Molecular modeling and UV-vis spectroscopic studies on the mechanism of action of reversed chloroquine (RCQ)

Reversed chloroquine (RCQ) is a multiple ligand compound active against chloroquine-sensitive and resistant falciparum malaria. It is composed by a 4-aminoquinoline moiety (like that present in chloroquine (CQ)) joined to imipramine (IMP), a modulating agent that also showed intrinsic antiplasmodial activity against Brazilian Plasmodium falciparum isolates resistant to CQ. Molecular modeling and ultraviolet-visible spectroscopy (UV-vis) studies strongly suggest that the interaction between RCQ and heme is predominant through the quinoline moiety in a mechanism of action similar to that observed for CQ. (C) 2010 Elsevier Ltd. All rights reserved.

The interaction between atoms of Au and Cu with clean Si(111) surface: A study combining synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations

In order to evaluate the interactions between Au/Cu atoms and clean Si(l 11) surface, we used synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations. Optimized geometries and energies on different adsorption sites indicate that the binding energies at different adsorption sites are high, suggesting a strong interaction between metal atom and silicon surface. The Au atom showed higher interaction than Cu atom. The theoretical and experimental data showed good agreement. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

The role of oxygen in the interaction of emeraldine base polyaniline with Cu(II) or Fe(III) ions in NMP solution

The influence of molecular oxygen in the interactions of emeraldine base form of polyaniline (EB-PANI) with Fe(III) or Cu(II) ions in 1-methyl-2-pyrrolidinone (NMP) solutions has been investigated by UV-vis-NIR, resonance Raman and electron paramagnetic resonance (EPR) spectroscopies. Through the set of spectroscopic results it was possible to rationalize the role Of O(2) and to construct a scheme of preferential routes occurring in the interaction of EB-PANI with Fe(III) or Cu(II). Solutions of 4.0 mmol L(-1) EB-PANI with 0.8, 2.0 and 20 mmol L(-1) Fe(III) or Cu(II) ions in NMP were investigated and the main observed reactions were EB-PANI oxidation to pernigraniline (PB-PANI) and EB-PANI doping process by pseudo-protonation, or by a two-step redox process. In the presence Of O(2), PB-PANI is observed in all Fe(III)/EB solutions and EB-PANI doping only occurs in solutions with high Fe(III) concentrations through pseudo-protonation. On the other hand, emeraldine salt (ES-PANI) is formed in all Fe(III)/EB solutions under N(2) atmosphere and, in this case, doping occurs both by the pseudo-protonation and two-step redox mechanisms. In all Cu(II)/EB solutions PB-PANI is formed both in the presence and absence of O(2), and only for solutions with high Cu(II) concentrations doping process occurs in a very low degree. The most important result from EPR spectra was providing evidence for redox steps. The determined Cu(II) signal areas under oxygen are higher than under N(2) and, further. the initial metal proportions (1:2:20) are maintained in these spectra, indicating that Cu(I) formed are re-oxidized by O(2) and. so, Cu(II) ions are being recycled. Consistently, for the solutions prepared under nitrogen, the corresponding areas and proportions in the spectra are much lower, confirming that a partial reduction of Cu(II) ions actually occurs. (C) 2009 Elsevier B.V. All rights reserved.

Crystal and molecular structures of three 2-sulphur-substituted cyclohexanones studied by X-ray crystallography and by ab initio molecular orbital calculations

