Signal transducer and activator of transcription 3 (STAT3) is a cancer-driving proto-oncoprotein that represents a novel target for the development of chemotherapeutics. In this study, the functional requirements to furnish a potent STAT3 inhibitor was investigated. First, a series of peptidomimetic inhibitors were rationally designed from lead parent peptides. Prepared peptidomimetics overcame the limitations normally associated with peptide agents and displayed improved activity in biophysical evaluations. Notably, lead peptidomimetic agents possessed micromolar cellular activity which was unobserved in both parent peptides. Peptidomimetic design relied on computational methods that were also employed in the design of purine based STAT3 inhibitory molecules. Docking studies with lead STAT3-SH2 domain inhibitory molecules identified key structural and chemical information required for the construction of a pharmacophore model. 2,6,9-heterotrisubstituted purines adequately fulfilled the pharmacophore model and a library of novel purine-based STAT3 inhibitory molecules was prepared utilizing Mitsunobu chemistry. Several agents from this new library displayed high affinity for the STAT3 protein and effectively disrupted the STAT3:STAT3-DNA complex. Furthermore, these agents displayed cancer-cell specific toxicity through a STAT3 dependant mechanism. While purine agents elicited cellular effects, the dose required for cellular efficacy was much higher than those observed for in vitro STAT3 dimer disruption. The diminished cellular activity could be attributed to the apparent poor cell permeability of the first generation purine library; thus, a second library of purine molecules was constructed to improve cell penetration. Unfortunately, iii 2nd generation purine inhibitors failed to disrupt phosphorylated STAT3 activity and suffered from poor cell permeability. However, a lead sulfamate agent was discovered that showed potent activity against multiple myeloma cancer cells. Investigations revealed potential kinase inhibitory activity as the source of the sulfamate purine’s biological effect. Explorations into the development of a potent STAT3 SH2 domain binder, including the creation of salicylic purine and constrained pyrimidine molecules, are ongoing. Finally, progress towards the creation of a macrocyclic purine combinatorial library has been pursued and is reported herein.

Noncovalent interactions in complex chemical systems are examined by considering model systems which capture the essential physics of the interactions and applying correlated electronic structure techniques to these systems. Noncovalent interactions are critical to understanding a host of energetic and structural properties in complex chemical systems, from base pair stacking in DNA to protein folding in organic solids. Complex chemical and biophysical systems, such as enzymes and proteins, are too large to be studied using computational techniques rigorous enough to capture the subtleties of noncovalent interactions. Thus, the larger chemical system must be truncated to a smaller model system to which rigorous methods can be applied in order to capture the essential physics of the interaction. Computational methodologies which can account for high levels of electron correlation, such as second-order perturbation theory and coupled-cluster theory, must be used. These computational techniques will be used to study several types (pi stacking, S/pi, and C-H/pi) of noncovalent interactions in two chemical contexts: biophysical systems and organic solids.

Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains xvii, 271 p.; also includes graphics. Includes bibliographical references (p. 245-269). Available online via OhioLINK's ETD Center

No description available.

Les foldamères – structures oligomériques artificielles adoptant une forme repliée définie – permettent la conception de récepteurs moléculaires de type capsule capables de reconnaitre sélectivement certains analytes pertinents du vin. En particulier, des récepteurs sélectifs et affins du fructose, de l’acide tartrique et de l’acide malique ont été identifiés au cours de ces dernières années. Le développement d’une méthodologie de synthèse sur support solide d’un récepteur moléculaire de l’acide gluconique sera abordé dans ce manuscrit. Cette thèse montre également comment certains de ces récepteurs peuvent être convertis en détecteurs capables d’émettre un signal en présence de l’analyte. La démarche est centrée sur l’incorporation d’un fluorophore au sein du site de reconnaissance. Une preuve de concept a ainsi été effectuée avec le dosage par fluorescence de l’acide tartrique. Enfin, le greffage de ce détecteur moléculaire à la surface de particules de silice a été réalisé et ouvre la voie au développement de dispositifs portables pour le dosage des analytes reconnus. De tels détecteurs sont requis par l’industrie du vin afin d’assurer le contrôle des processus biologiques, en particulier durant la fermentation. / Some relevant wine small molecular components can be selectively recognized by foldamer capsules – artificial oligomeric compounds able to fold into well-defined objects possessing an inner cavity. In recent years, selective and high affinity receptors for fructose, tartaric acid and malic acid have been reported. Here, a new methodology, using solid phase synthetic techniques, for the preparation of a gluconic acid receptor will be discussed. To transform these receptors into sensors, a fluorescent moiety has been incorporated in the binding site. A proof of concept has been achieved using a fluorescence titration of tartaric acid. Indeed, when the guest is encapsulated, a modification of the fluorescence emission is observed. Finally, these fluorescent receptors have been anchored to silica surfaces and pave the way to the development of mobile detection devices. Such sensors could be useful to the wine industry to ensure proper control of biological processes for example during fermentation.

