Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand-Based Virtual Screening (LBVS) and Target-Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled-rank-by-number, rank-by-rank and rank-by-vote, with the most thriving the scaled-rank-by-number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand-based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.

Natural products biological screening and ligand-based virtual screening for the discovery of new antileishmanial agents

In the course of our research program to discover novel antileishmanial agents, a biological screening of natural products against Leishmania major promastigotes allowed the identification of a furoquinoline alkaloid (1) and a furanocoumarin (2) as new hits. Subsequently, an integrated ligand-based virtual screening approach was employed to search for new antileishmanial compounds using these naturally occurring molecules as templates. Fourteen out of 40 compounds selected from a database of about 800,000 compounds (extracted from ZINC, a free database for virtual screening) were experimentally confirmed to possess significant in vitro antileishmanial properties. The application of ligand-based virtual screening as a complementary approach to experimental natural product screening was a useful strategy to facilitate the identification of new promising lead candidates.

Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example

Alzheimer`s disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. 128 BACE-1 inhibitors recently disclosed by GlaxoSmithKline R&D were selected specifically because the crystal structures of 9 of these compounds complexed to BACE-1, as well as five closely related analogs, have been made available. A new fragment-guided approach was designed to incorporate this wealth of structural information into a CoMFA study, and the methodology was systematically compared to other popular approaches, such as docking, for generating a molecular alignment. The influence of the partial charges calculation method was also analyzed. Several consistent and predictive models are reported, including one with r (2) = 0.88, q (2) = 0.69 and r (pred) (2) = 0.72. The models obtained with the new methodology performed consistently better than those obtained by other methodologies, particularly in terms of external predictive power. The visual analyses of the contour maps in the context of the enzyme drew attention to a number of possible opportunities for the development of analogs with improved potency. These results suggest that 3D-QSAR studies may benefit from the additional structural information added by the presented methodology.

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

Based on its essential role in the life cycle of Trypanosoma cruzi, the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH) has been considered a promising target for the development of novel chemotherapeutic agents for the treatment of Chagas` disease. In the course of our research program to discover novel inhibitors of this trypanosomatid enzyme, we have explored a combination of structure and ligand-based virtual screening techniques as a complementary approach to a biochemical screening of natural products using a standard biochemical assay. Seven natural products, including anacardic acids,. avonoid derivatives, and one glucosylxanthone were identified as novel inhibitors of T. cruzi GAPDH. Promiscuous inhibition induced by nonspecific aggregation has been discarded as specific inhibition was not reversed or affected in all cases in the presence of Triton X-100, demonstrating the ability of the assay to find authentic inhibitors of the enzyme. The structural diversity of this series of promising natural products is of special interest in drug design, and should therefore be useful in future medicinal chemistry efforts aimed at the development of new GAPDH inhibitors having increased potency. (C) 2009 Elsevier Ltd. All rights reserved.

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.

Role of Halogen Bonds in Thyroid Hormone Receptor Selectivity: Pharmacophore-Based 3D-QSSR Studies

Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TR alpha and TR beta. Several pharmacological effects mediated by TR beta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TR beta activation may elicit these effects while maintaining an acceptable safety profile, To understand the molecular determinants of affinity and subtype selectivity of TR ligands, we have successfully employed a ligand- and structure-guided pharmacophore-based approach to obtain the molecular alignment of a large series of thyromimetics. Statistically reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models were obtained using the comparative molecular field analysis (CoMFA) method, and the visual analyses of the contour maps drew attention to a number of possible opportunities for the development of analogs with improved affinity and selectivity. Furthermore, the 3D-QSSR analysis allowed the identification of a novel and previously unmentioned halogen bond, bringing new insights to the mechanism of activity and selectivity of thyromimetics.

