Le travail présenté dans cette thèse porte sur le développement de chimie de surface et de biocapteurs pouvant être utilisés dans le milieu hospitalier afin d’améliorer les méthodes de dépistages et de suivi de traitement de diverses maladies et cancers. Les méthodes actuelles de dépistage du cancer reposent principalement sur l’analyse histologique des cellules par des experts dans le domaine. Cela complique la transmission de l’information au patient et retarde le moment où un traitement approprié peut être entamé. Grâce à de nouvelles techniques d’analyses simples et peu coûteuses comme la spectroscopie de résonance des plasmons de surface (SPR), il est possible de développer des tests qui pourront être effectués par le personnel de l’hôpital, en peu de temps et à peu de frais. Afin de pouvoir utiliser la SPR en milieu clinique, une chimie de surface appropriée doit être développée afin d’empêcher les matrices biologiques de masquer le signal des analytes d’intérêt. En effet, qu’il s’agisse de lysat cellulaire, de sérum ou de tout autre fluide biologique, le contenu protéique et lipidique peut s’adsorber de façon non-spécifique aux surfaces d’analyse, compromettant ainsi les résultats obtenus. Afin de pallier ce problème, le développement de chimie de surface a été effectué. Des monocouches de peptides et de liquides ioniques ont été utilisées afin de réduire l’adsorption non-spécifique de lysat cellulaire non-dilué sur des capteurs SPR. Parmi les peptides, le plus efficace s’est avéré être le 3 MPA (His)2(Leu)2(Phe)2 OH, un peptide chargé positivement formé de 6 acides aminés plutôt hydrophobes. Grâce à cette surface, l’adsorption non-spécifique de lysat cellulaire a pu être réduite jusqu’à 159 ± 27 ng/cm2, par rapport à 929 ± 186 ng/cm2 sur une surface d’or non protégée. Une étude en spectrométrie de masse a permis de mieux comprendre le phénomène d’adsorption non-spécifique de lysat cellulaire et de confirmer que ce sont principalement des lipides qui s’adsorbent non-spécifiquement au capteur SPR lorsque celui-ci est exposé à du lysat cellulaire. Malgré la nette amélioration par rapport à un capteur non protégé, le phénomène d’adsorption non-spécifique était encore significativement présent avec les monocouches de peptides. L’adsorption non-spécifique de lysat cellulaire a ensuite été drastiquement réduite grâce aux liquides ioniques hydrophobes et chargés. Le liquide ionique le plus performant a montré une adsorption non-spécifique d’à peine 2 ± 2 ng/cm2. Par la suite, un biocapteur permettant la détection de HER2, un biomarqueur de cancer du sein présent dans environ 30% des cas de cancers du sein agressifs, a été développé. Cela a permis de démontrer que le liquide ionique pouvait être utilisé pour la construction d’un biocapteur, ouvrant ainsi la porte à un large domaine d’analyses en lysat cellulaire. Finalement, les défis de l’analyse SPR avec des échantillons cliniques ont été explorés par le développement d’un biocapteur pour l’anti-asparaginase, permettant de faire le suivi de traitement de patients atteints de leucémie. L’asparaginase est administrée aux patients leucémiques, en combinaison avec plusieurs autres composés chimiothérapiques, afin de combattre ce cancer. Toutefois, plusieurs patients ont une réaction allergique à cette protéine de source bactérienne, mais ne démontrent pas de symptômes physiques. Le biocapteur développé visait donc à détecter les réactions immunitaires des patients afin de modifier leur traitement lorsque cela s’avère nécessaire. Un biocapteur pour la détection de l’anti-asparaginase dans le sérum non-dilué de patients leucémiques a donc été développé. Des échantillons cliniques ont été étudiés et les résultats obtenus pour le nouveau biocapteur SPR ont montré une bonne concordance avec les résultats obtenus en ELISA. / This thesis describes the development of clinical biosensors. These biosensors were developed with the aim of improving diagnostic and treatment monitoring methods. Actual monitoring methods often rely on histological analysis performed by experts. This complicates the transmission of the information to the patient and delays the onset of an appropriate treatment. It is envisioned to develop simple experiments at low cost, which will allow untrained personnel to perform the testing on-site with biosensing technologies such as surface plasmon resonance (SPR). In order to perform SPR in clinical analysis, appropriate surface chemistry must be developed to prevent nonspecific adsorption. Nonspecific adsorption is the fouling of surfaces with biomolecules contained in the sample matrix such as proteins or lipids of biofluids. This leads to false positive signals preventing the correct measurement of the analyte concentration. Peptide and ionic liquid monolayers have been studied in this thesis to prevent nonspecific adsorption of undiluted cell lysate. The most efficient peptide was the 3 MPA (His)2(Leu)2(Phe)2 OH peptide, a 6 amino acids hydrophobic and positively charged peptide. The nonspecific adsorption of cell lysate was reduced to 159 ± 27 ng/cm2, compared to 929 ± 186 ng/cm2 on a bare gold surface. Also, mass spectrometry was performed to better understand the cell lysate nonspecific adsorption phenomenon. This study showed lipids were mostly adsorbed on the sensor when exposed to cell lysate. Despite a significant reduction of nonspecific adsorption with peptides, it remained unoptimal and should be improved. The newly developed hydrophobic and charged ionic liquids nearly eliminated the nonspecific adsorption of undiluted cell lysate, with only 2 ± 2 ng/cm2 of nonspecific material adsorbed on the surface. Then, a biosensor of an aggressive breast cancer biomarker, HER2, was developed. This proved that the ionic liquids could be used in the development of clinical biosensors. Finally, the challenges of the analysis of clinical samples with SPR sensing were explored with the development of an anti-asparaginase biosensor for leukemic patients. Asparaginase is a chemotherapeutic drug administered to patients in combination with various other drugs to treat leukemia. However, many patients suffer from silent allergic reactions due to the bacterial source of this drug. Therefore, a biosensor was developed to detect the antibodies in undiluted serum produced against the drug, which could ultimately serve to modify the patient’s treatment when necessary. Clinical samples from leukemia patients were studied and the results were in good agreement with ELISA experiments.