Ce travail de thèse porte sur l’optimisation des propriétés de nanotubes de carbone pour la détection de gaz.Pour cette application, les nanotubes de carbone ont été déposés sur deux types de transducteur sérigraphiés, résistif et résonant. Les nanotubes de carbone à multi-parois traités par plasma d’oxygène (O-MWCNTs) ont été le point de départ de ces travaux. Les performances de ces nanomatériaux déposés par air-brushing sur le transducteur de type résistif comportant deux électrodes de platine interdigitées préalablement déposées sur un substrat d’alumine ont été étudiées en présence de composés organiques volatils (COVs). Par comparaison aux réponses obtenues sous éthanol et acétone,une meilleure sensibilité et un meilleur temps de recouvrement ont été observés en présence de benzène et de toluène. Les nanotubes de carbone O-MWCNTs ont été ensuite déposés sur une micropoutre piézoélectrique sérigraphiée. Cette dernière, à base de PZT placé entre 2 électrodes, permet simultanément l’actionnement et la mesure de sa fréquence de résonance. De plus, le remplacement de l’électrode supérieure de géométrie rectangulaire par deux électrodes interdigitées a permis la mesure simultanée de la résistance des nanotubes de carbone et de la fréquence de résonance. Grâce à cette nouvelle génération de transducteur, la variation de résistance de la couche de nanotubes de carbone et la variation de masse ont pu être mesurés en présence de COVs mais aussi de monoxyde de carbone et de dioxyde d’azote. Sous forte concentration de vapeurs/gaz, la prise de masse de la couche sensible entraîne des variations de fréquence négatives. En revanche, à plus faible concentration, des variations de fréquence positives ont été observées. Ce phénomène est attribué à une modification de la rigidité de la poutre résonante suite à l’adsorption sur la poutre de l’espèce à détecter enfaible quantité. La mesure simultanée de la résistance des OMWCNTs de type-p a de plus permis la discrimination du caractère oxydant ou réducteur des gaz/vapeurs. Finalement,face à la difficulté de détecter le benzène à faible concentration, une approche basée sur la reconnaissance moléculaire « host-guest » a été proposée. Afin de promouvoir des interactions spécifiques avec le benzène, les MWCNTs ont été fonctionnalisés avec une molécule de type quinoxaléine en conformation de cavité. Ainsi, la mesure de la résistance de ce nanomatériau hybride a permis la détection de 2,5 ppb de benzène sous air sec avec une limite de détection (LOD) proche de 600 ppt. Ces résultats remarquables démontrent les potentialités des nanotubes de carbone fonctionnalisés pour la détection de faibles traces de composés aromatiques. / Multiwall carbon nanotubes (MWCNTs) base sensitive layers have been deposited onto different transducer substrates for gas sensing application. Oxygen plasma treated MWCNTs, so-called O-MWCNTs, have been a building blockfor developing other gas sensitive nanomaterials. At first, OMWCNTs have been studied as resistive gas sensors. Volatile organic compounds (VOCs) such as benzene, toluene, ethanol, methanol and acetone have been used to characterize this sensitive layer. The sensors show good sensitivity and excellent baseline recovery in the presence of benzene or toluene vapors compared to the others tested VOCs. OMWCNTs have been studied as adsorbent nanomaterials deposited on PZT piezoelectric resonant cantilevers fabricated by multilayer screen-printing. In the second step, a modification of the rectangular top electrode to become an interdigitated electrode was implemented in order to have a sensor transducer employing two transduction mechanisms. This configuration allowed us to measure, for a single device, the resistance change of the carbon nanotube film and the resonance frequency shift of the PZT cantilever up on exposure to VOCs. The sensing properties of such systems have been studied for benzene, CO, and NO2 contaminants. Positive and negative shifts of the resonance frequency are observed at lowand high gas concentrations, respectively. These are attributed to stress or to mass effects becoming dominant at low or high gas concentration levels. Monitoring the resistance of the p type O-MWCNT film helps discriminating gases/ vapours according to their oxidizing or reducing character. The interest of the double transduction has been demonstrated in the detection of CO. Finally, in front of the difficulty to detect benzene at low concentrations, a different approach based on the host-guest molecular recognition is proposed. To promote specific interaction toward benzene, quinoxaline-walled thioether-legged deep cavit and functionalized MWCNTs are used. The detection of 2.5 ppb of benzene in dry air is demonstrated with a limit of detection (LOD) near 600 ppt.These remarkable results show the potentiality of functionalized carbon nanotubes in aromatic vapor sensing at traces level.

