaleza a partir de patrones de comportamiento, propiedades asociadas u otros rasgos distintivos. Por otro lado, como segundo nivel de evaluación, el entendimiento de esta naturaleza permite al ser humano conocer/estimar la relación de los elementos con él mismo, así como sus implicaciones en cuanto a nivel de riesgo se refiere. El establecimiento de estas relaciones semánticas -llamado cognición- es la única forma de definir el nivel de riesgo de manera absoluta y de generar una respuesta adecuada al mismo. No necesariamente proporcional, sino coherente con el riesgo al que se enfrenta. La investigación que presenta esta tesis describe el trabajo realizado para trasladar esta metodología de análisis y funcionamiento a la robótica. Este se ha centrado especialmente en la nevegación de los robots aéreos, diseñando e implementado procedimientos de inspiración humana para garantizar la seguridad de la misma. Para ello se han estudiado y evaluado los mecanismos de percepción, cognición y reacción humanas en relación al manejo de riesgos. También se ha analizado como los estímulos son capturados, procesados y transformados por condicionantes psicológicos, sociológicos y antropológicos de los seres humanos. Finalmente, también se ha analizado como estos factores motivan y descandenan las reacciones humanas frente a los peligros. Como resultado de este estudio, todos estos procesos, comportamientos y condicionantes de la conducta humana se han reproducido en un framework que se ha estructurado basadandose en factores análogos. Este emplea el conocimiento obtenido experimentalmente en forma de algoritmos, técnicas y estrategias, emulando el comportamiento humano en las mismas circunstancias. Diseñado, implementeado y validado tanto en simulación como con datos reales, este framework propone una manera innovadora -tanto en metodología como en procedimiento- de entender y reaccionar frente a las amenazas potenciales de una misión robótica. ABSTRACT Robotics has undergone a great revolution in the last decades. Nowadays this technology is able to perform really complex tasks with a high degree of accuracy and speed, however this is only true in precisely defined situations with fully controlled variables. Since the real world is dynamic, changing and unstructured, flexible and non context-dependent systems are required. The ability to understand situations, acknowledge changes and balance reactions is required by robots to successfully interact with their surroundings in a fully autonomous fashion. In fact, it is those very processes that define human interactions with the environment. Social relationships, driving or risk/incertitude management... in all these activities and systems, context understanding and adaptability are what allow human beings to survive: contrarily to the traditional robotics, people do not evaluate obstacles according to their position but according to the potential risk their presence imply. In this sense, human perception looks for information which goes beyond location, speed and dynamics (the usual data used in traditional obstacle avoidance systems). Specific features in the behaviour of a particular element allows the understanding of that element’s nature and therefore the comprehension of the risk posed by it. This process defines the second main difference between traditional obstacle avoidance systems and human behaviour: the ability to understand a situation/scenario allows to get to know the implications of the elements and their relationship with the observer. Establishing these semantic relationships -named cognition- is the only way to estimate the actual danger level of an element. Furthermore, only the application of this knowledge allows the generation of coherent, suitable and adjusted responses to deal with any risk faced. The research presented in this thesis summarizes the work done towards translating these human cognitive/reasoning procedures to the field of robotics. More specifically, the work done has been focused on employing human-based methodologies to enable aerial robots to navigate safely. To this effect, human perception, cognition and reaction processes concerning risk management have been experimentally studied; as well as the acquisition and processing of stimuli. How psychological, sociological and anthropological factors modify, balance and give shape to those stimuli has been researched. And finally, the way in which these factors motivate the human behaviour according to different mindsets and priorities has been established. This associative workflow has been reproduced by establishing an equivalent structure and defining similar factors and sources. Besides, all the knowledge obtained experimentally has been applied in the form of algorithms, techniques and strategies which emulate the analogous human behaviours. As a result, a framework capable of understanding and reacting in response to stimuli has been implemented and validated.