Polyglutamine monomer structure and its implications for molecular self-assembly

Polyglutamine is a naturally occurring peptide found within several proteins in neuronal cells of the brain, and its aggregation has been implicated in several neurodegenerative diseases, including Huntington's disease. The resulting aggregates have been demonstrated to possess ~-sheet structure, and aggregation has been shown to start with a single misfolded peptide. The current project sought to computationally examine the structural tendencies of three mutant poly glutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing, and were analyzed quantitatively by various geometry- and energy-based methods. According to the results, the experimentally-observed inhibition of aggregation appears to be due to localized conformational restraint placed on the peptide backbone by inserted prolines, which in tum confines the peptide to native coil structure, discouraging transition towards the ~sheet structure required for aggregation. Such knowledge could prove quite useful to the design of future treatments for Huntington's and other related diseases.

Development of a Blood Antigen Molecular Profiling Panel using Genotyping Technologies for Patients Requiring Frequent Transfusions

Contexte. Les phénotypes ABO et Rh(D) des donneurs de sang ainsi que des patients transfusés sont analysés de façon routinière pour assurer une complète compatibilité. Ces analyses sont accomplies par agglutination suite à une réaction anticorps-antigènes. Cependant, pour des questions de coûts et de temps d’analyses faramineux, les dons de sang ne sont pas testés sur une base routinière pour les antigènes mineurs du sang. Cette lacune peut résulter à une allo-immunisation des patients receveurs contre un ou plusieurs antigènes mineurs et ainsi amener des sévères complications pour de futures transfusions. Plan d’étude et Méthodes. Pour ainsi aborder le problème, nous avons produit un panel génétique basé sur la technologie « GenomeLab _SNPstream» de Beckman Coulter, dans l’optique d’analyser simultanément 22 antigènes mineurs du sang. La source d’ADN provient des globules blancs des patients préalablement isolés sur papiers FTA. Résultats. Les résultats démontrent que le taux de discordance des génotypes, mesuré par la corrélation des résultats de génotypage venant des deux directions de l’ADN, ainsi que le taux d’échec de génotypage sont très bas (0,1%). Également, la corrélation entre les résultats de phénotypes prédit par génotypage et les phénotypes réels obtenus par sérologie des globules rouges et plaquettes sanguines, varient entre 97% et 100%. Les erreurs expérimentales ou encore de traitement des bases de données ainsi que de rares polymorphismes influençant la conformation des antigènes, pourraient expliquer les différences de résultats. Cependant, compte tenu du fait que les résultats de phénotypages obtenus par génotypes seront toujours co-vérifiés avant toute transfusion sanguine par les technologies standards approuvés par les instances gouvernementales, les taux de corrélation obtenus sont de loin supérieurs aux critères de succès attendus pour le projet. Conclusion. Le profilage génétique des antigènes mineurs du sang permettra de créer une banque informatique centralisée des phénotypes des donneurs, permettant ainsi aux banques de sang de rapidement retrouver les profiles compatibles entre les donneurs et les receveurs.

Novel molecular mechanisms of neuronal and vascular protection in experimental glaucoma