L’approche analytique d’interrogation sur puce par spectrométrie de masse est une techniqueparticulièrement bien adaptée à l’analyse multiplexée requise pour la recherche de biomarqueurs dansle diagnostic moderne. L’objectif a été de contribuer aux développements technologiques etméthodologiques d’une plateforme d’analyse baptisée SUPRA-MS (Imagerie par Résonance desPlasmons de Surface en array combinée à la Spectrométrie de Masse). Des puces d’or compatiblesavec la SPRi et la MS ont été conçues et réalisées à l’aide des techniques de dépôt sous vide. Uneétude originale couplant la SPRi avec l’AFM a permis d’établir une relation entre le signal SPRmesuré et la quantité réelle de protéines fixées sur des puces nanostructurées. Nous avons ensuitedéveloppé une procédure d’immobilisation en format array (16 à λ6 spots) par liaison covalente enmonocouche des anticorps spécifiques, dirigés contre un biomarqueur du cancer du sein (LAG3) pourune analyse multiplexée d’échantillons biologiques. Du plasma humain contenant 300 ng/mL deLAGγ est injecté à la surface de la puce. L’injection est suivie en temps réel par SPRi et conduit à unecapture du biomarqueur à l’échelle de la femtomole par spots. Un traitement collectif des spots parspray pour la digestion in situ des protéines et le dépôt de matrice en vue d’une interrogation MS enMALDI-TOF a été mis au point par l’équipe du Dr Patrick Ducoroy (CLIPP-CHU Dijon). Lesrésultats MS obtenues ont permis 100 % d’identification du biomarqueur. Cette technologie sansmarquages spécifiques est particulièrement bien adaptée à la caractérisation fine des biomarqueurs et àla discrimination de variants protéiques. / The analytic approach of interrogation on chip by mass spectrometry is a suitable technique tomultiplexed analysis required for biomarker research in modern diagnosis. The aim was to contributeto the technological and methodological developments of analysis platform called SUPRA-MS(Surface Plasmon Resonance in Array coupled to Mass Spectrometry) whose goal is to provideadditional data to assay on the target protein by mass spectrometry. At first, gold chips compatiblewith SPRi and MS were designed and fabricated using vacuum deposition techniques. An originalstudy coupling SPRi with AFM has established a relationship between the SPR signal measured andthe real amount of proteins bound to nanostructured chips. We developed an immobilization procedurein array format (spots 16-96) by covalent monolayer of specific antibodies directed against the proteinLAG3, a biomarker of breast cancer for multiplex analysis of human biological samples (plasma).Human plasma containing 300 ng/mL of LAG3 is injected to the chip surface. The injection ismonitored in real time by SPRi and leads to the biomarker capture at the femtomole scale. After thebiosensing step, a collective treatment of spots by spray for in situ protein digestion and matrixdeposition in view of a MS analysis was developed by Dr. Patrick Ducoroy's team (CLIPP-CHUDijon). The MS and MS-MS analysis by MALDI-TOF was developed to analyze all spotsautomatically and determine their peptide mapping leading to 100% of the biomarker identification.This technology does not require the use of specific markers, is suitable to the biomarkerscharacterization and discrimination of protein variants.

