Depuis une trentaine d’années, l’archéologie biomoléculaire s’est principalement attachée à étudier les substances organiques, notamment lipidiques, qui s’absorbent au sein des parois des récipients céramiques au cours de leur utilisation, grâce à des méthodes d’analyse séparative, structurale et isotopique. De façon à étudier les interactions entre la matrice céramique et les substances lipidiques, encore mal comprises, nous avons travaillé dans une perspective globale en prenant en considération l’ensemble du sous-système céramique, depuis l’acquisition des matières premières jusqu’à l’abandon du récipient. Nous avons étudié des tessons archéologiques issus de contextes variés, du point de vue chronologique, géographique et culturel (du Jura à la Sardaigne, entre le VIème et le Ier millénaire BC.), avec les méthodes classiques de l’archéologie biomoléculaire. Cette approche a été complétée avec diverses expérimentations et des méthodes d’analyse complémentaires, issues de la collaboration avec différents champs disciplinaires (étude des méthodes de façonnage, pétrographie des céramiques, sciences des matériaux, étude des sols, etc.). Grâce au formidable potentiel informatif des composés lipidiques et à la compréhension de leurs mécanismes d’absorption et de préservation, nous avons d’une part, identifié des chaînes opératoires de fabrication spécifiques (cuissons à basse température et/ou de courte durée, traitements des surfaces à chaud) et d’autre part, éclairé les modalités d’exploitation et de consommation des produits d’origine naturelle dans les céramiques par les populations pré- et protohistoriques de Méditerranée et du Jura. / For more than 30 years, biomolecular archaeology has been concerned with investigating organic products, mainly lipids, absorbed within archaeological pottery walls during their use thanks to separation, structural and isotopic techniques. To study interactions between the ceramic matrix and lipids, still poorly understood, this doctoral project have been built through a holistic approach that aims to consider the entire pottery subsystem, from the sourcing of raw materials to the disposal of the vessel. For this purpose, archaeological potsherds from various chronological, geographical and cultural contexts (from the Jura to Sardinia, between the VIth and the Ist millennium BC) have been investigated using classical methods of biomolecular archaeology. Additionally a wide range of experiments and complementary analyses were undertaken through collaborative projects involving diverse fields (study of manufacturing techniques, petrography, material science, soil study, etc.). By exploring the considerable informative potential of lipids and precisely understanding their absorption and preservation mechanisms, specific chaînes opératoires (low temperature and/or short firing, post-firing surface treatments) have been revealed and vessel use and resource exploitation by Pre- and Protohistoric society from the Mediterranean and the Jura regions have been explored.

Although seasonal influenza epidemics represent a significant threat to public health, their treatment options remain limited. With deaths from the 1918 influenza pandemic estimated at >50,000,000 worldwide and future pandemics predicted, the need for a potent broad-spectrum influenza therapy is critical. In this thesis, I describe the use of a structurally modified zanamivir, an influenza neuraminidase inhibitor that blocks the release of nascent virus, to deliver attached therapeutic agents specifically to the surfaces of viruses and virus-infected cells, leading to simultaneous inhibition of virus release and immune-mediated destruction of both free virus and virus-infected cells. Chapter 1 describes the major characteristics of the influenza virus, the morbidity and mortality associated with annual infections by current strains of the virus, and the treatments available to reduce the disease burden associated with these infections. Chapter 2 describes the design, synthesis, and evaluation of a zanamivir-related targeting ligand and its conjugation to two orthogonal imaging agents which are then used to characterize the binding specificity and biodistribution of the targeting ligand in influenza virus-infected cells and in infected mice. Chapter 3 describes the development of an influenza virus-targeted immunotherapy, where a zanamivir-targeted hapten is exploited to redirect the immune system to destroy influenza virus and virus-infected cells. When tested in vivo, this immunotherapy is shown to be significantly superior to zanamivir in protecting mice from lethal influenza virus infections. Finally, both a zanamivir-targeted chemotherapy and a CAR-T cell therapy with different mechanisms of cytotoxicity against neuraminidase expressing cells are introduced in Chapter 4.

