Desenvolupament computacional de la semblança molecular quàntica

La present Tesi Doctoral, titulada desenvolupament computacional de la semblança molecular quàntica, tracta, fonamentalment, els aspectes de càlcul de mesures de semblança basades en la comparació de funcions de densitat electrònica.El primer capítol, Semblança quàntica, és introductori. S'hi descriuen les funcions de densitat de probabilitat electrònica i llur significança en el marc de la mecànica quàntica. Se n'expliciten els aspectes essencials i les condicions matemàtiques a satisfer, cara a una millor comprensió dels models de densitat electrònica que es proposen. Hom presenta les densitats electròniques, mencionant els teoremes de Hohenberg i Kohn i esquematitzant la teoria de Bader, com magnituds fonamentals en la descripció de les molècules i en la comprensió de llurs propietats.En el capítol Models de densitats electròniques moleculars es presenten procediments computacionals originals per l'ajust de funcions densitat a models expandits en termes de gaussianes 1s centrades en els nuclis. Les restriccions físico-matemàtiques associades a les distribucions de probabilitat s'introdueixen de manera rigorosa, en el procediment anomenat Atomic Shell Approximation (ASA). Aquest procediment, implementat en el programa ASAC, parteix d'un espai funcional quasi complert, d'on se seleccionen variacionalment les funcions o capes de l'expansió, d'acord als requisits de no negativitat. La qualitat d'aquestes densitats i de les mesures de semblança derivades es verifica abastament. Aquest model ASA s'estén a representacions dinàmiques, físicament més acurades, en quant que afectades per les vibracions nuclears, cara a una exploració de l'efecte de l'esmorteïment dels pics nuclears en les mesures de semblança molecular. La comparació de les densitats dinàmiques respecte les estàtiques evidencia un reordenament en les densitats dinàmiques, d'acord al que constituiria una manifestació del Principi quàntic de Le Chatelier. El procediment ASA, explícitament consistent amb les condicions de N-representabilitat, s'aplica també a la determinació directe de densitats electròniques hidrogenoides, en un context de teoria del funcional de la densitat.El capítol Maximització global de la funció de semblança presenta algorismes originals per la determinació de la màxima sobreposició de les densitats electròniques moleculars. Les mesures de semblança molecular quàntica s'identifiquen amb el màxim solapament, de manera es mesuri la distància entre les molècules, independentment dels sistemes de referència on es defineixen les densitats electròniques. Partint de la solució global en el límit de densitats infinitament compactades en els nuclis, es proposen tres nivells de aproximació per l'exploració sistemàtica, no estocàstica, de la funció de semblança, possibilitant la identificació eficient del màxim global, així com també dels diferents màxims locals. Es proposa també una parametrització original de les integrals de recobriment a través d'ajustos a funcions lorentzianes, en quant que tècnica d'acceleració computacional. En la pràctica de les relacions estructura-activitat, aquests avenços possibiliten la implementació eficient de mesures de semblança quantitatives, i, paral·lelament, proporcionen una metodologia totalment automàtica d'alineació molecular. El capítol Semblances d'àtoms en molècules descriu un algorisme de comparació dels àtoms de Bader, o regions tridimensionals delimitades per superfícies de flux zero de la funció de densitat electrònica. El caràcter quantitatiu d'aquestes semblances possibilita la mesura rigorosa de la noció química de transferibilitat d'àtoms i grups funcionals. Les superfícies de flux zero i els algorismes d'integració usats han estat publicats recentment i constitueixen l'aproximació més acurada pel càlcul de les propietats atòmiques. Finalment, en el capítol Semblances en estructures cristal·lines hom proposa una definició original de semblança, específica per la comparació dels conceptes de suavitat o softness en la distribució de fonons associats a l'estructura cristal·lina. Aquests conceptes apareixen en estudis de superconductivitat a causa de la influència de les interaccions electró-fonó en les temperatures de transició a l'estat superconductor. En aplicar-se aquesta metodologia a l'anàlisi de sals de BEDT-TTF, s'evidencien correlacions estructurals entre sals superconductores i no superconductores, en consonància amb les hipòtesis apuntades a la literatura sobre la rellevància de determinades interaccions.Conclouen aquesta tesi un apèndix que conté el programa ASAC, implementació de l'algorisme ASA, i un capítol final amb referències bibliogràfiques.