Le glaucome est la deuxième cause de cécité irréversible dans le monde. La perte de vision qui se produit lors du glaucome s’explique par une dégénérescence du nerf optique et une mort progressive et sélective des cellules ganglionnaires de la rétine (CRG). L'hypertension oculaire est un facteur de risque majeur dans le glaucome, mais des défauts du champ visuel continuent à se développer chez un contingent de patients malgré l'administration de médicaments qui abaissent la pression intraoculaire (PIO). Par conséquent, bien que la PIO représente le seul facteur de risque modifiable dans le développement du glaucome, son contrôle ne suffit pas à protéger les CRGs et préserver la fonction visuelle chez de nombreux patients. Dans ce contexte, j'ai avancé l'hypothèse centrale voulant que les stratégies de traitement du glaucome visant à promouvoir la protection structurale et fonctionnelle des CRGs doivent agir sur les mécanismes moléculaires qui conduisent à la mort des ces neurones. Dans la première partie de ma thèse, j'ai caractérisé l'effet neuroprotecteur de la galantamine, un inhibiteur de l'acétylcholinestérase qui est utilisé cliniquement dans le traitement de la maladie d'Alzheimer. Cette étude s’est basée sur l'hypothèse que la galantamine, en modulant l'activité du récepteur de l'acétylcholine, puisse améliorer la survie des CRGs lors du glaucome. Nous avons utilisé un modèle expérimental bien caractérisé d'hypertension oculaire induite par l’administration d'une solution saline hypertonique dans une veine épisclérale de rats Brown Norway. Les résultats de cette étude (Almasieh et al. Cell Death and Disease, 2010) ont démontré que l'administration quotidienne de galantamine améliore de manière significative la survie des corps cellulaires et des axones CRGs. La protection structurelle des CRGs s’accompagne d’une préservation remarquable de la fonction visuelle, évaluée par l'enregistrement des potentiels évoqués visuels (PEV) dans le collicule supérieur, la cible principale des CRGs chez le rongeur. Une autre constatation intéressante de cette étude est la perte substantielle de capillaires rétiniens et la réduction du débit sanguin associé à la perte des CRGs dans le glaucome expérimental. Il est très intéressant que la galantamine ait également favorisé la protection de la microvascularisation et amélioré le débit sanguin rétinien des animaux glaucomateux (Almasieh et al. en préparation). J'ai notamment démontré que les neuro-et vasoprotections médiées par la galantamine se produisent par iv l'activation des récepteurs muscariniques de l'acétylcholine. Dans la deuxième partie de ma thèse, j'ai étudié le rôle du stress oxydatif ainsi que l'utilisation de composés réducteurs pour tester l'hypothèse que le blocage d'une augmentation de superoxyde puisse retarder la mort des CRG lors du glaucome expérimental. J'ai profité d'un composé novateur, un antioxydant à base de phosphineborane (PB1), pour tester sur son effet neuroprotecteur et examiner son mécanisme d'action dans le glaucome expérimental. Les données démontrent que l'administration intraoculaire de PB1 entraîne une protection significative des corps cellulaire et axones des CRGs. Les voies moléculaires conduisant à la survie neuronale médiée par PB1 ont été explorées en déterminant la cascade de signalisation apoptotique en cause. Les résultats démontrent que la survie des CRGs médiée par PB1 ne dépend pas d’une inhibition de signalisation de protéines kinases activées par le stress, y compris ASK1, JNK ou p38. Par contre, PB1 induit une augmentation marquée des niveaux rétiniens de BDNF et une activation en aval de la voie de survie des ERK1 / 2 (Almasieh et al. Journal of Neurochemistry, 2011). En conclusion, les résultats présentés dans cette thèse contribuent à une meilleure compréhension des mécanismes pathologiques qui conduisent à la perte de CRGs dans le glaucome et pourraient fournir des pistes pour la conception de nouvelles stratégies neuroprotectrices et vasoprotectrices pour le traitement et la gestion de cette maladie.

Molecular Networks Created by Charge-Assisted Hydrogen Bonds Between Bis(aminidinium) Cations and Carboxylates, Sulfonates, Phosphonates and Phosphates

L'objectif de cette étude est d'apprendre à créer de nouveaux matériaux moléculaires par design. À l'heure actuelle, il n'existe aucune méthode générale pour la prédiction des structures et des propriétés, mais des progrès importants ont été accomplis, en particulier dans la fabrication de matériaux moléculaires ordonnés tels que des cristaux. En ces matériaux, l'organisation peut être contrôlée efficacement par la stratégie de la tectonique moléculaire. Cette approche utilise des molécules appelées “tectons”, qui peuvent s’associer de manière dirigée par des interactions non covalentes prévisibles. De cette façon, la position de chaque molécule par rapport à ses voisins peut être programmée avec un degré élevé de fiabilité pour créer des cristaux et d'autres matériaux organisés avec des caractéristiques et des propriétés structurelles souhaitables. Le travail que nous allons décrire est axé sur l'utilisation de l'association des cations bis(aminidinium) avec des carboxylates, sulfonates, phosphonates et phosphates, afin de créer des réseaux moléculaires prévisibles. Ces réseaux promettent d'être particulièrement robuste, car ils sont maintenus ensemble par de multiples liaisons hydrogène assistées par des interactions électrostatiques.