Stimuli sensitive polymers and hydrogels respond with large property changes to small physical and chemical stimuli (e.g. temperature, pH, ionic strength). The bulk behavior of these polymers is widely studied and they show an isotropic swelling. However, thin hydrogel layers of polymers on a substrate show a swelling behavior, which is constrained in some way. Therefore, size, confinement, patternability, response time and transition temperature of thin hydrogel layers are the most important parameters in technological applications and this study focuses on the investigation of these above-mentioned parameters. The aim of this study involves synthesis, characterization and application of thin photo-crosslinked hydrogel layers. Dimethylmaleimide (DMI) moiety was incorporated in the polymers chains and was used to introduce photo-crosslinking by [2+2] cyclodimerization reaction in the presence of UV irradiation. The following photo-crosslinkers based on DMI group were synthesized ? - Acrylate photo-crosslinker (DMIAm) - Acrylamide photo-crosslinker (DMIAAm) - Polyol photo-crosslinker (DMIPA, DMIPACl) The conventional free radical polymerization of above listed photo-crosslinker with its respective monomer resulted in formation of photo-crosslinkable polymers of (a) HEMA, (b) DMAAm, (c) NIPAAm/DMAAm, (d) NIPAAm/Cyclam. The properties of these polymers were investigated by NMR, UV-VIS spectroscopy, GPC and SPR. Thin hydrogel layers were prepared by spin coating on gold-coated LaSFN9 glass. The covalent attachment to the surface was achieved through an adhesion promoter. Swelling behavior of the thin polymer layers was thoroughly investigated by Surface Plasmon Resonance (SPR) Spectroscopy and Optical Waveguide Spectroscopy (OWS). SPR and OWS gave a wide range of information regarding the film thickness, swelling ratio, refractive index, and volume degree of swelling of the thin hydrogel layer. For hydrophilic photo-crosslinked hydrogel layers of HEMA and DMAAm, it was observed that the volume degree of swelling was independent of temperature changes but was dependent on the photo-crosslinker mol-% in the polymer. These surface attached thin hydrogel layer exhibited an anisotropic swelling. For NIPAAm photo-crosslinked hydrogel layers with DMAAm as a hydrophilic monomer, it was observed that both transition temperature (Tc) and volume degree of swelling increases with increase in the mol-% of DMAAm. To study the effect of film thickness on Tc and volume degree of swelling, hydrogels with wide range of film thickness were prepared and investigated by SPR. These results provided vital information on the swelling behavior of surface attached hydrogel layer and showed the versatility of SPR instrument for studying thin hydrogel layers. Later part of project involved synthesis of multilayer hydrogel assembly involving a thermoresponsive polymer and a hydrophilic polymer. The combination of two layers with photo-crosslinkable DMAAm polymer as base layer and photo-crosslinkable NIPAAm polymer as top layer formulate a multilayer assembly where, the base layer only swells in response to temperature and the top layer shows temperature dependent swelling. Photo-crosslinked hydrogel layers of NIPAAm, DMAAm and HEMA shows a high-resolution patterns when irradiated by UV light through a chromium mask. At last this study focused on an important application of these hydrogel layers for cell attachment processes. Cell growth, proliferation and spreading shows a biocompatible nature of these hydrogel surfaces. Such thermoresponsive photo-crosslinkable multilayer structure forms bases for future projects involving their use in actuator material and cell-attachment processes.