Calixarene and Resorcarene Based Receptors: From Structural and Thermodynamic Studies to the Synthesis of a New Mercury(II) Selective Material

Materials used in current technological approaches for the removal of mercury lack selectivity. Given that this is one of the main features of supramolecular chemistry, receptors based on calix[4]arene and calix[4]resorcarene containing functional groups able to interact selectively with polluting ions while discriminating against biologically essential ones were designed. Thus two receptors, a partially functionalized calix[4]arene derivative, namely, 5,11,17,23-tetra-tert-butyl [25-27-bis(diethyl thiophosphate amino)dihydroxy] calix[4]arene (1) and a fully functionalized calix[4]resorcarene, 4,6,10,12,16,18,22,24-diethyl thiophosphate calix[4]resorcarene (2) are introduced. Mercury(II) was the identified target due to the environmental and health problems associated with its presence in water Thus following the synthesis and characterization of 1 and 2 in solution ((1)HNMR) and in the solid state (X-ray crystallography) the sequence of experimental events leading to cation complexation studies in acetonitrile and methanol ((1)H NMR, conductance, potentiometric, and calorimetric measurements) with the aim of assessing their behavior as mercury selective receptors are described. The cation selectivity pattern observed in acetonitrile follows the sequence Hg(II) > Cu(II) > Ag(I). In methanol 1 is also selective for Hg(II) relative to Ag(I) but no interaction takes place between this receptor and Cu(II) in this solvent. Based on previous results and experimental facts shown in this paper, it is concluded that the complexation observed with Cu(II) in acetonitrile occurs through the acetonitrile-receptor adduct rather than through the free ligand. Receptor 2 has an enhanced capacity for uptaking Hg(II) but forms metalate complexes with Cu(II). These studies in solution guided the inmobilization of receptor 1 into a silica support to produce a new and recyclable material for the removal of Hg(II) from water. An assessment on its capacity to extract this cation from water relative to Cu(II) and Ag (I) shows that the cation selectivity pattern of the inmobilized receptor is the same as that observed for the free receptor in methanol. These findings demonstrate that fundamental studies play a critical role in the selection of the receptor to be attached to silicates as well as in the reaction medium used for the synthesis of the new decontaminating agent.

Tetrachlorocarbonyliridates: Water-Soluble Carbon Monoxide Releasing Molecules Rate-Modulated by the Sixth Ligand

A new family of compounds is presented as potential carbon monoxide releasing molecules (CORMs). These compounds, based on tetrachlorocarbonyliridate(III) derivatives, were synthesized and fully characterized by X-ray diffraction, electrospray mass spectrometry, IR. NMR, and density functional theory calculations. The rate of CO release was studied via the myoglobin assay. The results showed that the rate depends on the nature of the sixth ligand, trans to CO, and that a significant modulation on the release rate can be produced by changing the ligand. The reported compounds are soluble in aqueous media, and the rates of CO release are comparable with those for known CORMs, releasing CO at a rate of 0.03-0.58 mu M min(-1) in a 10 mu M solution of myoglobin and 10 mu M of the complexes.

Novel electroluminescent devices containing Eu(3+)-(2-acyl-1,3-indandionate) complexes with TPPO ligand

Fabrication and electroluminescent properties of devices containing europium complexes of general formula [Eu(ACIND)(3)(TPPO)(2)], where ACIND, 2-acyl-1,3-indandionate ligands: and TPPO, triphenylphosphine oxide. as emitter layers are discussed. The double-layer devices based on these complexes present the following configurations: device 1: ITO/TPD/[Eu(AlND)(3)(TPPO)(2)]/Al: device 2: ITO/TPD/[Eu(ISOV-IND)(3)(TPPO)(2)]/Al and device 3: ITO/TPD/[Eu(BIND)(3)(TPPO)(2)]/Al, where AlND, 2-acetyl-1,3-indandionate; ISOVIND, 2-isovaleryl-1,3-indandionate; and BIND, 2-benzoyl-1,3-indandionate, respectively. These devices exhibited photo and electroluminescent emissions. An important characteristic presented by devices is that their electroluminescent (EL) spectra, in the region of (5)D(0) -> (7)F(J) (J = 0, 1, 2, 3 and 4) transitions of Eu(3+) ion, show profiles that are different from photoluminescent (PL) ones. In addition to narrow bands arising from intraconfigurational-4f(6) transitions, devices 1 and 2 also exhibited a broad band with maximum at around 500 nm which is assigned to electrophosphorescence from the indandionate ligands. On the other hand, EL spectra of device 3 present only narrow bands from (5)D(0) -> (7)F(J) transitions. [Eu(ACIND)(3)(TPPO)(2)] complexes are promising candidates to prepare efficient organic light-emitting devices (OLEDs) when compared with those containing Eu(3+)-complexes of aliphatic beta-diketonate anions. (C) 2009 Elsevier B.V. All rights reserved.