Molecular quantum similarity in QSAR: applications in computer-aided molecular design

La present tesi està centrada en l'ús de la Teoria de Semblança Quàntica per a calcular descriptors moleculars. Aquests descriptors s'utilitzen com a paràmetres estructurals per a derivar correlacions entre l'estructura i la funció o activitat experimental per a un conjunt de compostos. Els estudis de Relacions Quantitatives Estructura-Activitat són d'especial interès per al disseny racional de molècules assistit per ordinador i, en particular, per al disseny de fàrmacs. Aquesta memòria consta de quatre parts diferenciades. En els dos primers blocs es revisen els fonaments de la teoria de semblança quàntica, així com l'aproximació topològica basada en la teoria de grafs. Ambdues teories es fan servir per a calcular els descriptors moleculars. En el segon bloc, s'ha de remarcar la programació i implementació de programari per a calcular els anomenats índexs topològics de semblança quàntica. La tercera secció detalla les bases de les Relacions Quantitatives Estructura-Activitat i, finalment, el darrer apartat recull els resultats d'aplicació obtinguts per a diferents sistemes biològics.

Unravelling the conundrum of tannins in animal nutrition and health

This paper examines the nutritional and veterinary effects of tannins on ruminants and makes some comparisons with non-ruminants. Tannin chemistry per se is not covered and readers are referred to several excellent reviews instead: (a) Okuda T et al. Heterocycles 30:1195-1218 (1990); (b) Ferreira D and Slade D. Nat Prod Rep 19:517-541 (2002); (c) Yoshida T et al. In Studies in Natural Product Chemistry. Elsevier Science, Amsterdam, pp. 395-453 (2000); (d) Khanbabaee K and van Ree T. Nat Prod Rep 18:641-649 (2001); (e) Okuda et al. Phytochemistvy 55:513-529 (2000). The effects of tannins on rumen micro-organisms are also not reviewed, as these have been addressed by others: (a) McSweeney CS et al. Anim Feed Sci Technol 91:83-93 (2001); (b) Smith AH and Mackie RI. Appl Environ Microbiol 70:1104-1115 (2004). This paper deals first with the nutritional effects of tannins in animal feeds, their qualitative and quantitative diversity, and the implications of tannin-protein complexation. It then summarises the known physiological and harmful effects and discusses the equivocal evidence of the bioavailability of tannins. Issues concerning tannin metabolism and systemic effects are also considered. Opportunities are presented on how to treat feeds with high tannin contents, and some lesser-known but successful feeding strategies are highlighted. Recent research has explored the use of tannins for preventing animal deaths from bloat, for reducing intestinal parasites and for lowering gaseous ammonia and methane emissions. Finally, several tannin assays and a hypothesis are discussed that merit further investigation in order to assess their suitability for predicting animal responses. The aim is to provoke discussion and spur readers into new approaches. An attempt is made to synthesise the emerging information for relating tannin structures with their activities. Although many plants with high levels of tannins produce negative effects and require treatments, others are very useful animal feeds. Our ability to predict whether tannin-containing feeds confer positive or negative effects will depend on interdisciplinary research between animal nutritionists and plant chemists. The elucidation of tannin structure-activity relationships presents exciting opportunities for future feeding strategies that will benefit ruminants and the environment within the contexts of extensive, semi-intensive and some intensive agricultural systems. (c) 2006 Society of Chemical Industry