Synthesis of dimethyl acetal of ketones: design of solid acid catalysts for one-pot acetalization reaction

The synthesis of dimethyl acetals of carbonyl compounds such as cyclohexanone, acetophenone, and benzophenone has successfully been carried out by the reaction between ketones and methanol using different solid acid catalysts. The strong influence of the textural properties of the catalysts such as acid amount and adsorption properties (surface area and pore volume) determine the catalytic activity. The molecular size of the reactants and products determine the acetalization ability of a particular ketone. The hydrophobicity of the various rare earth exchanged Mg–Y zeolites, K-10 montmorillonite clay, and cerium exchanged montmorillonite (which shows maximum activity) is more determinant than the number of active sites present on the catalyst. The optimum number of acidic sites as well as dehydrating ability of Ce3+-montmorillonite and K-10 montmorillonite clays and various rare earth exchanged Mg–Y zeolites seem to work well in shifting the equilibrium to the product side.

Phenylethynylarene Based Donor-Acceptor Systems: Design, Synthesis and Photophysical Studies

This thesis Entitled phenylethynylarene based Donor-Acceptor systems:Desigh,Synthesis and Photophysical studies. A strategy for the design of donor-acceptor dyads, wherein decay of the charge separated (CS) state to low lying local triplet levels could possibly be prevented, is proposed. In order to examine this strategy, a linked donor-acceptor dyad BPEPPT with bis(phenylethYlly/)pyrene (BPEP) as the light absorber and acceptor and phenothiazine (PT) as donor was designed and photoinduced electron transfer in the dyad investigated. Absorption spectra of the dyad can be obtained by adding contributions due 10 the BPEP and PT moieties indicating that the constituents do not interact in the ground stale. Fluorescence of the BPEP moiety was efficiently quenched by the PT donor and this was attributed to electron lransfer from PT to BPEP. Picosecond transient absorption studies suggested formation of a charge separated state directly from the singlet excited state of BPEP. Nanosecond flash photolysis experiments gave long-ived transient absorptions assignable to PT radical cation and BPEP radical anion. These assignments were confirmed by oxygen quenching studies and secondary electron transfer experiments. Based on the available data, energy level diagram for BPEP-PT was constructed. The long lifetime of the charge separated state was attributed to the inverted region effects. The CS state did not undergo decay to low lying BPEP triplet indicating the success of our strategy

Design Of Metal Architectures: Synthesis And Study Of Their Photophysical And Biomolecular Recognition Properties

Design and study of molecular receptors capable of mimicking natural processes has found applications in basic research as well as in the development of potentially useful technologies. Of the various receptors reported, the cyclophanes are known to encapsulate guest molecules in their cavity utilizing various non–covalent interactions resulting in significant changes in their optical properties. This unique property of the cyclophanes has been widely exploited for the development of selective and sensitive probes for a variety of guest molecules including complex biomolecules. Further, the incorporation of metal centres into these systems added new possibilities for designing receptors such as the metallocyclophanes and transition metal complexes, which can target a large variety of Lewis basic functional groups that act as selective synthetic receptors. The ligands that form complexes with the metal ions, and are capable of further binding to Lewis-basic substrates through open coordination sites present in various biomolecules are particularly important as biomolecular receptors. In this context, we synthesized a few anthracene and acridine based metal complexes and novel metallocyclophanes and have investigated their photophysical and biomolecular recognition properties.