The conformational features of three 2-sulphur-substituted cyclohexanone derivatives, which differ in the number of sulphur-bound oxygen atoms, i.e. zero (I), one (II) and two (III), were investigated by single crystal X-ray crystallography and geometry optimized structures determined using Hartree-Fock method. In each of (I)-(III) an intramolecular S center dot center dot center dot O(carbonyl) interaction is found with the magnitude correlated with the oxidation state of the sulphur atom, i.e. 2.838(3) angstrom in (I) to 2.924(2) angstrom in (II) to 3.0973(18) angstrom in (III). There is an inverse relationship between the strength of this interaction and the magnitude of the carbonyl bond. The supramolecular aggregation patterns are primarily determined by C-H center dot center dot center dot O contacts and are similarly influenced by the number of oxygen atoms in the molecular structures. Thus, a supramolecular chain is found in the crystal structure of (I). With an additional oxygen atom available to participate in C-H center dot center dot center dot O interactions, as in (II), a two-dimensional array is found. Finally, a three-dimensional network is found for (III). Despite there being differences in conformations between the experimental structures and those calculated in the gas-phase, the S center dot center dot center dot O interactions persist. The presence of intermolecular C-H center dot center dot center dot O interactions involving the cyclohexanone-carbonyl group in the solid-state, disrupts the stabilising intramolecular C-H center dot center dot center dot O interaction in the energetically-favoured conformation. (I): C(12)H(13)NO(3)S, triclinic space group P (1) over bar with a = 5.392(3) angstrom b = 10.731(6) angstrom, c = 11.075(6) angstrom, alpha = 113.424(4)degrees, beta = 94.167(9)degrees, gamma = 98.444(6)degrees, V = 575.5(6) angstrom(3), Z = 2, R(1) = 0.052; (II): C(12)H(13)NO(4)S, monoclinic P2(1)/n, a = 7.3506(15) angstrom, b = 6.7814(14) angstrom, c = 23.479(5) angstrom, beta = 92.94(3)degrees, V = 1168.8(4) angstrom(3), Z = 4, R(1) = 0.046; (III): C(12)H(13)NO(5)S, monoclinic P2(1)/c, a = 5.5491(11) angstrom, b = 24.146(3) angstrom, c = 11.124(3) angstrom, beta = 114.590(10)degrees, V = 1355.3(5) angstrom(3), Z = 4, R(1) = 0.051.

Stereochemical and electronic interaction studies of some N-methoxy-N-methyl-2-[(4 `-substituted)phenylsulfinyl]propanamides

The (1)H NMR spectra of N-methoxy-N-methyl-2-[(4`-substituted)phenylsulfinyl]-propanamides [Y-Ph-S(O)CH(Me)C(O)N(OMe)Me; Y = OMe 1, Me 2, H 3. Cl 4, NO(2) 5] along with the X-ray diffraction analysis of the nitro-derivative (5). have shown the existence of two pairs of diastereomers (racemic mixture) [C(R)S(S)/C(S)S(R) (diast(1)) and C(R)S(R)/C(S)S(S) (diast(2))] in the ratio of ca. 7:3. respectively. The v(CO) IR analysis of the title compounds supported by HF and B3LYP/6-31G** calculations of 3 and of the parent N-methoxy-N-methyl-propanamide (6) by HF, have shown that diast(1) exists in an equilibrium between the two more polar and more stable quasi-cis (q-c(1) and q-c(2)) conformers and the gauche(g) conformer. The population of the g conformer in the equilibrium increases with the increase in the solvent polarity, which is attributed to a larger solvation effect on the carbonyl and sulfinyl groups. Diast(2) of compound 3 occurs in the gas phase as an equilibrium between the most stable quasi-gauche (q-g) conformer and the quasi-cis (q-c) conformer, both presenting very similar dipole moments. The former is stabilized by electrostatic and charge transfer interactions, which results in a less solvated spatial arrangement. Moreover, all conformers of both diastereomers are stabilized by several intramolecular hydrogen bonds. X-ray single crystal analysis performed for diast(1) and for diast(2) of 5 indicates that both stereoisomers assume, in the solid state, the anti-clinal (gauche) conformation. For the crystal packing, diast(1) of 5 is made up of three molecules joined through two centro-symmetric H center dot center dot center dot O hydrogen bonds. (C) 2008 Elsevier B.V. All rights reserved.

Interaction of giant extracellular Glossoscolex paulistus hemoglobin (HbGp) with zwitterionic surfactant N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS): Effects of oligomeric dissociation

