2D QSAR and similarity studies on cruzain inhibitors aimed at improving selectivity over cathepsin L

Hologram quantitative structure-activity relationships (HQSAR) were applied to a data set of 41 cruzain inhibitors. The best HQSAR model (Q(2) = 0.77; R-2 = 0.90) employing Surflex-Sim, as training and test sets generator, was obtained using atoms, bonds, and connections as fragment distinctions and 4-7 as fragment size. This model was then used to predict the potencies of 12 test set compounds, giving satisfactory predictive R-2 value of 0,88. The contribution maps obtained from the best HQSAR model are in agreement with the biological activities of the study compounds. The Trypanosoma cruzi cruzain shares high similarity with the mammalian homolog cathepsin L. The selectivity toward cruzam was checked by a database of 123 compounds, which corresponds to the 41 cruzain inhibitors used in the HQSAR model development plus 82 cathepsin L inhibitors. We screened these compounds by ROCS (Rapid Overlay of Chemical Structures), a Gaussian-shape volume overlap filter that can rapidly identify shapes that match the query molecule. Remarkably, ROCS was able to rank the first 37 hits as being only cruzain inhibitors. In addition, the area under the curve (AUC) obtained with ROCS was 0.96, indicating that the method was very efficient to distinguishing between cruzain and cathepsin L inhibitors. (c) 2007 Elsevier Ltd. All rights reserved.

Investigating the Nature of Noble Gas-Copper Bonds by the Quantum Theory of Atoms in Molecules

We investigated noble gas copper bonds in linear complexes represented by the NgCuX general formula in which Ng and X stand for a noble gas (neon, argon, krypton, or xenon) and a halogen (fluorine, chlorine or bromine), respectively, by coupled cluster methods and modified cc-pVQZ basis sets. The quantum theory of atoms in molecules (QTAIM) shows a linear relation between the dissociation energy or noble gas-copper bonds and the amount of electronic charge transferred mainly from the noble gas to copper during complexation. Large changes in the QTAIM quadrupole moments of copper and noble gases resulting from this bonding and a comparison between NgCuX and NgNaCl systems indicate that these noble gas-copper bonds should be better interpreted as predominantly covalent. Finally, QTAIM atomic dipoles of noble gases in NgNaCl systems agree satisfactorily with atomic dipoles given by a simple model for these NgNa van der Waals bonds.

A quantum chemical study on a set of non-imidazole H(3) antihistamine molecules

Molecular orbital calculations were carried out on a set of 28 non-imidazole H(3) antihistamine compounds using the Hartree-Fock method in order to investigate the possible relationships between electronic structural properties and binding affinity for H3 receptors (pK(i)). It was observed that the frontier effective-for-reaction molecular orbital (FERMO) energies were better correlated with pK(i) values than highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy values. Exploratory data analysis through hierarchical cluster (HCA) and principal component analysis (PCA) showed a separation of the compounds in two sets, one grouping the molecules with high pK(i) values, the other gathering low pK(i) value compounds. This separation was obtained with the use of the following descriptors: FERMO energies (epsilon(FERMO)), charges derived from the electrostatic potential on the nitrogen atom (N(1)), electronic density indexes for FERMO on the N(1) atom (Sigma((FERMO))c(i)(2)). and electrophilicity (omega`). These electronic descriptors were used to construct a quantitative structure-activity relationship (QSAR) model through the partial least-squares (PLS) method with three principal components. This model generated Q(2) = 0.88 and R(2) = 0.927 values obtained from a training set and external validation of 23 and 5 molecules, respectively. After the analysis of the PLS regression equation and the values for the selected electronic descriptors, it is suggested that high values of FERMO energies and of Sigma((FERMO))c(i)(2), together with low values of electrophilicity and pronounced negative charges on N(1) appear as desirable properties for the conception of new molecules which might have high binding affinity. 2010 Elsevier Inc. All rights reserved.

A quantum chemical study on the formation of phosphorus mononitride

The chemical mechanism of the (1)PN formation was successfully studied by using the CCSD(T)/6-311++G(3df,3pd) level of theory. The (1)NH(3) + (3)PH and (4)P + NH(3) reaction paths are not energetically favorable to form the (1)PN molecule. However, the (3)NH + (3)PH, (4)N + (3)PH(3), (4)N + (3)PH, (4)P + (3)NH, and (4)P + (2)NH(2) reaction paths to form the (1)PN molecule are only energetically favorable by taking place through specific transition states to form the (1)PN molecule. The NH(3) + (3)PH, (4)N + (1)PH(3), NH(3) + (4)P, and (4)N + (2)PH(2) reactions are spin-forbidden and the probability of hopping for these reactions was estimated to be 0 by the Landau-Zener theory. This is the first detailed study on the chemical mechanism for the (1)PN formation. (C) 2009 Elsevier B.V. All rights reserved.