Extracellular β-glucosidase Production by a Marine Aspergillus sydowii BTMFS 55 under Solid State Fermentation Using Statistical Experimental Design

A potential fungal strain producing extracellular β-glucosidase enzyme was isolated from sea water and identified as ^ëéÉêJ Öáääìë=ëóÇçïáá BTMFS 55 by a molecular approach based on 28S rDNA sequence homology which showed 93% identity with already reported sequences of ^ëéÉêÖáääìë=ëóÇçïáá in the GenBank. A sequential optimization strategy was used to enhance the production of β-glucosidase under solid state fermentation (SSF) with wheat bran (WB) as the growth medium. The two-level Plackett-Burman (PB) design was implemented to screen medium components that influence β-glucosidase production and among the 11 variables, moisture content, inoculums, and peptone were identified as the most significant factors for β-glucosidase production. The enzyme was purified by (NH4)2SO4 precipitation followed by ion exchange chromatography on DEAE sepharose. The enzyme was a monomeric protein with a molecular weight of ~95 kDa as determined by SDS-PAGE. It was optimally active at pH 5.0 and 50°C. It showed high affinity towards éNPG and enzyme has a hã and sã~ñ of 0.67 mM and 83.3 U/mL, respectively. The enzyme was tolerant to glucose inhibition with a há of 17 mM. Low concentration of alcohols (10%), especially ethanol, could activate the enzyme. A considerable level of ethanol could produce from wheat bran and rice straw after 48 and 24 h, respectively, with the help of p~ÅÅÜ~êçãóÅÉë=ÅÉêÉîáëá~É in presence of cellulase and the purified β-glucosidase of ^ëéÉêÖáääìë=ëóÇçïáá BTMFS 55.

Design and study of self-assembled functional organic and hybrid systems for biological applications