Unravelling the conundrum of tannins in animal nutrition and health

This paper examines the nutritional and veterinary effects of tannins on ruminants and makes some comparisons with non-ruminants. Tannin chemistry per se is not covered and readers are referred to several excellent reviews instead: (a) Okuda T et al. Heterocycles 30:1195-1218 (1990); (b) Ferreira D and Slade D. Nat Prod Rep 19:517-541 (2002); (c) Yoshida T et al. In Studies in Natural Product Chemistry. Elsevier Science, Amsterdam, pp. 395-453 (2000); (d) Khanbabaee K and van Ree T. Nat Prod Rep 18:641-649 (2001); (e) Okuda et al. Phytochemistvy 55:513-529 (2000). The effects of tannins on rumen micro-organisms are also not reviewed, as these have been addressed by others: (a) McSweeney CS et al. Anim Feed Sci Technol 91:83-93 (2001); (b) Smith AH and Mackie RI. Appl Environ Microbiol 70:1104-1115 (2004). This paper deals first with the nutritional effects of tannins in animal feeds, their qualitative and quantitative diversity, and the implications of tannin-protein complexation. It then summarises the known physiological and harmful effects and discusses the equivocal evidence of the bioavailability of tannins. Issues concerning tannin metabolism and systemic effects are also considered. Opportunities are presented on how to treat feeds with high tannin contents, and some lesser-known but successful feeding strategies are highlighted. Recent research has explored the use of tannins for preventing animal deaths from bloat, for reducing intestinal parasites and for lowering gaseous ammonia and methane emissions. Finally, several tannin assays and a hypothesis are discussed that merit further investigation in order to assess their suitability for predicting animal responses. The aim is to provoke discussion and spur readers into new approaches. An attempt is made to synthesise the emerging information for relating tannin structures with their activities. Although many plants with high levels of tannins produce negative effects and require treatments, others are very useful animal feeds. Our ability to predict whether tannin-containing feeds confer positive or negative effects will depend on interdisciplinary research between animal nutritionists and plant chemists. The elucidation of tannin structure-activity relationships presents exciting opportunities for future feeding strategies that will benefit ruminants and the environment within the contexts of extensive, semi-intensive and some intensive agricultural systems. (c) 2006 Society of Chemical Industry

The extrapolation problem and how population modeling can help

We argue that population modeling can add value to ecological risk assessment by reducing uncertainty when extrapolating from ecotoxicological observations to relevant ecological effects. We review other methods of extrapolation, ranging from application factors to species sensitivity distributions to suborganismal (biomarker and "-omics'') responses to quantitative structure activity relationships and model ecosystems, drawing attention to the limitations of each. We suggest a simple classification of population models and critically examine each model in an extrapolation context. We conclude that population models have the potential for adding value to ecological risk assessment by incorporating better understanding of the links between individual responses and population size and structure and by incorporating greater levels of ecological complexity. A number of issues, however, need to be addressed before such models are likely to become more widely used. In a science context, these involve challenges in parameterization, questions about appropriate levels of complexity, issues concerning how specific or general the models need to be, and the extent to which interactions through competition and trophic relationships can be easily incorporated.

AT(1) receptor ligands: virtual-screening-based design with TOPP descriptors, synthesis, and biological evaluation of pyrrolidine derivatives

As a continuing effort to establish the structure-activity relationships (SARs) within the series of the angiotensin II antagonists (sartans), a pharmacophoric model was built by using novel TOPP 3D descriptors. Statistical values were satisfactory (PC4: r(2)=0.96, q(2) ((5) (random) (groups))=0.84; SDEP=0.26) and encouraged the synthesis and consequent biological evaluation of a series of new pyrrolidine derivatives. SAR together with a combined 3D quantitative SAR and high-throughput virtual screening showed that the newly synthesized 1-acyl-N-(biphenyl-4-ylmethyl)pyrrolidine-2-carboxamides may represent an interesting starting point for the design of new antihypertensive agents. In particular, biological tests performed on CHO-hAT(1) cells stably expressing the human AT(1) receptor showed that the length of the acyl chain is crucial for the receptor interaction and that the valeric chain is the optimal one.