[pt] A espectroscopia de ressonância de plásmon superficial (SPR) é uma técnica óptica baseada na excitação coletiva dos elétrons livres de metais nobres, tradicionalmente utilizada em sensoriamento de analitos de diferente natureza. Neste trabalho foi otimizado o processo de fabricação de sensores plasmônicos baseados em filmes finos de ouro e interfaces ouro-grafeno. As plataformas de sensoriamento SPR foram usadas para a detecção de íons de metais tóxicos pesados de Pb(2+), Hg(2+) e Cd(2+) em concentrações de 0.1ppm até 1ppm. Os sensores baseados em interfaces ouro-grafeno, onde o grafeno foi crescido mediante o método CVD, demonstraram uma sensitividade entre 3 até 6 vezes maior que os sensores constituídos por filmes finos de ouro, apontando para uma absorção química devida à transferência de elétrons do grafeno para os íons. / [en] Surface plásmon resonance (SPR) spectroscopy is an optical technique based on the collective excitation of free electrons of noble metals, traditionally used in sensing different types of analytes. In this work the fabrication process of plásmonic sensors based on thin gold films and gold-graphene interfaces was optimized. SPR sensing platforms were used for the detection of toxic heavy metals ions Pb(2+), Hg(2+) and Cd(2+) in concentrations ranging from 0.1ppm to 1ppm. The sensors based on gold-graphene interfaces, where graphene was grown using the CVD method, demonstrated a sensitivity between 3 and 6 times greater than the sensor made of thin films of gold, pointing to a chemical absorption due to the transfer of electrons from the graphene to the ions.

Surface-plasmon-resonance (SPR) sensors are widely used in biological, chemical, medical, and environmental sensing. This dissertation describes the design and development of dual-mode, self-referencing SPR sensors supporting two surface-plasmon modes (long- and short-range) which can differentiate surface binding interactions from bulk index changes at a single sensing location. Dual-mode SPR sensors have been optimized for surface limit of detection (LOD). In a wavelength interrogated optical setup, both surface plasmons are simultaneously excited at the same location and incident angle but at different wavelengths. To improve the sensor performance, a new approach to dual-mode SPR sensing is presented that offers improved differentiation between surface and bulk effects. By using an angular interrogation, both surface plasmons are simultaneously excited at the same location and wavelength but at different angles. Angular interrogation offers at least a factor of 3.6 improvement in surface and bulk cross-sensitivity compared to wavelength-interrogated dual-mode SPR sensors. Multi-mode SPR sensors supporting at least three surface-plasmon modes can differentiate a target surface effect from interfering surface effects and bulk index changes. This dissertation describes a tri-mode SPR sensor which supports three surface plasmon resonance modes at one single sensing position, where each mode is excited at a different wavelength. The tri-mode SPR sensor can successfully differentiate specific binding from the non-specific binding and bulk index changes.

Le développement important des biocapteurs pour des applications médicales entraînent, depuis ces dernières années, à envisager d'autres façons de construire des plans d'expérience. Ainsi, les travaux ici présentés tentent de répondre à une problématique originale consistant à détecter des événements ayant une faible probabilité de se produire selon deux approches "antagonistes" ; d'une part, le criblage pharmaceutique de molécules chimiques et d'autre part, la détection de toxines à usage bioterroriste. Alternativement, ce sont les sondes et les cibles qui présentent une activité inconnue vis-à-vis de leur partenaire. Pour y répondre, nous avons envisagé la combinaison de la technique d'imagerie par résonance plasmonique de surface (SPRi) et l'utilisation de biopuces. L'immobilisation de composés chimiques issus de la chimie combinatoire est effectuée selon une conception préalable des molécules afin qu'elles soient compatibles en vue d'une immobilisation dans un polymère fin de polypyrrole. Appliquée à la recherche de nouvelles molécules interagissant avec l'ARN polymérase bactérienne, enzyme cible pour l'élaboration de molécules à activité antibiotique, ce procédé a permis d'isoler plusieurs molécules appartenant à la famille des hydantoïnes et des quinazoline-2,4-diones capables de réagir avec la cible pharmacologique choisie. Une miniaturisation des procédés de fabrication ouvre la voie vers une augmentation des débits de criblage de ce type de méthode. Dans le cadre de la détection de toxines, la chaîne B de la ricine a été prise pour modèle d'étude. Afin de surmonter les limitations de la technique par SPRi, un protocole d'amplification du signal a été mis au point. Celui-ci a permis de déceler jusqu'à 10 pM en analyte, c'est-à-dire une sensibilité comparable aux autres méthodes de transduction. Grâce à cette stratégie analytique multi-étape, une gamme dynamique de 3 ordres de grandeur a été établie. Une extension de cette approche analytique pourra à court terme amener à doser simultanément plusieurs toxines.