In this thesis molecular interactions between polypeptide conjugates and protein targets were investigated. Polypeptides were derivatized with small organic molecules, peptides and oligonucleotides. New strategies were developed with the aim to increase affinities for proteins of biological interest. A 42-residue polypeptide (4-C15L8) conjugated to a small organic molecule 3,5-bis[[bis(2-pyridylmethyl)amino]methyl]benzoic acid (PP1), was shown to bind glycogen phosphorylase a (GPa) in the presence of zinc ions. Under the assumption that hydrophobic interactions dominated the binding energy, the hydrophobic residues of 4-C15L8-PP1 were systematically replaced in order to study their contribution to the affinity enhancement. The replacement of the Nle, Ile and Leu residues by Ala amino acids reduced affinities. The introduction of non-natural L-2-aminooctanoic acid (Aoc) residues into the peptide sequence enhanced the binding affinity for GPa. A decreased KD of 27nM was obtained when Nle5, Ile9 and Leu12 were replaced by Aoc residues, in comparison to the KD value of 280nM obtained for the unmodified 4-C15L8-PP1. It is evident that there are non-obvious hydrophobic binding sites on the surfaces of proteins that could be identified by introducing the more hydrophobic and conformationally flexible Aoc residues. The downsizing of the 42-mer peptide to an 11-mer and the incorporation of three Aoc residues gave rise to a KD of 550 nM, comparable to that of  4-C15L8-PP1 suggesting that bioactive peptides can be downsized by the introduction of Aoc. Aiming to improve in vivo stability, the affinity for human serum albumin (HSA) of hydrophobic, positively and negatively charged polypeptide-PP1 conjugates was evaluated. Increased hydrophobicity due to the introduction of Aoc residues did not significantly increase the affinity for HSA. No binding was observed in the case of the most negatively charged polypeptides whereas the slightly negatively and positively charged polypeptides conjugated to PP1 bound HSA with affinities that increased with the positive charge. It was found that polypeptide-PP1 conjugates target the zinc binding site of the HSA. Affinity enhancement was obtained due to the incorporation of PP1 and increased by charge to charge interactions between the positively charged amino acids of the polypeptide and the negatively charged residues of HSA, in close proximity to the HSA zinc binding site. The survival times of the peptide-PP1 conjugates in human serum were extended as a result of binding to HSA. Zn2+ ion chelating agents can be incorporated in potential peptide therapeutics with a short plasma half-life, without increasing their molecular weights.

No description available.

Both technological and experimental advancements in the field of biotechnology have allowed scientists to make leaps in areas such nucleic acid, antibody, and recombinant protein technologies. Here we focus on the use of recombinant proteins as molecular recognition motifs, wound healing biomaterials, and agents for cell cycle pathway elucidation are discussed. The author's primary project is described in chapters 2 and 3, and is focused on designed leucine-rich repeat proteins which offer increased stability, modularity, and surface area for binding interactions. These proteins bind at least two muramyl dipeptide ligands with picomolar to nanomolar affinity (Kd1 = 0.04 – 3.5 nM); as measured by fluorescence quenching experiments and ITC. The longest designed repeat, CLRR8, has a Kd app value of 1.0 nM which is comparable to full length native NOD2 protein. Molecular docking simulations revealed the locations of two potential binding sites and their respective interactions. The series of proteins represents a foundation for a high affinity and highly specific molecular recognition scaffold that has the potential to bind a variety of ligands. Previously the author contributed to the design of recombinant keratin proteins, and the work in Chapter 4 builds on the original design to allow for controlled degradation in wound healing systems. Site-directed mutagenesis was utilized to introduce these degradation sites, and modified keratin proteins were expressed with no differences to native recombinant keratin proteins. Success in engineering a variation of native keratin protein with no issues in expression lay the foundation for further engineering of native keratin or other relevant proteins for improved functionality. Chapter 5 describes steps towards producing human Aurora borealis (Bora) protein, an important substrate in cell cycle regulation, by in vitro transcription-translation with locked Ser–Pro analogues. This will allow for the elucidation of the active isomerization form to ensure proper cell division. Site-directed mutagenesis successfully introduced the amber codon to relevant Ser-Pro sites at positions 274 and 278. These mutated Bora genes along with modified ribosomes and aminoacyl tRNA will allow for the incorporation of locked dipeptide analogues. Expression of native Bora was carried out as a control, and appeared to express in dimeric form. The experiments carried out in Chapter 5 describe and outline all the molecular biology work completed and to be completed for this novel method of studying cis-trans isomerization in living cells. / Doctor of Philosophy / Sequencing of the human genome and the rapid development of gene editing and recombinant DNA technologies paved the way for a massive shift in the pharmaceutical industry. The first pharmaceutical companies in the 19th century started as fine chemicals businesses. The discovery of penicillin introduced antibiotics, and improved synthetic techniques led to the giants we know as big pharma today. Today, in the 21st century both computing and biotechnology has allowed for great leaps forward in precision medicine. Biotechnology refers to the manipulation of living organisms or their components to produce useful commercial products. In the pharmaceutical industry this refers to genetic engineering for novel pharmaceuticals. Here, we focus on the use of recombinant technology to create proteins for use in biomedical applications. Recombinant proteins are proteins formed by laboratory methods of molecular cloning. Through this technology, we are able to elucidate sequence-structure-function relationships of proteins, and determine their specific functions. Additionally, recombinant methods allow us to fine tune or modify the sequences of natural proteins to be more effective scaffolds or reagents. Chapter 3 focuses on the development of synthetic proteins for medical diagnostics. We designed a protein scaffold, based on natural innate immunity proteins, to detect bacteria cell wall components. Chapter 4 focuses on the engineering of keratin protein with applications in wound healing. We introduce controlled degradation of the biomaterial for use in potential drug delivery systems at the wound site. Chapter 5 focuses on the use of recombinant technologies aiding in the elucidation of a regulatory protein's function in cell division.