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has been widely accepted the CF lung airway consists of a complex codependent community of bacteria, viruses, and fungi. To elucidate the interplay among the members of this community, within the constraint of lung uptake regime, I developed a community metabolic network model comprising of >380 metabolites obtained after modeling 39 most abundant bacterial genera across 279 sputum specimens collected from 79 individuals over 10 years from a study by LiPuma et. al. by 16S rRNA gene sequencing, accounting for >89% of reads across samples. The community metabolic model was contrasted with the 16S relative abundance data through standard data mining techniques employed for the analysis of multidimensional data. I further attempted to quantitatively analyze and elucidate the correlations among patient lung function, disease progression, community diversity, microbial compositions, and metabolic capabilities by standard classical hypothesis testing methods. Comparison through linear dimensionality reduction (PCA) of the 16S data and the model data revealed slightly higher variance explained by the model, indicating presence of relatively smaller number of metabolite-based than the 16S-based polymicrobial communities. A deeper analysis elucidated both the phenomena, consolidation of compositionally different communities due to metabolic closeness, as well as splitting of other communities into metabolically distinct clusters due to minor changes in composition and increase in diversity. Clustering of 16S-based relative abundance data and the model data revealed that the rare Burkholderia infections are metabolically distinct from other CF communities, and are heavily dominated by this genus. It was also reiterated that Achromobacter infections are highly resilient to treatment. Linear regression analysis between lung function and microbiota diversity revealed no strong correlation across the population, however, diversity was found to first increase and then subsequently decrease drastically with disease severity.

Molecular recognition, defined as the specific interactions between two or more molecules, is at the center of many biological processes including catalysis, signal transduction, gene regulation and allostery. Allosteric regulation is the modification of function caused by an intermolecular interaction. Allosteric proteins modify their activity in response to a biological signal that is often transmitted through the interaction with a small effector molecule. Therefore, determination of the origins of intermolecular interactions involved in molecular recognition and allostery are essential for understanding biological processes. Classically, molecular recognition and allosteric regulation have been associated to structural changes of the system. NMR spectroscopic methods have indicated that changes in protein dynamics may also contribute to molecular recognition and allostery. This thesis is an investigation of the contributions of both structure and dynamics in molecular binding phenomena. In chapter I, I describe molecular recognition, allostery and examples of allostery and cooperativity. Then I discuss the contribution of protein dynamics to function with a special focus on allosteric regulation. Lastly I introduce the hemoglobin homodimer, HbI of Scapharca inaequivalvis and the mRNA binding protein TIS11d. Chapter II is the primary focus of this thesis on the contribution of protein dynamics to allostery in the dimeric hemoglobin of scapharca inaequivalvis, HbI. Thereafter I concentrate on the mechanism of adenine recognition of the Tristetraprolin-like (TTP) protein TIS11d; this study is detailed in Chapter III. In Chapter IV I discuss broader impacts and future directions of my research. This thesis presents an example of the use of protein NMR spectroscopy to probe ligand binding. The studies presented in this thesis emphasize the importance of dynamics in understanding protein function. Measurements of protein motions will be an element of future studies to understand protein function in health and disease.

Mesoporous silica nanoparticles (MSNPs) possess large surface areas and ample pore space that can be readily modified with specific functional groups for targeted binding of bioactive materials to be transported through cellular barriers. Engineered silica nanoparticles (ESNP) have been used extensively to deliver bio-active materials to target intracellular sites, including as non-viral vectors for nucleic acid (DNA/RNA) delivery such as for siRNA induced interference. The reverse process guided by the same principles is called “nanoharvesting”, where valuable biomolecules are carried out and separated from living and functioning organisms using nano-carriers. This dissertation focuses on ESNP design principles for both applications. To investigate the bioactive materials loading, the adsorption of antioxidant flavonoids was investigated on titania (TiO2) functionalized MSNPs (mean particle diameter ~170 nm). The amount of flavonoid adsorbed onto particle surface was a strong function of active group (TiO2) grafting and a 100-fold increase in the adsorption capacity was observed relative to nonporous particles with similar TiO2 coverage. Active flavonoid was released from the particle surface using citric acid-mediated ligand displacement. Afterwards, nanoharvesting of flavonoids from plant hairy roots is demonstrated using ESNP in which TiO2 and amine functional groups are used as specific binding sites and positive surface charge source, respectively. Isolation of therapeutics was confirmed by increased pharmacological activity of the particles. After nanoharvesting, roots are found to be viable and capable of therapeutic re-synthesis. In order to identify the underlying nanoparticle uptake mechanism, TiO2 content of the plant roots was quantified with exposure to nanoparticles. Temperature (4 or 23 °C) dependent particle recovery, in which time dependent release of ESNP from plant cells showed a similar trend, indicated an energy independent process (passive transport). To achieve the selective separation and nanoharvesting of higher value therapeutics, amine functionalized MSNPs were conjugated with specific functional oligopeptides using a hetero-bifunctional linker. Fluorescence spectroscopy was used to confirm and determine binding efficiency using fluorescently attached peptides. Binding of targeted compounds was confirmed by solution depletion using liquid chromatography–mass spectrometry. The conjugation strategy is generalizable and applicable to harvest the pharmaceuticals produced in plants by selecting a specific oligopeptide that mimic the appropriate binding sites. For related gene delivery applications, the thermodynamic interaction of amine functionalized MSNPs with double-stranded (ds) RNA was investigated by isothermal titration calorimetry (ITC). The heat of interaction was significantly different for particles with larger pore size (3.2 and 7.6 nm) compared to that of small pore particles (1.6 nm) and nonporous particles. Interaction of dsRNA also depended on molecular length, as longer RNA (282 base pair) was unable to load into 1.6 nm particles, consistent with previous confocal microscopy observations. Calculated thermodynamic parameters (enthalpy, entropy and free energy of interaction) are essential to design pore size dependent dsRNA loading, protection and delivery using MSNP carriers. While seemingly diverse, the highly tunable nature of ESNP and their interactions with cells are broadly applicable, and enable facile nano-harvesting and delivery based on a continuous uptake-expulsion mechanism.

