Designing Novel Antitrypanosomal Agents from a Mixed Graph-Theoretical Substructural Approach

Chagas disease is nowadays the most serious parasitic health problem. This disease is caused by Trypanosoma cruzi. The great number of deaths and the insufficient effectiveness of drugs against this parasite have alarmed the scientific community worldwide. In an attempt to overcome this problem, a model for the design and prediction of new antitrypanosomal agents was obtained. This used a mixed approach, containing simple descriptors based on fragments and topological substructural molecular design descriptors. A data set was made up of 188 compounds, 99 of them characterized an antitrypanosomal activity and 88 compounds that belong to other pharmaceutical categories. The model showed sensitivity, specificity and accuracy values above 85%. Quantitative fragmental contributions were also calculated. Then, and to confirm the quality of the model, 15 structures of molecules tested as antitrypanosomal compounds (that we did not include in this study) were predicted, taking into account the information on the abovementioned calculated fragmental contributions. The model showed an accuracy of 100% which means that the ""in silico"" methodology developed by our team is promising for the rational design of new antitrypanosomal drugs. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 882-894. 2010

Three-Dimensional Quantitative Structure-Activity Relationship Study of Antitumor 2-Formylpyridine Thiosemicarbazones Derivatives as Inhibitors of Ribonucleotide Reductase

In order to extend previous SAR and QSAR studies, 3D-QSAR analysis has been performed using CoMFA and CoMSIA approaches applied to a set of 39 alpha-(N)-heterocyclic carboxaldehydes thiosemicarbazones with their inhibitory activity values (IC(50)) evaluated against ribonucleotide reductase (RNR) of H.Ep.-2 cells (human epidermoid carcinoma), taken from selected literature. Both rigid and field alignment methods, taking the unsubstituted 2-formylpyridine thiosemicarbazone in its syn conformation as template, have been used to generate multiple predictive CoMFA and CoMSIA models derived from training sets and validated with the corresponding test sets. Acceptable predictive correlation coefficients (Q(cv)(2) from 0.360 to 0.609 for CoMFA and Q(cv)(2) from 0.394 to 0.580 for CoMSIA models) with high fitted correlation coefficients (r` from 0.881 to 0.981 for CoMFA and r(2) from 0.938 to 0.993 for CoMSIA models) and low standard errors (s from 0.135 to 0.383 for CoMFA and s from 0.098 to 0.240 for CoMSIA models) were obtained. More precise CoMFA and CoMSIA models have been derived considering the subset of thiosemicarbazones (TSC) substituted only at 5-position of the pyridine ring (n=22). Reasonable predictive correlation coefficients (Q(cv)(2) from 0.486 to 0.683 for CoMFA and Q(cv)(2) from 0.565 to 0.791 for CoMSIA models) with high fitted correlation coefficients (r(2) from 0.896 to 0.997 for CoMFA and r(2) from 0.991 to 0.998 for CoMSIA models) and very low standard errors (s from 0.040 to 0.179 for CoMFA and s from 0.029 to 0.068 for CoMSIA models) were obtained. The stability of each CoMFA and CoMSIA models was further assessed by performing bootstrapping analysis. For the two sets the generated CoMSIA models showed, in general, better statistics than the corresponding CoMFA models. The analysis of CoMFA and CoMSIA contour maps suggest that a hydrogen bond acceptor near the nitrogen of the pyridine ring can enhance inhibitory activity values. This observation agrees with literature data, which suggests that the nitrogen pyridine lone pairs can complex with the iron ion leading to species that inhibits RNR. The derived CoMFA and CoMSIA models contribute to understand the structural features of this class of TSC as antitumor agents in terms of steric, electrostatic, hydrophobic and hydrogen bond donor and hydrogen bond acceptor fields as well as to the rational design of this key enzyme inhibitors.