Résumé : Les méthodes de détection de similarités de sites de liaison servent entre autres à la prédiction de fonction et à la prédiction de cibles croisées. Ces méthodes peuvent aider à prévenir les effets secondaires, suggérer le repositionnement de médicament existants, identifier des cibles polypharmacologiques et des remplacements bio-isostériques. La plupart des méthodes utilisent des représentations basées sur les atomes, même si les champs d’interaction moléculaire (MIFs) représentent plus directement ce qui cherche à être identifié. Nous avons développé une méthode bio-informatique, IsoMif, qui détecte les similarités de MIF entre différents sites de liaisons et qui ne nécessite aucun alignement de séquence ou de structure. Sa performance a été comparée à d’autres méthodes avec des bancs d’essais, ce qui n’a jamais été fait pour une méthode basée sur les MIFs. IsoMif performe mieux en moyenne et est plus robuste. Nous avons noté des limites intrinsèques à la méthodologie et d’autres qui proviennent de la nature. L’impact de choix de conception sur la performance est discuté. Nous avons développé une interface en ligne qui permet la détection de similarités entre une protéine et différents ensembles de MIFs précalculés ou à des MIFs choisis par l’utilisateur. Des sessions PyMOL peuvent être téléchargées afin de visualiser les similarités identifiées pour différentes interactions intermoléculaires. Nous avons appliqué IsoMif pour identifier des cibles croisées potentielles de drogues lors d’une analyse à large échelle (5,6 millions de comparaisons). Des simulations d’arrimage moléculaire ont également été effectuées pour les prédictions significatives. L’objectif est de générer des hypothèses de repositionnement et de mécanismes d’effets secondaires observés. Plusieurs exemples sont présentés à cet égard. / Abstract : Methods that detect binding site similarities between proteins serve for the prediction of function and the identification of potential off-targets. These methods can help prevent side-effects, suggest drug repurposing and polypharmacological strategies and suggest bioisosteric replacements. Most methods use atom-based representations despite the fact that molecular interaction fields (MIFs) represents more closely the nature of what is meant to be identified. We developped a computational algorithm, IsoMif, that detects MIF similarities between binding sites. We benchmark IsoMif to other methods which has not been previously done for a MIF-based method. IsoMif performed best in average and more consistently accross datasets. We highlight limitations intrinsic to the methodology or to nature. The impact of design choices on performance is discussed. We built a freely available web interface that allows the detection of similarities between a protein and pre-calculated MIFs or user defined MIFs. PyMOL sessions can be downloaded to visualize similarities for the different intermolecular interactions. IsoMif was applied for a large-scale analysis (5,6 millions of comparisons) to predict offtargets of drugs. Docking simulations of the drugs in the binding site of their top hits were performed. The primary objective is to generate hypotheses that can be further investigated and validated regarding drug repurposing opportunities and side-effect mechanisms.