In this thesis, we study the problem of protein side chain assignment (SCA) given multiple sources of experimental and modeling data. In particular, the mechanism of X-ray crystallography (X-ray) is re-examined using Fourier analysis, and a novel probabilistic model of X-ray is proposed for SCA's decision making. The relationship between the measurements in X-ray and the desired structure is reformulated in terms of Discrete Fourier Transform (DFT). The decision making is performed by developing a new resolution-dependent electron density map (EDM) model and applying Maximum Likelihood (ML) estimation, which simply reduces to the Least Squares (LS) solution. Calculation of the condence probability associated with this decision making is also given. One possible extension of this novel model is the real-space refinement when the continuous conformational space is used. Furthermore, we present a data fusion scheme combining multi-sources of data to solve SCA problem. The merit of our framework is the capability of exploiting multi-sources of information to make decisions in a probabilistic perspective based on Bayesian inference. Although our approach aims at SCA problem, it can be easily transplanted to solving for the entire protein structure.

<p>The proteasome is a multi-subunit protease complex responsible for most of the non-lysosomal protein turnover in eukaryotic cells. This degradation process can be conducted dependent or independent of ubiquitination as different isoforms with different substrate preferences coexist in the cell. Proteasomal activity declines during aging due to a decreased expression of proteasome subunits, complex disassembly, and oxidative stress. This malfunction leads to protein accumulation, subsequent aggregation, and ultimately diseased states. Considering the shared feature of aggregation and accumulation of intrinsically disordered proteins (IDPs) in age-related diseases, and the substrate preference of the 20S isoform for misfolded proteins, enhancing the proteolytic activity of the 20S proteasome has arisen as an attractive strategy to minimize the burden associated with this increased protein load. Recently, we identified the FDA-approved drug miconazole (MO) as a stimulator of the 20S isoform and validated its activity profile in biochemical and cell-based assays. Given its FDA-approved drug status, we considered that to successfully repurpose it, information regarding its binding location within the 20S and network of binding partners, as well as its value in protein homeostasis in age-related diseases are necessary. Herein, we (1) conduct SAR studies to determine MO’s key features responsible for proteasomal activation and obtain molecules with enhanced ability to activate the 20S proteasome; next, using the developed SAR model, we (2) design a diazirine-based photoreactive probe that allows for the identification of MO’s binding partners and location within the 20S proteasome. Lastly, we (3) explore the use of MO to restore the activity of impaired proteasomes by Parkinson’s disease-associated toxic oligomers. This work expands upon previous research avenues by using newer approaches to study this enzymatic complex, and describes methods that can be further used to better establish the role of the 20S proteasome in age-related diseases.</p>

<p>Deep vein thrombosis (DVT) and Pulmonary embolism (PE) are responsible for over 900,000 cases and 100,000 deaths each year in the US. Direct fibrinolytic agents such as plasmin are being investigated for their treatment. However, plasmin administration is not widely studied as low plasmin concentrations are rapidly inactivated by antiplasmin in vivo, whereas high plasmin doses would deplete endogenous antiplasmin and impose bleeding risks. Thus, a plasmin delivery system that can achieve efficient clot lysis while minimizing inactivation by antiplasmin and has reduced bleeding risks is needed. To address this, we propose using reversible inhibitors of plasmin that can sequester plasmin from antiplasmin and release it on the surface of a fibrin clot to achieve clot lysis. The inhibition must be tuned such that it is strong enough to protect plasmin from antiplasmin and weak enough to release plasmin at the clot for lysis. To achieve this, we utilize principles of multivalency to synthesize three classes of inhibitors with varying potencies and mechanisms of inhibition: (i) Multivalent benzamidines (ii) Multivalent tranexamic acids (TXA), and (iii) Hetero-multivalent inhibitors having both benzamidine and TXA. Benzamidine is a competitive inhibitor of plasmin’s active site. TXA, on the other hand, is an FDA-approved weak active site inhibitor that is primarily used to disrupt plasmin(ogen) from binding to fibrin on the clot by inhibiting plasmin’s kringle domains. Multivalent inhibitors were synthesized using amine-reactive chemistry, purified using RP-HPLC and confirmed with Mass Spectrometry. Inhibition assays were performed to assess inhibition potency by determining Ki values (inhibition constants). Lower Ki values indicate stronger inhibition. With multivalent benzamidine derivatives, it was observed that changing valency and linker length substantially impacted inhibition and resulted in Ki values ranging from 2.1 to 1,395 μM. Inhibitors of higher valencies and shorter linker lengths exhibited stronger inhibition. Multivalent TXAs of valencies 1 to 16 were also tested and they exhibited Ki values varying from 2.5 to 21,370 μM indicating up to 8,548-fold improvement in inhibition due to valency. It was found that monovalent TXA, primarily a kringle inhibitor, can be converted into a stronger active site inhibitor by multivalency. With hetero-bivalent TXA-dPEG36-AMB, simultaneous binding of benzamidine to the active site and TXA to the kringle domains was achieved to attain improved inhibition. These results indicate that multivalency can significantly alter the potency of inhibitors and can modulate plasmin inhibition for drug delivery.</p>