The present work focuses on the interaction between the zwitterionic surfactant N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS) and the giant extracellular hemoglobin of Glossoscolex paulistus (HbGp). Electronic optical absorption, fluorescence emission and circular dichroism spectroscopy techniques, together with Gel-filtration chromatography, were used in order to evaluate the oligomeric dissociation as well as the autoxidation of HbGp as a function of the interaction with HPS. A peculiar behavior was observed for the HPS-HbGp interaction: a complex ferric species formation equilibrium was promoted, as a consequence of the autoxidation and oligomeric dissociation processes. At pH 7.0, HPS is more effective up to 1 mM while at pH 9.0 the surfactant effect is more intense above 1 mM. Furthermore, the interaction of HPS with HbGp was clearly less intense than the interaction of this hemoglobin with cationic (CTAC) and anionic (SDS) surfactants. Probably, this lower interaction with HPS is due to two factors: (i) the lower electrostatic attraction between the HPS surfactant and the protein surface ionic sites when compared to the electrostatic interaction between HbGp and cationic and anionic surfactants, and (ii) the low cmc of HPS, which probably reduces the interaction of the surfactant in the monomeric form with the protein. The present work emphasizes the importance of the electrostatic contribution in the interaction between ionic surfactants and HbGp. Furthermore, in the whole HPS concentration range used in this study, no folding and autoxidation decrease induced by this surfactant were observed. This is quite different from the literature data on the interaction between surfactants and tetrameric hemoglobins, that supports the occurrence of this behavior for the intracellular hemoglobins at low surfactant concentration range. Spectroscopic data are discussed and compared with the literature in order to improve the understanding of hemoglobin-surfactant interaction as well as the acid isoelectric point (pI) influence of the giant extracellular hemoglobins on their structure-activity relationship. (c) 2007 Elsevier B.V. All rights reserved.

Stoichiometry and thermodynamics of the interaction between the C-terminus of human 90 kDa heat shock protein Hsp90 and the mitochondrial translocase of outer membrane Tom70

A large majority of the 1000-1500 proteins in the mitochondria are encoded by the nuclear genome, and therefore, they are translated in the cytosol in the form and contain signals to enable the import of proteins into the organelle. The TOM complex is the major translocase of the outer membrane responsible for preprotein translocation. It consists of a general import pore complex and two membrane import receptors, Tom20 and Tom70. Tom70 contains a characteristic TPR domain, which is a docking site for the Hsp70 and Hsp90 chaperones. These chaperones are involved in protecting cytosolic preproteins from aggregation and then in delivering them to the TOM complex. Although highly significant, many aspects of the interaction between Tom70 and Hsp90 are still uncertain. Thus, we used biophysical tools to study the interaction between the C-terminal domain of Hsp90 (C-Hsp90), which contains the EEVD motif that binds to TPR domains, and the cytosolic fragment of Tom70. The results indicate a stoichiometry of binding of one monomer of Tom70 per dimer of C-Hsp90 with a K(D) of 360 30 nM, and the stoichiometry and thermodynamic parameters obtained suggested that Tom70 presents a different mechanism of interaction with Hsp90 when compared with other TPR proteins investigated. (C) 2011 Elsevier Inc. All rights reserved.

Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.

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.

Host-guest system of 4-nerolidylcatechol in 2-hydroxypropyl-beta-cyclodextrin: preparation, characterization and molecular modeling

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genotype by environment interaction in Nelore cattle from five Brazilian states

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

Enhanced stabilization of aerosol-OT surfactant monolayer upon interaction with small amounts of bovine serum albumin at the air-water interface

An investigation is made of the influence from small amounts of the protein bovine serum albumin (BSA) on the lateral organization of low molecular weight surfactant sodium bis-2-ethylhexyl sulfosuccinate (AOT) at the air-water interface. Surface pressure (pi - A), surface potential (DeltaV - A) and Brewster angle microscopy (BAM) experiments were carried out, with particular emphasis on the monolayer stability under successive compression-expansion cycles. AOT monolayer is not stable at the air-water interface, which means that the majority of AOT molecules go into the aqueous subphase as monomers and/or normal micelles. When a waiting time elapses between spreading and compression, the surfactant monolayer tends to reorganize partially at the air-water interface, with a monolayer expansion being observed for waiting times as large as 12 h. The incorporation of very small amount of BSA (10(-9) M) at the interface, also inferred from BAM, increases the monolayer stability as revealed by pi - A and DeltaV - A results. For a waiting time of circa 3 h, the mixed monolayer reaches its maximum stability. This must be related to protein (and/or protein-surfactant complexes) adsorbed onto the AOT monolayer, thus altering the BSA conformation to accommodate its hydrophobic/hydrophilic residues. Furthermore, the effects from such small amounts of BSA in the monolayer formation and stabilization mean that the AOT monolayer responds cooperatively to BSA. (C) 2004 Elsevier B.V. All rights reserved.

