Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)

Solving the structure of protein-protein complexes is one of the most important tasks in structural biology. Even though there has been great progress in recent years there still a small number of protein complexes structures deposited in the Protein Data Bank in comparison to isolated partners. In this sense, the computational prediction of protein complexes starting from the unbound structures, protein-protein Docking algorithms, has emerged as a reasonable alternative. Many docking programs employ Fast Fourier Transform (FFT) correlations as an efficient search strategy. We describe an implementation of a protein-protein docking program based on FFT surface complementarity that runs entirely on a Graphics Processing Unit (GPU), including grid generation, rotation and scoring. We evaluate its performance, and show that it can be up to 13 times faster than conventional CPU based implementations.Sociedad Argentina de Informática e Investigación Operativ

Solvents to Fragments to Drugs: MD Applications in Drug Design

Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates

Omics data integration facilitates target selection for new antiparasitic drugs against TriTryp infections

Introduction:Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp., commonly referred to as TriTryps, are a group of protozoan parasites that cause important human diseases affecting millions of people belonging to the most vulnerable populations worldwide. Current treatments have limited efficiencies and can cause serious side effects, so there is an urgent need to develop new control strategies. Presently, the identification and prioritization of appropriate targets can be aided by integrative genomic and computational approaches.Methods: In this work, we conducted a genome-wide multidimensional data integration strategy to prioritize drug targets. We included genomic, transcriptomic, metabolic, and protein structural data sources, to delineate candidate proteins with relevant features for target selection in drug development.Results and Discussion: Our final ranked list includes proteins shared by TriTryps and covers a range of biological functions including essential proteins for parasite survival or growth, oxidative stress-related enzymes, virulence factors, and proteins that are exclusive to these parasites. Our strategy found previously described candidates, which validates our approach as well as new proteins that can be attractive targets to consider during the initial steps of drug discovery

Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile

The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also wellrepresented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.Centro de Investigaciones Geológica

Interacción de la melatonina con radicales libres

El objetivo de este trabajo de tesis fue el estudio a nivel molecular de la interacción de la melatonina (N-acetil-S-metoxitriptamina) con dos radicales libres de relevancia biológica, el radical oxhidrilo (OH·) y el óxido nítrico (NO). Para el desarrollo del presente trabajo se analizaron estas interacciones químicas desde un enfoque teórico, mediante técnicas de simulación computacional, desde un enfoque experimental, a través del estudio de las mismas en condiciones aisladas y controladas, y a través de la evaluación de los alcances fisiológicos de las reacciones propuestas. Para evaluar las interacciones con los diferentes blancos se analizó, en primer término, la superficie de energía potencial de la melatonina mediante técnicas de dinámica molécular basadas en campos de fuerzas clásicos y métodos semiempíricos. Se prestó especial atención a los aspectos relacionados con su libertad conformacional en vacío y en solución acuosa. Asimismo, se analizó la dependencia de las propiedades moleculares con la conformación. La reacción con el radical oxhidrilo se estudió mediante técnicas de estructura electrónica, evaluando los posibles mecanismos de reacción y realizando una exhaustiva caracterización de los intermediarios. El estudio de la interacción con NO se puede dividir en dos partes: i) la identificación y caracterización de los productos de reacción y la elucidación de los mecanismos operantes en diversos medios; y ii) el estudio del efecto de la melatonina sobre la biosíntesis de NO en la retina de hámster. Finalmente, mediante el uso de técnicas de resonancia magnética nuclear y de dinámica molecular, se realizó un estudio detallado de la interacción entre la melatonina y la calmodulina, una proteína con probado efecto estimulatorio en la biosíntesis del NO.The goal of this thesis was the study at a molecular level of the interactions of melatonin (N-Acetyl-5-metoxytriptamine) with two free radicals of biological relevance, hydroxyl (OH·) radical and nitric oxide (NO). The evaluation of the different interactions has been performed by a theoretical approach using molecular modeling tools; through the study of these reactions in isolated and controlled conditions, and finally by the evaluation of their physiological relevance. In order to evaluate the interactions with these different targets, the potential energy surface of melatonin has been analyzed by classical molecular dynamics and semiempirical electronic structure methodologies. Special attention has been paid to the conformational behavior in vacuum and aqueous solution. Moreover, the influence of conformation on several properties has been studied. The reaction with OH· has been analyzed with electronic structure methods. Feasible reaction mechanisms have been evaluated along with a thorough characterization of the intermediates. The research on the interaction with NO consisted of: i) the identification and characterization of the products, and the elucidation of the mechanisms operative in different environments ii) by the analysis of the effect of melatonin on NO biosynthesis in the hamster retina. Finally, by means of nuclear magnetic resonance and molecular dynamics techniques, a detailed study of the interaction of melatonin with calmodulin, a stimulatory protein of NO biosynthesis has been carried out.Fil:Turjanski, Adrián G.. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Molecular structure effects on the kinetics of hydroxyl radical addition to azo dyes

The effect of the molecular structure of azobenzene and related azo dyes on their reactivity towards .OH radicals in water was investigated by performing ultrasonic irradiation experiments on their aqueous solutions and density functional theory (DFT) calculations. Sonolysis of azobenzene, methyl orange, o-methyl red and p-methyl red was performed at a frequency of 500 kHz and 50 W applied power under air saturation. Under such irradiation conditions, these molecules were shown to decompose through .OH radical addition reactions taking place in the bulk liquid. The ortho isomer of methyl red reacted at significantly higher rates (nearly 30% higher) than the other three studied compounds in non-buffered aqueous solutions. In contrast, measurements performed at lower pH (10 mM HNO3), at which the carboxylic group vicinal to the azo group is protonated, yielded a similar reaction rate for all four substrates, i.e. the specific acceleration observed in the ortho-substituted dye disappeared with protonation. These results were rationalized by the computation of formation energies of the adduct originated in the .OH addition to the azo group, performing DFT calculations combined with the polarized continuum model (PCM) of solvation. The calculations suggest that intramolecular H-bonding in the o-methyl red–OH adduct provides extra stabilization in that particular case, which correlates with the observed higher addition rates of .OH radical to the anionic form of that isomer in non-buffered solutions. On the other hand, the energy changes calculated for the .OH addition to an o-methyl red molecule which is protonated in the carboxylic group (representative of the situation at pH 2) do not differ significantly from those computed for the other three molecules studied