<p> The development of high-quality screening assays for the identification of biologically active ligands is critical in drug discovery. This thesis is aimed at developing new advances m capillary electrophoresis (CE) for the characterization of the conformational stability and enzymatic activity of protein targets with small molecules. CE provides a convenient platform for unbiased assessment of multiple thermodynamic and kinetic parameters associated with biomolecular interactions involving regulatory protein or isomerase enzymes, where various sample pretreatment steps can be integrated directly in-capillary during analysis. The first two chapters of the thesis (Chapters II, III) outline the development of dynamic ligand exchange-affinity capillary electrophoresis (DLEACE) as a novel strategy for the screening of allosteric ligands based on the differential stability of urea-induced unfolding of various apolholo-protein states of cAMP receptor protein constructs. This work introduced a label-free and multivariate approach for ligand selection based on complementary thermodynamic parameters that allowed for determination of the dissociation constant of protein-ligand interactions over a wide dynamic range (> 10^4, Kd = nM-mM). The subsequent two chapters of the thesis (Chapters IV, V) describe the development of a novel kinetic assay for unbiased characterization of isomerase activity associated with D/L-amino acid metabolism using hydroxyproline epimerase as a model system. Stereoselective resolution of various hydroxyproline isomers was accomplished via off-line or on-line chemical derivatization with dynamic complexation usmg chiral selector(s) in order to screen potential inhibitors for putative epimerase and racemase activity. The integration of both thermodynamic and kinetic strategies for differentiation of mutant from wild-type enzymes was important for revealing the function of a catalytic acid/base cysteine pair in the epimerase active site. Overall, this thesis outlines an integrative framework based on CE for high-quality screening, which is relevant in reducing the high attrition rate of lead candidates in drug development. </p> / Thesis / Doctor of Philosophy (PhD)

Over the course of more than ten years, there has been a significant increase in the approach employed to inhibit the function of soluble epoxide hydrolase (sEH). The phenomenon of upregulating soluble epoxide hydrolase (sEH) has been found to result in a decrease in the ratio of epoxyeicosatrienoic acids (EETs) to dihydroeicosatrienoic acids (DHETs) in the body. This has garnered significant attention due to the diverse biological functions attributed to EETs, including the regulation of vasodilation, neuroprotection, increased fibrinolysis, calcium ion influx, and anti-inflammatory effects. Consequently, there has been a growing interest in developing and discovering sEH inhibitors through chemical syntheses and natural extracts, with the aim of increasing the availability of these anti-inflammatory molecules by reducing their hydrolysis. A comprehensive examination of this project was conducted to explore the inhibitory effects of YMSV, a tetrapeptide derived from the castor bean (Ricinus communis), on sEH, as well as to elucidate its underlying mechanism of action. YMSV was determined to function as a mixed-competitive inhibitor of soluble epoxide hydrolase (sEH), and the interaction between the peptide and the protein resulted in the disruption of the secondary structural composition of sEH. Furthermore, the hydrogen bond interactions between YMSV and the Asp 333 residue in the active region of soluble epoxide hydrolase (sEH) were demonstrated using molecular docking investigations. However, quantitative structure-activity relationship (QSAR) research revealed that nonpolar, hydrophobic, and bulky amino acids are favored at the N- and C- terminals of peptides for sEH inhibition. The results of this study indicate that peptides obtained from dietary sources possess unique characteristics as inhibitors of soluble epoxide hydrolase (sEH), displaying significant potency. Consequently, these peptides have promise for further development as therapeutic medicines targeting inflammation and depression in the future.