Studies toward the structural optimization of novel thiazolylhydrazone-based potent antitrypanosomal agents

In previous studies, we identified promising anti-Trypanosoma cruzi cruzain inhibitors based on thiazolylhydrazones. To optimize this series, a number of medicinal chemistry directions were explored and new thiazolylhydrazones and thiosemicarbazones were thus synthesized. Potent cruzain inhibitors were identified, such as thiazolylhydrazones 3b and 3j, which exhibited IC(50) of 200-400 nM. Furthermore, molecular docking studies showed concordance with experimentally derived structure-activity relationships (SAR) data. In the course of this work, lead compounds exhibiting in vitro activity against both the epimastigote and trypomastigote forms of T. cruzi were identified and in vivo general toxicity analysis was subsequently performed. Novel SAR were documented, including the importance of the thiocarbonyl carbon attached to the thiazolyl ring and the direct comparison between thiosemicarbazones and thiazolylhydrazones. (C) 2010 Elsevier Ltd. All rights reserved.

Topliss method in the optimization of salicylic acid derivatives as potential antimycobacterial agents

The Topliss method was used to guide a synthetic path in support of drug discovery efforts toward the identification of potent antimycobacterial agents. Salicylic acid and its derivatives, p-chloro, p-methoxy, and m-chlorosalicylic acid, exemplify a series of synthetic compounds whose minimum inhibitory concentrations for a strain of Mycobacterium were determined and compared to those of the reference drug, p-aminosalicylic acid. Several physicochemical descriptors (including Hammett's sigma constant, ionization constant, dipole moment, Hansch constant, calculated partition coefficient, Sterimol-L and -B-4 and molecular volume) were considered to elucidate structure-activity relationships. Molecular electrostatic potential and molecular dipole moment maps were also calculated using the AM1 semi-empirical method. Among the new derivatives, m-chlorosalicylic acid showed the lowest minimum inhibitory concentration. The overall results suggest that both physicochemical properties and electronic features may influence the biological activity of this series of antimycobacterial agents and thus should be considered in designing new p-aminosalicylic acid analogs.

Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid

Tuberculosis made a resurgence in the mid-1980s and now kills approximately 3 million people a year. The re-emergence of tuberculosis as a public health threat, the high susceptibility of HIV-infected persons and the proliferation of multi-drug-resistant strains have created a need to develop new drugs. Shikimate kinase and other enzymes in the shikimate pathway are attractive targets for development of non-toxic antimicrobial agents, herbicides and anti-parasitic drugs, because the pathway is essential in these species whereas it is absent from mammals. The crystal structure of shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid ( shikimate) has been determined at 2.3 Angstrom resolution, clearly revealing the amino-acid residues involved in shikimate binding. This is the first three-dimensional structure of shikimate kinase complexed with shikimate. In MtSK, the Glu61 residue that is strictly conserved in shikimate kinases forms a hydrogen bond and salt bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for shikimate binding. The carboxyl group of shikimate interacts with Arg58, Gly81 and Arg136 and the hydroxyl groups interact with Asp34 and Gly80. The crystal structure of MtSK-MgADP-shikimate will provide crucial information for the elucidation of the mechanism of the shikimate kinase-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.

Cardioplegia using low volumic cardioplegic agents: morphological study in isolated rabbit hearts