Quantum control of electromagnetically induced transparency dispersion via atomic tunneling in a double-well Bose-Einstein condensate

Electromagnetically induced transparency (EIT) is an important tool for controlling light propagation and nonlinear wave mixing in atomic gases with potential applications ranging from quantum computing to table top tests of general relativity. Here we consider EIT in an atomic Bose-Einstein condensate (BEC) trapped in a double-well potential. A weak probe laser propagates through one of the wells and interacts with atoms in a three-level Lambda configuration. The well through which the probe propagates is dressed by a strong control laser with Rabi frequency Omega(mu), as in standard EIT systems. Tunneling between the wells at the frequency g provides a coherent coupling between identical electronic states in the two wells, which leads to the formation of interwell dressed states. The macroscopic interwell coherence of the BEC wave function results in the formation of two ultranarrow absorption resonances for the probe field that are inside of the ordinary EIT transparency window. We show that these new resonances can be interpreted in terms of the interwell dressed states and the formation of a type of dark state involving the control laser and the interwell tunneling. To either side of these ultranarrow resonances there is normal dispersion with very large slope controlled by g. We discuss prospects for observing these ultranarrow resonances and the corresponding regions of high dispersion experimentally.

Interação heparina-antitrombina : reconhecimento molecular caracterizado por ferramentas de modelagem molecular

A heparina foi isolada no início do século XX e permanece, até os dias atuais, como um dos mais importantes e eficientes agentes terapêuticos de ação antitrombótica. Sua atividade anticoagulante deve-se à ativação da antitrombina (AT), uma serpina responsável pela inibição fisiológica de serino-proteinases plasmáticas, tais como fIIa e fXa. Os esforços no sentido da elucidação dos aspectos estruturais e dinâmicos associados ao reconhecimento molecular da heparina pela AT, em nível atômico, vêm encontrando diversas dificuldades, principalmente associadas aos compostos sacarídicos. Em decorrência de sua elevada polaridade e flexibilidade, glicosaminoglicanos como a heparina são difíceis de estudar e modelar. Soma-se a isto o fato de que os resíduos de iduronato presentes na heparina (IdoA) apresentam um incomum equilíbrio conformacional entre estados de cadeira (1C4) e bote-torcido (2SO), sendo esta última estrutura postulada como a possível conformação bioativa. Sendo assim, este trabalho apresenta um estudo de modelagem molecular do perfil conformacional da heparina, tanto em solução quanto complexada à AT, utilizando cálculos ab initio e simulações de dinâmica molecular (DM) Em decorrência da ausência de parâmetros capazes de descrever polissacarídeos nos campos de força atualmente disponíveis, cargas atômicas foram geradas, utilizando-se os esquemas de Mulliken, Löwdin e cargas ajustadas ao Potencial Eletrostático, através de cálculos quantum-mecânicos na base 6-31G** e testadas na simulação de DM da heparina. Diversas condições de simulação, tais como modelos de água, concentrações de sais e as conformações 1C4 e 2SO do IdoA, foram avaliadas de forma a identificar as melhores condições para a descrição conformacional da heparina em solução. O protocolo de DM obtido foi então utilizado no estudo do complexo AT-heparina. Os resultados obtidos estão de acordo com os dados experimentais atualmente disponíveis acerca da conformação da heparina e da contribuição energética de cada resíduo de aminoácido da AT para a formação do complexo com a heparina. A partir dos cálculos ab initio realizados, foi proposto um refinamento na estrutura da heparina determinada por RMN, enquanto que as simulações de DM permitiram reinterpretar aspectos da estrutura tridimensional da AT determinada por cristalografia de raios-X. Adicionalmente, os dados obtidos sugerem que não há requerimento conformacional para a interação do IdoA com a AT Globalmente, os dados indicam que simulações de DM podem ser utilizadas para representar adequadamente a conformação da heparina, assim como para caracterizar e quantificar suas interações com a AT. Assim sendo, propomos o uso de simulações de DM do complexo entre a AT e a heparina, ou entre a AT e compostos derivados da heparina, como uma ferramenta útil no processo de desenvolvimento de novos agentes antitrombóticos e anticoagulantes.

Biosystematics of the Genus Andryala L. (Asteraceae)