The focus of self-assembly as a strategy for the synthesis has been confined largely to molecules, because of the importance of manipulating the structure of matter at the molecular scale. We have investigated the influence of temperature and pH, in addition to the concentration of the capping agent used for the formation of the nano-bio conjugates. For example, the formation of the narrower size distribution of the nanoparticles was observed with the increase in the concentration of the protein, which supports the fact that γ-globulin acts both as a controller of nucleation as well as stabiliser. As analyzed through various photophysical, biophysical and microscopic techniques such as TEM, AFM, C-AFM, SEM, DLS, OPM, CD and FTIR, we observed that the initial photoactivation of γ-globulin at pH 12 for 3 h resulted in small protein fibres of ca. Further irradiation for 24 h, led to the formation of selfassembled long fibres of the protein of ca. 5-6 nm and observation of surface plasmon resonance band at around 520 nm with the concomitant quenching of luminescence intensity at 680 nm. The observation of light triggered self-assembly of the protein and its effect on controlling the fate of the anchored nanoparticles can be compared with the naturally occurring process such as photomorphogenesis.Furthermore,our approach offers a way to understand the role played by the self-assembly of the protein in ordering and knock out of the metal nanoparticles and also in the design of nano-biohybrid materials for medicinal and optoelectronic applications. Investigation of the potential applications of NIR absorbing and water soluble squaraine dyes 1-3 for protein labeling and anti-amyloid agents forms the subject matter of the third chapter of the thesis. The study of their interactions with various proteins revealed that 1-3 showed unique interactions towards serum albumins as well as lysozyme. 69%, 71% and 49% in the absorption spectra as well as significant quenching in the fluorescence intensity of the dyes 1-3, respectively. Half-reciprocal analysis of the absorption data and isothermal titration calorimetric (ITC) analysis of the titration experiments gave a 1:1 stoichiometry for the complexes formed between the lysozyme and squaraine dyes with association constants (Kass) in the range 104-105 M-1. We have determined the changes in the free energy (ΔG) for the complex formation and the values are found to be -30.78, -32.31 and -28.58 kJmol-1, respectively for the dyes 1, 2 and 3. Furthermore, we have observed a strong induced CD (ICD) signal corresponding to the squaraine chromophore in the case of the halogenated squaraine dyes 2 and 3 at 636 and 637 nm confirming the complex formation in these cases. To understand the nature of interaction of the squaraine dyes 1-3 with lysozyme, we have investigated the interaction of dyes 1-3 with different amino acids. These results indicated that the dyes 1-3 showed significant interactions with cysteine and glutamic acid which are present in the side chains of lysozyme. In addition the temperature dependent studies have revealed that the interaction of the dye and the lysozyme are irreversible. Furthermore, we have investigated the interactions of these NIR dyes 1-3 with β- amyloid fibres derived from lysozyme to evaluate their potential as inhibitors of this biologically important protein aggregation. These β-amyloid fibrils were insoluble protein aggregates that have been associated with a range of neurodegenerative diseases, including Huntington, Alzheimer’s, Parkinson’s, and Creutzfeldt-Jakob diseases. We have synthesized amyloid fibres from lysozyme through its incubation in acidic solution below pH 4 and by allowing to form amyloid fibres at elevated temperature. To quantify the binding affinities of the squaraine dyes 1-3 with β-amyloids, we have carried out the isothermal titration calorimetric (ITC) measurements. The association constants were determined and are found to be 1.2 × 105, 3.6× 105 and 3.2 × 105 M-1 for the dyes, 1-3, respectively. To gain more insights into the amyloid inhibiting nature of the squaraine dyes under investigations, we have carried out thioflavin assay, CD, isothermal titration calorimetry and microscopic analysis. The addition of the dyes 1-3 (5μM) led to the complete quenching in the apparent thioflavin fluorescence, thereby indicating the destabilization of β-amyloid fibres in the presence of the squaraine dyes. Further, the inhibition of the amyloid fibres by the squaraine dyes 1-3, has been evidenced though the DLS, TEM AFM and SAED, wherein we observed the complete destabilization of the amyloid fibre and transformation of the fibre into spherical particles of ca. These results demonstrate the fact that the squaraine dyes 1-3 can act as protein labeling agents as well as the inhibitors of the protein amyloidogenesis. The last chapter of the thesis describes the synthesis and investigation of selfassembly as well as bio-imaging aspects of a few novel tetraphenylethene conjugates 4-6.Expectedly, these conjugates showed significant solvatochromism and exhibited a hypsochromic shift (negative solvatochromism) as the solvent polarity increased, and these observations were justified though theoretical studies employing the B3LYP/6-31g method. We have investigated the self-assembly properties of these D-A conjugates though variation in the percentage of water in acetonitrile solution due to the formation of nanoaggregates. Further the contour map of the observed fluorescence intensity as a function of the fluorescence excitation and emission wavelength confirmed the formation of J-type aggregates in these cases. To have a better understanding of the type of self-assemblies formed from the TPE conjugates 4-6, we have carried out the morphological analysis through various microscopic techniques such as DLS, SEM and TEM. 70%, we observed rod shape architectures having ~ 780 nm in diameter and ~ 12 μM in length as evidenced through TEM and SEM analysis. We have made similar observations with the dodecyl conjugate 5 at ca. 70% and 50% water/acetonitrile mixtures, the aggregates formed from 4 and 5 were found to be highly crystalline and such structures were transformed to amorphous nature as the water fraction was increased to 99%. To evaluate the potential of the conjugate as bio-imaging agents, we have carried out their in vitro cytotoxicity and cellular uptake studies though MTT assay, flow cytometric and confocal laser scanning microscopic techniques. Thus nanoparticle of these conjugates which exhibited efficient emission, large stoke shift, good stability, biocompatibility and excellent cellular imaging properties can have potential applications for tracking cells as well as in cell-based therapies. In summary we have synthesized novel functional organic chromophores and have studied systematic investigation of self-assembly of these synthetic and biological building blocks under a variety of conditions. The investigation of interaction of water soluble NIR squaraine dyes with lysozyme indicates that these dyes can act as the protein labeling agents and the efficiency of inhibition of β-amyloid indicate, thereby their potential as anti-amyloid agents.