This thesis is focused on enzymatic studies of the secreted aspartic proteases (Saps) from Candida albicans as a tool for discovery of anti-candida drugs. C. albicans causes infections in a number of different locations, which differ widely in the protein substrates available and pH. Since C. albicans needs Saps during virulent growth, these enzymes are good targets for drug development. In order to investigate the catalytic characteristics of Saps and their inhibitor affinities, substrate-based kinetic assays were developed. Due to the low sensitivity of these assays, especially at the sub-optimal pH required to mimic the different locations of infections, these assays were not satisfactory. Therefore, a biosensor assay was developed whereby, it was possible to study interaction between Saps and inhibitors without the need to optimise catalytic efficacy. Furthermore, the biosensor assay allowed determination of affinity, as well as the individual association and dissociation rates for inhibitor interactions. Knowledge about substrate specificity, Sap subsite adaptivity, and the pH dependencies of catalytic efficacy has been accumulated. Also, screening of transition-state analogue inhibitors designed for HIV-1 protease has revealed inhibitors with affinity for Saps. Furthermore, the kinetics and pH dependencies of their interaction with Saps have been investigated. One of these inhibitors, BEA-440, displayed a complex interaction with Saps, indicating a conformational change upon binding and a very slow dissociation rate. A time dependent interaction was further supported by inhibition measurements. The structural information obtained affords possibilities for design of new more potent inhibitors that might ultimately become drugs against candidiasis. The strategy to combine substrate specificity studies with inhibitor screening has led to complementary results that generate a framework for further development of potent inhibitors.

Plasmonics techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), have been widely used for chemical and biochemical sensing applications. One approach to excite surface plasmons is through the coupling of light into metallic grating nanostructures. Those grating nanostructures can be fabricated using state-of-the-art nanofabrication methods. Laser interference lithography (LIL) is one of those methods that allow the rapid fabrication of nanostructures with a high-throughput. In this thesis, LIL was combined with other microfabrication techniques, such as photolithography and template stripping, to fabricate different types of plasmonic sensors. Firstly, template stripping was applied to transfer LIL-fabricated patterns of one-dimensional nanogratings onto planar supports (e.g., glass slides and plane-cut optical fiber tips). A thin adhesive layer of epoxy resin was used to facilitate the transfer. The UV-Vis spectroscopic response of the nanogratings supported on glass slides demonstrated a strong dependency on the polarization of the incident light. The bulk refractive index sensitivities of the glass-supported nanogratings were dependent on the type of metal (Ag or Au) and the thickness of the metal film. The described methodology provided an efficient low-cost fabrication alternative to produce metallic nanostructures for plasmonic chemical sensing applications. Secondly, we demonstrated a versatile procedure (LIL either alone or combined with traditional laser photolithography) to prepare both large area (i.e. one inch2) and microarrays (μarrays) of metallic gratings structures capable of supporting SPR excitation (and SERS). The fabrication procedure was simple, high-throughput, and reproducible, with less than 5 % array-to-array variations in geometrical properties. The nanostructured gold μarrays were integrated on a chip for SERS detection of ppm-level of 8-quinolinol, an emerging water-borne pharmaceutical contaminant. Lastly, the LIL-fabricated large area nanogratings have been applied for SERS detection of the mixtures of quinolone antibiotics, enrofloxacin, an approved veterinary antibiotic, and one of its active metabolite, ciprofloxacin. The quantification of these analytes (enrofloxacin and ciprofloxacin) in aqueous mixtures were achieved by employing chemometric analysis. The limit of quantification of the method described in this work is in the ppm-level, with <10 % SERS spatial variation. Isotope-edited internal calibration method was attempted to improve the accuracy and reproducibility of the SERS methodology. / Graduate / 2018-02-17

Cancer, group of diseases characterized by an uncontrolled cell growth, represents one of the great challenges of modern clinical research. Currently, the standard treatment of the cancer disease relies mainly on the whole body exposition to various factors, which targets the dividing cells, combined with surgical resection of the tumor. Unfortunately, this treatment is sometimes accompanied by numerous severe side-effects (e.g., nausea, loss of hair, infertility etc.). Therefore, in the past 40 years enormous resources and effort have been invested into finding a way how to specifically target and destroy the cancerous cells. This goal has been primarily addressed by the search for molecules, mainly proteins, which are predominantly expressed in the cancerous tissues compared to the healthy cells. Glutamate carboxypeptidase II (GCPII), also known as prostate specific membrane antigen (PSMA), represents such a target since it is highly expressed in a prostate carcinoma as well as in a solid tumor neovasculature. Additionally, GCPII is widely used as a model target molecule for proof-of-principle studies on targeted drug delivery. GCPII thorough biochemical characterization is essential for its appropriate use. Therefore, our laboratory has been investigating GCPII from various perspectives for more...

Orientador: Ronei Miotto. / Dissertação (mestrado) - Universidade Federal do ABC. Programa de Pós Graduação em Nanociências e Materiais Avançados, 2010.