Andryala (Asteraceae: Cichorieae) is a little-known Mediterranean-Macaronesian genus whose taxonomy is much in need of revision. The aim of the present biosystematic study was to elucidate species relationships within this genus based on morphological and molecular data. In this study several taxa are recognised: 17 species, 14 subspecies, and 3 hybrids. Among these, 5 species are Macaronesian endemics (A. glandulosa, A. sparsiflora, A. crithmifolia Aiton, A. pinnatifida, and A. perezii), 4 species are Northwest African endemics (A. mogadorensis, A. maroccana, A. chevallieri, and A. nigricans) and one species is endemic to Romania (A. laevitomentosa). Historical background regarding taxonomic delimitation in the genus is addressed from Linnaean to present day concepts, as well as the origin of the name Andryala. The origin of Asteraceae and the systematic position of Andryala is shortly summarised. The morphological study was based on a bibliographic review and the revision of 1066 specimens of 13 herbaria as well as additional material collected during fieldwork. The variability of the morphological characters of the genus, including both vegetative taxonomic characters (root, stem, leaf and indumentum characters) and reproductive ones (inflorescence, floret, fruit and pappus characters), is assessed. Numerical analysis of the morphological data was performed using different similarity or dissimilarity measures and coefficients, as well as ordination and clustering methods. Results support the segregation of the recognised taxa and the congruence of the several analyses in the separation of the recognised taxa (using quantitative, binary or multi-state characters). The proposed taxonomy for Andryala includes a new infra-generic classification, new taxa and new combinations and ranks, typifications and diagnostic keys (one for the species and several for subspecies). For each taxon a list of synonyms, typification comments and a detailed description are provided, just as comments on taxonomy and nomenclature, and a brief discussion on karyology. Additionally, information on ecology and conservation status as well as on distribution and a list of studied material are also presented. Phylogenetic analyses based on different nuclear and chloroplast DNA markers, using Bayesian and maximum parsimony methods of inference, were performed. Results support three main lineages: separate ones for the relict species A. agardhii and A. laevitomentosa and a third including the majority of the Andryala species that underwent a relatively rapid and recent speciation. They also suggest a single colonization event of Madeira and the Canary Islands from the Mediterranean region, followed by insular speciation. Biogeography and speciation within the genus are briefly discussed, including a proposal for the centre of origin of the genus and possible dispersal routes.

Modelagem molecular na caracterização eletrônica de oligopeptídeos e na descrição quântica da interação fármaco-receptor

In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicosídico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced.

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation

Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by PCR reaction using specific oligonucleotide primers for the 16S rRNA gene. The PCR products were cloned into a pGEM-T-Easy vector (Promega), and Escherichia coli was used as the host cell for recombinant DNAs. The partial clone sequencing was obtained using universal oligonucleotide primers from the vector. The genetic library obtained generated 431 clones. All the sequenced clones presented similarity to phylum Proteobacteria, with Gammaproteobacteria the most present group (49.8 % of the clones), followed by Alphaproteobacteira (44.8 %) and Betaproteobacteria (5.4 %). The Pseudomonas genus was the most abundant in the metagenomic library, followed by the Parvibaculum and the Sphingobium genus, respectively. After partial sequencing of the 16S rRNA, the diversity of the bacterial consortium was estimated using DOTUR software. When comparing these sequences to the database from the National Center for Biotechnology Information (NCBI), a strong correlation was found between the data generated by the software used and the data deposited in NCBI.

Caracterização molecular de isolados de Flavobacterium columnare de tilapia do nilo e piracanjuba por meio de RAPD-PCR

Flavobacterium columnare is a cosmopolite bacteria and it is one of the main problem in Brazilian aquaculture, causing high mortalities index and economic damage. The main factors that contribute to columnaris disease are inadequate water quality, excess handling, high density of fish and temperature variations. For a successful epidemiological study and disease control, it is essential to differentiate the F. columnare from other yellow pigmentation bacteria. The present study used molecular techniques to characterize, by RAPD-PCR, two strains of F. columnare isolated from Oreochromis niloticus and Brycon orbignyanus. Data were analyzed as binary (0 and 1) and a genetic similarity matrix was generated by Jaccard's coefficient. Cluster analysis was performed by the neighbor joining method. The RAPD-PCR technique confirmed to be a usefull tool to obtain genetic profiles from F. columnare isolates based on the oligonucleotides used and to verify genetic similarity.

Molecular epidemiology of Staphylococcus aureus isolates at different sites in the milk producing dairy farms

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Caracterização molecular através da técnica fAFLP de isolados de Diaporthe citri

A citricultura é um mercado em expansão, principalmente no Estado de São Paulo, cuja importância na balança comercial já é reconhecida. Como em qualquer espécie cultivada, o crescimento das áreas de cultivo favorecem também o crescimento de problemas fitossanitários. Desta forma, as espécies de citros são afetadas por diversas doenças destacando-se entre elas a melanose, causada por Diaporthe citri (Wolf.), à qual a grande maioria das variedades comerciais são suscetíveis. O conhecimento da diversidade intra-específica é de grande importância, já que esta poderá auxiliar na seleção de variedades com resistência. O objetivo deste trabalho foi avaliar a variabilidade genética em isolados de Diaporthe citri, originários de diferentes locais, variedades e partes da planta, utilizando marcadores moleculares. Marcadores do tipo AFLP (Amplified Fragment Length Polymorphism) foram utilizados para caracterização de dez isolados do patógeno. Os DNAs genômicos extraídos da massa micelial foram utilizados nas reações de amplificação. A técnica fluorescent AFLP permitiu a distinção dos isolados estudados, tendo sido classificados em quatro grupos distintos. Contudo, estes grupos não foram formados em razão da região geográfica, parte da planta ou variedade.

Molecular characterization of group A bovine rotavirus in southeastern and central-western Brazil, 2009-2010

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular and serological detection of Leishmania spp. in captive wild animals from Ilha Solteira, SP, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)