Incorporation of Ag nanoparticles into membrane mimetic systems composed by phospholipid layer-by-layer (LbL) films to achieve surface-enhanced Raman scattering as a tool in drug interaction studies

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

Study of the interaction between cardiolipin bilayers and methylene blue in polymer-based Layer-by-Layer and Langmuir films applied as membrane mimetic systems

An increase of the reports involving mimetic systems has been observed. Briefly, these systems use biological phospholipids to exploit specific interactions between membrane-models and drugs. Here, the Layer-by-Layer (LbL) and Langmuir techniques were used to investigate the interaction between cardiolipin (CLP-negative phospholipid) and a cationic-like drug methylene blue (MB). Supported by a cationic polyelectrolyte (PAH), LbL films containing PAH/(CLP + MB) and PAH/(CLP + MB + AgNP) were grown up to 14 bilayers. The optical microscopy analysis revealed a decrease of the CLP vesicle sizes in the presence of MB as a possible consequence of the MB action onto the mechanical properties of the CLP membrane. From FTIR spectra, changes mainly related to peak position and band intensity and shape were observed in the spectra from PAH/CLP when in the presence of MB. The latter supports that the interactions between the phosphate and amine charged groups from CLP and PAH, respectively, established during the LbL film fabrication, besides the CLP hydrocarbon environment, are influenced by the presence of MB. Using the micro-Raman technique, a chemical mapping was build based on MB spectrum by resonance Raman scattering (RRS) and surface-enhanced resonance Raman scattering (SERRS). The later phenomenon was activated by Ag nanoparticles (AgNPs) trapped within the LbL film allowing collecting spectra for a single bilayer of PAH/(CLP + MB + AgNP). A rough estimation showed a SERRS amplification of 10(3) in comparison to RRS spectra. As a complementary approach, Langmuir films of CLP in the presence of co-spread MB were investigated through surface pressure vs mean molecular area (pi-A) isotherms. The results showed that for concentrations of MB below 100 mol%, the drug is expelled to water subphase for high values of surface pressure (condensed phase). For concentration at 100% and higher, the MB keeps bound to CLP floating monolayer. (C) 2010 Elsevier B.V. All rights reserved.

Pathogenesis II: Fungal responses to host responses: interaction of host cells with fungi

Most of our knowledge concerning the virulence determinants of pathogenic fungi comes from the infected host, mainly from animal models and more recently from in vitro studies with cell cultures. The fungi usually present intra- and/or extracellular host-parasite interfaces, with the parasitism phenomenon dependent on complementary surface molecules. Among living organisms, this has been characterized as a cohabitation event, where the fungus is able to recognize specific host tissues acting as an attractant, creating stable conditions for its survival. Several fungi pathogenic for humans and animals have evolved special strategies to deliver elements to their cellular targets that may be relevant to their pathogenicity. Most of these pathogens express surface factors that mediate binding to host cells either directly or indirectly, in the latter case binding to host adhesion components such as extracellular matrix (ECM) proteins, which act as 'interlinking' molecules. The entry of the pathogen into the host cell is initiated by fungal adherence to the cell surface, which generates an uptake signal that may induce its cytoplasmic internalization. Once this is accomplished, some fungi are able to alter the host cytoskeletal architecture, as manifested by a rearrangement of microtubule and microfilament proteins, and this can also induce epithelial host cells to become apoptotic. It is possible that fungal pathogens induce modulation of different host cell pathways in order to evade host defences and to foster their own proliferation. For a number of pathogens, the ability to bind ECM glycoproteins, the capability of internalization and the induction of apoptosis are considered important factors in virulence. Furthermore, specific recognition between fungal parasites and their host cell targets may be mediated by the interaction of carbohydrate-binding proteins, e.g., lectins on the surface of one type of cell, probably a parasite, that combine with complementary sugars on the surface of host-cell. These interactions supply precise models to study putative adhesins and receptor-containing molecules in the context of the fungus-host interface. The recognition of the host molecules by fungi such as Aspergillus fumigatus, Paracoccidioides brasiliensis and Histoplasma capsulatum, and their molecular mechanisms of adhesion and invasion, are reviewed in this paper.