BioJADE: A Design and Simulation Tool for Synthetic Biological Systems

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us with the ability to build cells that are capable of a plethora of activities, from computation to synthesizing nanostructures. To develop these systems, we must have a set of tools not only for synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible design and simulation platform for synthetic biology. BioJADE is a graphical design tool built in Java, utilizing a database back end, and supports a range of simulations using an XML communication protocol. BioJADE currently supports a library of over 100 parts with which it can compile designs into actual DNA, and then generate synthesis instructions to build the physical parts. The BioJADE project contributes several tools to Synthetic Biology. BioJADE in itself is a powerful tool for synthetic biology designers. Additionally, we developed and now make use of a centralized BioBricks repository, which enables the sharing of BioBrick components between researchers, and vastly reduces the barriers to entry for aspiring Synthetic Biologists.

Estructura computacional i aplicacions de la semblança molecular quàntica

La tesis tracta diferents aspectes relacionats amb el càlcul de la semblança quàntica, així com la seva aplicació en la racionalització i predicció de l'activitat de fàrmacs. Es poden destacar dos progressos importants en el desenvolupament de noves metodologies que faciliten el càlcul de les mesures de semblança quàntica. En primer lloc, la descripció de les molècules mitjançant les funciones densitat aproximades PASA (Promolecular Atomic Shell Approximation) ha permès descriure amb suficient precisió la densitat electrònica dels sistemes moleculars analitzats, reduint substancialment el temps de càlcul de les mesures de semblança. En segon lloc, el desenvolupament de tècniques de superposició molecular específiques de les mesures de semblança quàntica ha permès resoldre el problema de l'alineament en l'espai dels compostos comparats. El perfeccionament d'aquests nous procediments i algoritmes matemàtics associats a les mesures de semblança molecular quàntica, ha estat essencial per poder progressar en diferents disciplines de la química computacional, sobretot les relacionades amb les anàlisis quantitatives entre les estructures moleculars i les seves activitats biològiques, conegudes amb les sigles angleses QSAR (Quantitative Structure-Activity Relationships). Precisament en l'àrea de les relacions estructura-activitat s'han presentat dues aproximacions fonamentades en la semblança molecular quàntica que s'originen a partir de dues representacions diferents de les molècules. La primera descripció considera la densitat electrònica global de les molècules i és important, entre altres, la disposició dels objectes comparats en l'espai i la seva conformació tridimensional. El resultat és una matriu de semblança amb les mesures de semblança de tots els parells de compostos que formen el conjunt estudiat. La segona descripció es fonamenta en la partició de la densitat global de les molècules en fragments. S'utilitzen mesures d'autosemblança per analitzar els requeriments bàsics d'una determinada activitat des del punt de vista de la semblança quàntica. El procés permet la detecció de les regions moleculars que són responsables d'una alta resposta biològica. Això permet obtenir un patró amb les regions actives que és d'evident interès per als propòsits del disseny de fàrmacs. En definitiva, s'ha comprovat que mitjançant la simulació i manipulació informàtica de les molècules en tres dimensions es pot obtenir una informació essencial en l'estudi de la interacció entre els fàrmacs i els seus receptors macromoleculars.

O uso de nanoanticorpos no design de vacinas

Por volta da década de 90, foram descobertos na família Camelidae anticorpos desprovidos de cadeias leves e em que o seu domínio variável era constituído unicamente por cadeias pesadas (VHH) e dois domínios constantes (CH2 e CH3). Estes fragmentos passaram a ser conhecidos por Nanoanticorpos, não só pelo seu pequeno tamanho e flexibilidade, mas também por se tratar de uma nova geração de anticorpos terapêuticos, os quais apresentam várias vantagens face aos anticorpos convencionais, uma vez que não são imunogénicos e têm uma alta estabilidade térmica e química, entre tantas outras características inerentes. As suas aplicações são diversas: podem ser usados como tratamento e diagnóstico médico, na veiculação de fármacos e no desenvolvimento de vacinas. Uma das tecnologias moleculares mais usadas na clonagem e expressão dos Nanoanticorpos é a tecnologia de «Phage Display» que pode ser categorizada em duas vertentes: o sistema vector de fago e o sistema vector de fagemídeo. Os vectores fágicos mais usados são os bacteriófagos filamentosos, como o M13, capazes de infetar bactérias gram negativas, como a Escherichia coli. Trata-se de uma ferramenta biotecnológica poderosa e promissora, destacando-se na área da medicina.