INTRODUÇÃO: A solução cardioplégica farmacológica busca eliminar as conseqüências do dano isquêmico, que é o resultado do desbalanço entre a oferta e o consumo de energia durante a parada dos batimentos cardíacos, nas cirurgias cardíacas com circulação extracorpórea. OBJETIVO: Este trabalho avalia experimentalmente as alterações estruturais e ultra-estruturais em coração isolado de coelhos submetidos à parada protegida pela Solução para Cardioplegia de Baixo Volume (SCBV). MÉTODO: O estudo compreendeu um grupo controle e dois grupos experimentais. No grupo I, a parada cardíaca foi obtida pela infusão da SCBV por 2 horas. No grupo II, o experimento foi conduzido da mesma forma até a parada protegida pela SCBV por duas horas, imediatamente procedeu-se à reperfusão com solução oxigenada de Ringer Locke (RL) por uma hora. No grupo controle os corações foram perfundidos com solução oxigenada de RL por duas horas. Após os experimentos, oito amostras de parede lateral do ventrículo esquerdo foram fixadas em formaldeído 10% e glutaraldeído 2,5% para análises histológica e ultra-estrutural. RESULTADOS: As células do miocárdio, fibroblastos e células endoteliais, observadas nos grupos experimentais I e II, apresentaram marginalização da heterocromatina, compactação do nucléolo, alteração na forma das mitocôndrias, compactação das cristas e aumento da densidade da matriz mitocondrial, indicando que tanto a estrutura nuclear quanto a das organelas citoplasmáticas foram alteradas em relação às células do grupo controle. CONCLUSÃO: As modificações estruturais foram decorrentes de uma adaptação fisiológica da célula, não sendo indicativas de oncose ou apoptose, sugerindo, portanto, que a solução cardioplégica utilizada foi eficiente para a preservação das células.

New insights regarding HCV-NS5A structure/function and indication of genotypic differences

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

The X-ray crystallographic structure of the angiogenesis inhibitor angiostatin

Angiogenesis inhibitors have gained much public attention recently as anti-cancer agents and several are currently in clinical trials, including angiostatin (Phase I, Thomas Jefferson University Hospital, Philadelphia, PA). We report here the bowl-shaped structure of angiostatin kringles 1-3, the first multi-kringle structure to be determined. All three kringle lysine-binding sites contain a bound bicine molecule of crystallization while the former of kringle 2 and kringle 3 are cofacial. Moreover, the separation of the kringle 2 and kringle 3 lysiner binding sites is sufficient to accommodate the a-helix of the 30 residue pepticle VEK-30 found in the kringle 2/VEK-30 complex. Together the three kringles produce a central cavity suggestive of a unique domain where they may function in concert. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Bond strengths, degree of conversion of the cement and molecular structure of the adhesive-dentine joint in fibre post restorations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effects of Dimerization on the Structure and Biological Activity of Antimicrobial Peptide Ctx-Ha

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Pt(II) and Ag(I) complexes with acesulfame: Crystal structure and a study of their antitumoral, antimicrobial and antiviral activities

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

Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1

The crystal structures of five new non-electrophilic β-strand-templated thrombin active-site inhibitors have been determined bound to the enzyme. Four co-crystallize with hirugen and inhibitor isomorphously to produce thrombin-hirugen crystals (monoclinic, space group C2), while one co-crystallizes in the hexagonal system, space group P65. A 1,4-substituted cyclohexyl moiety is conserved at the P1 position of all the inhibitors, along with a fused hetero-bicyclic five- and six-membered ring that occupies the P2 site. Amino, amidino and aminoimidazole groups are attached to the cyclohexyl ring for recognition at the S1 specificity site, while benzylsulfonyl and diphenyl groups enhance the binding at the S3 subsite. The cyclohexyl groups at the P1 positions of three of the inhibitors appear to be in the energetically favored chair conformation, while the imidazole-substituted cyclohexyl rings are in a boat conformation. Somewhat unexpectedly, the two cyclohexyl-aminoimidazole groups bind differently in the specificity site; the unique binding of one is heretofore unreported. The other inhibitors generally mimic arginyl binding at S1. This group of inhibitors combines the nonelectrophilicity and selectivity of DAPA-like compounds and the more optimal binding features of the S1-S3 sites of thrombin for peptidic molecules, which results in highly potent (binding constants 12 nM-16 pM, one being 1.1 μM) and selective (ranging from 140 to 20 000 times more selective compared with trypsin) inhibitors of thrombin. The binding modes of these novel inhibitors are correlated with their binding constants, as is their selectivity, in order to provide further insight for the design of therapeutic antithrombotic agents that inhibit thrombin directly at the active site.