Photoswitches and Luminescent Rigidity Sensors Based on fac-[Re(CO)(3)(Me(4)phen)(L)](+)

The fac-[Re(CO)(3)(Me(4)phen)(trans-L)](+) complexes, Me(4)phen = 3,4,7,8-tetramethyl-1,10-phenanthroline and L = 4-styrylpyridine, stpy, or 1,2-bis(4-pyridyl)ethylene, bpe, were synthesized and characterized by their spectroscopic, photochemical, and photophysical properties. The complexes exhibit trans-to-cis isomerization upon 313, 334, 365, and 404 nm irradiation, and the true quantum yields can be efficiently determined by absorption changes combined with (1)H NMR data. For fac-[Re(CO)(3)(Me(4)phen)(trans-bpe)](+) similar quantum yields were determined at all wavelengths investigated. However, a lower value (phi(true) = 0.35) was determined for fac-[Re(CO)(3)(Me(4)phen)(trans-stpy)](+) at 404 nm irradiation, which indicates different pathways for the photoisomerization process. The photoproducts, fac-[Re(CO)(3)(Me(4)phen)(cis-L)](+), exhibit luminescence at room temperature with two maxima ascribed to the (3)IL(Me4phen) and (3)MLCT(Re -> Me4phen) excited states. The luminescence properties were investigated in different media, and the behavior in glassy EPA at 77 K showed that the contribution of each emissive state is dependent on the excitation wavelength. The photochemical and photophysical behavior of the complexes were rationalized in terms of the energy gap of excited states and can be exploited in photoswitchable luminescent rigidity sensors.

Triangular ruthenium acetate clusters containing the bis(pyridyl)propane ligand and their inclusion chemistry with beta-cyclodextrin

The triruthenium carboxylate cluster [Ru(3)O(OAc)(6)(py)(2)(bpp)](+) (OAc = acetate) containing the bridging 1,3-bis(4-pyridyl)propane (bpp) ligand, and its dimeric species [{Ru(3)O(OAc)(6)(py(2))}(2)(mu-bpp)](2+) were synthesized in order to investigate their inclusion compounds with beta-cyclodextrin (beta-CD). Characterization of the complexes was carried out based on spectroscopic, electrochemical and spectroelectrochemical techniques, while the formation of inclusion complexes was evaluated using (1)H NMR/NOESY spectroscopy. Since bpp is a flexible ligand, a DFT study was carried out in order to characterize its conformational isomers and their possible role in the host-guest chemistry with beta-CD. Instead of observing the formation of inclusion compounds with different stoichiometries, we observed the formation of 1:1 bpp/beta-CD compounds in which the bpp ligand assumes different conformations. The assembly of polymetallic rotaxane species was successfully demonstrated by monitoring the (1)H NMR spectra of the monomeric cluster species in the presence of aquapentacyanoferrate(II) ions and beta-CD.