Diverse signalling by different chemokines through the chemokine receptor CCR5

We have investigated the signalling properties of the chemokine receptor, CCR5, using several assays for agonism: stimulation of changes in intracellular Ca2+ or CCR5 internalisation in CHO cells expressing CCR5 or stimulation of [S-35]GTP gamma S binding in membranes of CHO cells expressing CCR5. Four isoforms of the chemokine CCL3 with different amino termini (CCL3, CCL3(2-70), CCL3(5-70), CCL3L1) were tested in these assays in order to probe structure/activity relationships. Each isoform exhibited agonism. The pattern of agonism (potency, maximal effect) was different in the three assays, although the rank order was the same with CCL3L1 being the most potent and efficacious. The data show that the amino terminus of the chemokine is important for signalling. A proline at position 2 (CCL3L1) provides for high potency and efficacy but the isoform with a serine at position 2 (CCL3(2-70)) is as efficacious in some assays showing that the proline is not the only determinant of high efficacy. We also increased the sensitivity of CCR5 signalling by treating cells with sodium butyrate, thus increasing the receptor/G protein ratio. This allowed the detection of a change in intracellular Ca2+ after treatment with CCL7 and Met-RANTES showing that these ligands possess measurable but low efficacy. This study therefore shows that sodium butyrate treatment increases the sensitivity of signalling assays and enables the detection of efficacy in ligands previously considered as antagonists. The use of different assay systems, therefore, provides different estimates of efficacy for some ligands at this receptor. (c) 2006 Elsevier Inc. All rights reserved.

Development and application of diazirines in biological and synthetic macromolecular systems

Many different reagents and methodologies have been utilised for the modification of synthetic and biological macromolecular systems. In addition, an area of intense research at present is the construction of hybrid biosynthetic polymers, comprised of biologically active species immobilised or complexed with synthetic polymers. One of the most useful and widely applicable techniques available for functionalisation of macromolecular systems involves indiscriminate carbene insertion processes. The highly reactive and non-specific nature of carbenes has enabled a multitude of macromolecular structures to be functionalised without the need for specialised reagents or additives. The use of diazirines as stable carbene precursors has increased dramatically over the past twenty years and these reagents are fast becoming the most popular photophors for photoaffinity labelling and biological applications in which covalent modification of macromolecular structures is the basis to understanding structure-activity relationships. This review reports the synthesis and application of a diverse range of diazirines in macromolecular systems.

QSAR studies of multidentate nitrogen ligands used in lanthanide and actinide extraction processes

Quantitative structure activity relationships (QSARs) have been developed to optimise the choice of nitrogen heterocyclic molecules that can be used to separate the minor actinides such as americium(III) from europium(III) in the aqueous PUREX raffinate of nuclear waste. Experimental data on distribution coefficients and separation factors (SFs) for 47 such ligands have been obtained and show SF values ranging from 0.61 to 100. The ligands were divided into a training set of 36 molecules to develop the QSAR and a test set of 11 molecules to validate the QSAR. Over 1500 molecular descriptors were calculated for each heterocycle and the Genetic Algorithm was used to select the most appropriate for use in multiple regression equations. Equations were developed fitting the separation factors to 6-8 molecular descriptors which gave r(2) values of >0.8 for the training set and values of >0.7 for the test set, thus showing good predictive quality. The descriptors used in the equations were primarily electronic and steric. These equations can be used to predict the separation factors of nitrogen heterocycles not yet synthesised and/or tested and hence obtain the most efficient ligands for lanthanide and actinide separation. (C) 2003 Elsevier B.V. All rights reserved.

Characterization of protein-polyphenol interactions

Dietary polyphenols have received attention for their biologically significant functions as antioxidants, anticarcinogens or antimutagens, which have led to their recognition as potential nutraceuticals. Polyphenols also characteristically possess a significant binding affinity for proteins, which can lead to the formation of soluble and insoluble protein-polyphenol complexes. Questions remain concerning whether and to what extent the protein-polyphenol interaction influences functionality. For example, is the formation of protein-polyphenol complexes an obstacle to the nutritional bioavailability of either species? This article discusses the development of suitable methodologies to investigate the physicochemical basis of protein-polyphenol interactions and the influence of structure-activity relationships on binding affinities. (C) 2003 Elsevier Ltd. All rights reserved.