Distributed mining of molecular fragments

In real world applications sequential algorithms of data mining and data exploration are often unsuitable for datasets with enormous size, high-dimensionality and complex data structure. Grid computing promises unprecedented opportunities for unlimited computing and storage resources. In this context there is the necessity to develop high performance distributed data mining algorithms. However, the computational complexity of the problem and the large amount of data to be explored often make the design of large scale applications particularly challenging. In this paper we present the first distributed formulation of a frequent subgraph mining algorithm for discriminative fragments of molecular compounds. Two distributed approaches have been developed and compared on the well known National Cancer Institute’s HIV-screening dataset. We present experimental results on a small-scale computing environment.

Can a consecutive double turn conformation be considered as a peptide based molecular scaffold for supramolecular helix in the solid state?

Helices and sheets are ubiquitous in nature. However, there are also some examples of self-assembling molecules forming supramolecular helices and sheets in unnatural systems. Unlike supramolecular sheets there are a very few examples of peptide sub-units that can be used to construct supramolecular helical architectures using the backbone hydrogen bonding functionalities of peptides. In this report we describe the design and synthesis of two single turn/bend forming peptides (Boc-Phe-Aib-Ile-OMe 1 and Boc-Ala-Leu-Aib-OMe 2) (Aib: alpha-aminoisobutyric acid) and a series of double-turn forming peptides (Boc-Phe-Aib-IIe-Aib-OMe 3, Boc-Leu-Aib-Gly-Aib-OMe 4 and Boc-gamma-Abu-Aib-Leu-Aib-OMe 5) (gamma-Abu: gamma-aminobutyric acid). It has been found that, in crystals, on self-assembly, single turn/bend forming peptides form either a supramolecular sheet (peptide 1) or a supramolecular helix (peptide 2). unlike self-associating double turn forming peptides, which have only the option of forming supramolecular helical assemblages. (c) 2005 Elsevier Ltd. All rights reserved.

Mapping antimalarial pharmacophores as a useful tool for the rapid discovery of drugs effective in vivo: design, construction, characterization, and pharmacology of metaquine

Resistant strains of Plasmodium falciparum and the unavailability of useful antimalarial vaccines reinforce the need to develop new efficacious antimalarials. This study details a pharmacophore model that has been used to identify a potent, soluble, orally bioavailable antimalarial bisquinoline, metaquine (N,N'-bis(7-chloroquinolin-4-yl)benzene-1,3-diamine) (dihydrochloride), which is active against Plasmodium berghei in vivo (oral ID50 of 25 mu mol/kg) and multidrug-resistant Plasmodium falciparum K1 in vitro (0.17 mu M). Metaquine shows strong affinity for the putative antimalarial receptor, heme at pH 7.4 in aqueous DMSO. Both crystallographic analyses and quantum mechanical calculations (HF/6-31+G*) reveal important regions of protonation and bonding thought to persist at parasitic vacuolar pH concordant with our receptor model. Formation of drug-heme adduct in solution was confirmed using high-resolution positive ion electrospray mass spectrometry. Metaquine showed strong binding with the receptor in a 1: 1 ratio (log K = 5.7 +/- 0.1) that was predicted by molecular mechanics calculations. This study illustrates a rational multidisciplinary approach for the development of new 4-aminoquinoline antimalarials, with efficacy superior to chloroquine, based on the use of a pharmacophore model.