New insights on surface-enhanced Raman scattering based on controlled aggregation and spectroscopic studies, DFT calculations and symmetry analysis for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine adsorbed onto citrate-stabilized gold nanoparticles

Asystematic study on the surface-enhanced Raman scattering (SERS) for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine (bptz) adsorbed onto citrate-modified gold nanoparticles (cit-AuNps) was carried out based on electronic and vibrational spectroscopy and density functional methods. The citrate/bptz exchange was carefully controlled by the stepwise addition of bptz to the cit-AuNps, inducing flocculation and leading to the rise of a characteristic plasmon coupling band in the visible region. Such stepwise procedure led to a uniform decrease of the citrate SERS signals and to the rise of characteristic peaks of bptz, consistent with surface binding via the N heterocyclic atoms. In contrast, single addition of a large amount of bptz promoted complete aggregation of the nanoparticles, leading to a strong enhancement of the SERS signals. In this case, from the distinct Raman profiles involved, the formation of a new SERS environment became apparent, conjugating the influence of the local hot spots and charge-transfer (CT) effects. The most strongly enhanced vibrations belong to a(1) and b(2) representations, and were interpreted in terms of the electromagnetic and the CT mechanisms: the latter involving significant contribution of vibronic coupling in the system. Copyright (C) 2010 John Wiley & Sons, Ltd.

Determination of carbaryl in tomato ""in natura"" using an amperometric biosensor based on the inhibition of acetylcholinesterase activity

This work reports the utilization of two methodologies for carbaryl determination in tomatoes. The measurements were carried out using an amperometric biosensor technique based on the inhibition of acetylcholinesterase activity due to carbaryl adsorption and a HPLC procedure. The electrochemical experiments were performed in 0.1 mol L-1 phosphate buffer solutions at pH 7.4 with an incubation time of 8 min. The analytical curve obtained in pure solutions showed excellent linearity in the 5.0 x 10(-5) to 75 x 10(-5) mol L-1 range, with the limit of detection at 0.4 x 10(-3) gL(-1). The application of such a methodology in tomato samples involved solely liquidising the samples, which were spiked with 6.0 x 10(-6) and 5.0 x 10(-5) mol L-1 carbaryl. Recovery in such samples presented values of 99.0 and 92.4%, respectively. In order to obtain a comparison, HPLC experiments were also conducted under similar conditions. However, the tomato samples have to be manipulated by an extraction procedure (MSPD), which yielded much lower recovery values (78.3 and 84.8%, respectively). On the other hand, the detection limit obtained was much lower than that for the biosensor, i.e., 3.2 x 10(-6) g L-1. Finally, the biosensor methodology was employed to analyze carbaryl directly inside the tomato, without any previous manipulation. In this case, the biosensor was immersed in the tomato pulp, which had previously been spiked with the pesticide for 8 min, removed and inserted in the electrochemical cell. A recovery of 83.4% was obtained, showing very low interference of the matrix constituents. (C) 2007 Elsevier B.V. All rights reserved.

The influence of perhydroazepine and piperidine as further ancillary ligands on Ru-PPh(3)-based catalysts for ROMP of norbornene and norbornadiene

Polynorbornadiene and polynorbornene were synthesized via ring opening metathesis polymerization (ROMP) with [RuCl(2)(PPh(3))(2)(amine)] as catalyst precursors, amine = piperidine (1) or perhydroazepine (2) in the presence of 5 mu L of ethyl diazoacetate (EDA) ([monomer]/[Ru] = 5000; 40 degrees C with 1; 25 degrees C with 2). The effects of the solvent volume (2-8 mL of CHCl(3)) reaction time (5-120 min) and atmosphere type (argon and air) on the yields were investigated to observe the behavior of the two different precursors. Quantitative yields were obtained for 60 or 120 min regardless of the starting volumes, either in argon or air, with both Ru species. However, low yields were obtained for short times (5-30 min) when the reactions are performed with large volumes (6-8 mL). In argon, the yields were larger with 2, associated to a faster propagation reaction controlled by the Ru active species. In air, the yields were larger with 1, associated to a higher resistance to O(2) of the starting and propagating Ru species. The different activities between 1 and 2 are discussed considering the steric hindrance and electronic characteristics of the amines such as ancillary ligands and their arrangements with PPh(3) and Cl(-) ions in the metal centers. (c) 2009 Elsevier B.V. All rights reserved.