Lethality of essential oil constituents towards the human louse, Pediculus humanus, and its eggs

Essential oils have been widely used in traditional medicine for the eradication of lice, including head lice, but due to the variability of their constitution the effects may not be reproducible. In an attempt to assess the contribution of their component monoterpenoids, a range of common individual compounds were tested in in vitro toxicity model against both human lice (Pediculus humanus, an accepted model of head lice lethality) and their eggs, at different concentrations. No detailed study into the relative potencies of their constituent terpenoids has so far been published. Adult lice were observed for lack of response to stimuli over 3 h and the LT50 calculated, and the percentage of eggs failing to hatch was used to generate ovicidal activity data. A ranking was compiled for adult lice and partially for eggs, enabling structure-activity relationships to be assessed for lethality to both, and showed that, for activity in both life-cycle stages, different structural criteria were required. (+)-Terpinen-4-ol was the most effective compound against adult lice, followed by other mono-oxygenated monocyclic compounds, whereas nerolidol was particularly lethal to eggs, but ineffective against adult lice. (c) 2006 Elsevier B.V. All rights reserved.

Diverse signalling by different chemokines through the chemokine receptor CCR5

We have investigated the signalling properties of the chemokine receptor, CCR5, using several assays for agonism: stimulation of changes in intracellular Ca(2+) or CCR5 internalisation in CHO cells expressing CCR5 or stimulation of [(35)S]GTPgammaS binding in membranes of CHO cells expressing CCR5. Four isoforms of the chemokine CCL3 with different amino termini (CCL3, CCL3(2-70), CCL3(5-70), CCL3L1) were tested in these assays in order to probe structure/activity relationships. Each isoform exhibited agonism. The pattern of agonism (potency, maximal effect) was different in the three assays, although the rank order was the same with CCL3L1 being the most potent and efficacious. The data show that the amino terminus of the chemokine is important for signalling. A proline at position 2 (CCL3L1) provides for high potency and efficacy but the isoform with a serine at position 2 (CCL3(2-70)) is as efficacious in some assays showing that the proline is not the only determinant of high efficacy. We also increased the sensitivity of CCR5 signalling by treating cells with sodium butyrate, thus increasing the receptor/G protein ratio. This allowed the detection of a change in intracellular Ca(2+) after treatment with CCL7 and Met-RANTES showing that these ligands possess measurable but low efficacy. This study therefore shows that sodium butyrate treatment increases the sensitivity of signalling assays and enables the detection of efficacy in ligands previously considered as antagonists. The use of different assay systems, therefore, provides different estimates of efficacy for some ligands at this receptor.

Classical and hologram QSAR studies on a series of inhibitors of trypanosomatid Glyceraldehyde-3-Phosphate Dehydrogenase

Leishmaniasis and trypanosomiasis are major causes of morbidity and mortality in both tropical and subtropical regions of the world. The current available drugs are limited, ineffective, and require long treatment regimens. Due to the high dependence of trypanosomatids on glycolysis as a source of energy, some glycolytic enzymes have been identified as attractive targets for drug design. In the present work, classical Two-Dimensional Quantitative Structure -Activity Relationships (2D QSAR) and Hologram QSAR (HQSAR) studies were performed on a series of adenosine derivatives as inhibitors of Leishmania mexicana Glyceraldehyde-3-Phosphate Dehydrogenase (LmGAPDH). Significant correlation coefficients (classical QSAR, r(2)=0.83 and q(2) =0.81; HQSAR, r(2)=0.91 and q(2) =0.86) were obtained for the 56 training set compounds, indicating the potential of the models for untested compounds. The models were then externally validated using a test set of 14 structurally related compounds and the predicted values were in good agreement with the experimental results (classical QSAR, r(pred)(2) = 0.94; HQSAR, r(pred)(2) = 0.92).

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.

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.