Effects of temperature and of the addition of accelerating and retarding agents on the kinetics of hydration of tricalcium silicate

The formation of calcium silicate hydrates (C-S-H) during the hydration of tricalcium silicate (C3S) in pure water and in water solutions containing 1% CaCl2 (accelerator) and 0.01% saccharose (retarder) was studied by small-angle X-ray scattering (SAXS). SAXS measurements were performed under isothermal conditions within the temperature range 25 °C T < 52 °C. The experimental results indicate that the time variation of the mass fraction of the C-S-H product phase, α(f), can be fitted, under all conditions of paste setting, by Avrami equation, α(t) = 1 -exp(-(kt)′), k being a rate parameter and n an exponent depending on the characteristics of the transformation. The parameter n is approximately equal to 2 for hydration of C^S in pure water. Depending on temperature, n varies from 2 to 2.65 for hydration in the presence of CaC^ and saccharose. The value n = 2 is theoretically expected for lateral growth of thin C-S-H plates of constant thickness. The time dependence of SAXS intensity indicates that the transformed phase (C-S-H) consists of colloidal particles in early stages of hydration, evolving by two-dimensional growth toward a disordered lamellar structure composed of very thin plates. The activation energy ΔE for the growth of C-S-H phase was determined from the time dependence of X-ray scattering intensity. These data were obtained by in situ measurements at different temperatures of hydration. The values of ΔE are 37.7, 49.4, and 44.3 kJ/mol for hydration in pure water and in water solutions containing CaCl2 and saccharose, respectively. © 2000 American Chemical Society.

Natural chromenes and chromene derivatives as potential anti-trypanosomal agents

The aim of the study was to investigate the anti-trypanocidal activities of natural chromene and chromene derivatives. Five chromenes were isolated from Piper gaudichaudianum and P. aduncum, and a further seven derivatives were prepared using standard reduction, methylation and acetylation procedures. These compounds were assayed in vitro against epimastigote forms of Trypanosoma cruzi, the causative agent of Chagas disease. The results showed that the most of the compounds, especially those possessing electron-donating groups as substituents on the aromatic ring, showed potent trypanocidal activity. The most active compound, [(2S)-methyl-2-methyl-8-(3″-methylbut-2″-enyl)-2- (4′-methylpent-3′-enyl)-2H-chromene-6-carboxylate], was almost four times more potent than benznidazole (the positive control) and showed an IC 50 of 2.82 μM. The results reveal that chromenes exhibit significant anti-trypanocidal activities and indicate that this class of natural product should be considered further in the development of new and more potent drugs for use in the treatment of Chagas disease. © 2008 Pharmaceutical Society of Japan.

Influence of mineralizer agents on the growth of crystalline CeO 2 nanospheres by the microwave-hydrothermal method

Cystalline ceria (CeO2) nanoparticles have been synthesized by a simple and fast microwave-assisted hydrothermal (MAH) under NaOH, KOH, and NH4OH mineralizers added to a cerium ammonium nitrate aqueous solution. The products were characterized by X-ray powder diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transformed-IR and Raman spectroscopies. Rietveld refinement reveals a cubic structure with a space group Fm3m while infrared data showed few traces of nitrates. Field emission scanning microcopy (FEG-SEM) revealed a homogeneous size distribution of nanometric CeO2 nanoparticles. The MAH process in KOH and NaOH showed most effective to dehydrate the adsorbed water and decrease the hydrogen bonding effect leaving a weakly agglomerated powder of hydrated ceria. TEM micrographs of CeO2 synthesized under MAH conditions reveal particles well-dispersed and homogeneously distributed. The MAH enabled cerium oxide to be synthesized at 100 °C for 8 min. © 2012 Elsevier B.V. All rights reserved.