Dissertations / Theses on the topic '030401 Biologically Active Molecules'

Diatoms are unicellular photosynthetic microalgae responsible for approximately 40% of marine primary productivity. This algal class has traditionally been regarded as providing the bulk of the food that sustains the marine food chain to top consumers and important fisheries. However, this beneficial role has recently been questioned on the basis of laboratory and field studies showing that although dominant zooplankton grazers such as copepods feed extensively on diatoms, the hatching success of eggs thus produced is seriously impaired. Short chain polyunsaturated aldehydes, such as 2,4,7-decatrienal and 2,4-decadienal, were correlated to the antiproliferative effect of diatoms on copepod reproduction. After establishing a method of analysis, the aldehyde profile of some ecologically relevant species of marine diatoms was assessed. The results showed that the production of aldehydes is species-specific. Detailed chemical analysis revealed the presence of fatty acid derivatives other than aldehydes such as hydroxyacids, ketoacids, oxoacids and epoxyalcohols, increasing the complexity of a chemical defence of diatoms mediated only by aldehydes. All these compounds belong to a class of compounds called oxylipins, that are oxygenated compounds biosynthesized from fatty acids by oxygenasecatalyzed oxygenation. Marine diatoms are able to produce the major antiproliferative oxylipins by a novel oxygenase-dependent oxidation of C16 fatty acids hexadecatrienoic acid (16:3 (w-4)) and hexadecatetrenoic acid (16:4 (w-1)), and C2o eicosapentaenoic acid (20:5 (w-3)). This process is triggered by lypolitic acyl hydrolase activity, that feeds the downstream lipoxygenase pathway. The ecological meaning of the oxylipin pathway in the diatom-copepod interactions is discussed, showing that attention should move from single compounds to complex biochemical process. The deleterious effect on copepod reproduction could be due to a biochemical process such as the generation of an high oxidative potential, rather than only by aldehydes or other secondary oxygenated products, that when present can co-occur to produce the final effect.

Pancratistatin and narciclasine are natural products isolated from Pancratium litorale1 and Narcissus poeticus2 respectively. Pancratistatin and Narciclasine have been shown to possess potent antitumour activity3 however they have never been widely exploited due to their limited availability from natural sources.4 Pancratistatin and narciclasine both contain a dihydroisoquinolinone framework. The work described in this thesis explores synthetic routes relating to this dihydroisoquinolinone framework, as well as comparable tetrahydroisoquinolines. An initial proposed synthetic route involved the synthesis of the dihydroisoquinolinone framework via the corresponding indanone. Indanones have also been shown to possess potential antitumour activity.5 A range of lactam and indanone analogues were synthesised and a selection were tested for biological activity against cancer cell lines. The most biologically active lactam analogue synthesised was lactam 170. Lactam 170 was synthesised via two steps from commercially available starting materials in an overall 51 % yield and was tested in the HT29 colon cancer cell line to give an IC50 value of 9 μM. Indanone 177 is an analogue of natural product indanocine and was synthesised via two steps in an overall 49 % yield. Analogue 177 was tested in the 60 cell line screen by the National Cancer Institute (NCI) to give a mean GI50 value of 1.29 μM and is currently under consideration for further testing. This thesis describes the synthesis and biological testing of the aforementioned compounds as well as an array of analogues.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2004.
Includes bibliographical references (p. 92-96).
Separation of biologically active molecules (BAM's) is a problem for the pharmaceutical and biotechnology industries. Current technologies addressing this problem require too many techniques, toxic additives, and time to filter desired materials. As a result, a new technology is needed. The objective of this thesis is to contribute towards the development of a new method for separating biologically active molecules in the size range of 0.5 nanometers to 500 nanometers. A normally open diaphragm valve is proposed that can control a gap formed by two flat surfaces. For accurate control of gap height, the valve was designed to ensure that the flat surfaces remain parallel during operation . Modularity was also part of design considerations to address issues of eventual biocompatibility breakdown specifically protein adsorption. Control of the gap has been achieved to increments of 1.8 nanometers.
by Mauricio R. Gutierrez.
S.M.

The post genomic era, set the challenge to develop drugs that target an ever-growing list of proteins associated with diseases. However, an increase in the number of drugs approved every year is nowadays still not observed. To overcome this gap, innovative approaches should be applied in drug discovery for target validation, and at the same time organic synthetic chemistry has to find new fruitful strategies to obtain biologically active small molecules not only as therapeutic agents, but also as diagnostic tools to identify possible cellular targets. In this context, in view of the multifactorial mechanistic nature of cancer, new chimeric molecules, which can be either antitumor lead candidates, or valuable chemical tools to study molecular pathways in cancer cells, were developed using a multitarget-directed drug design strategy. According to this approach, the desired hybrid compounds were obtained by combining in a single chemical entity SAHA analogues, targeting histone deacetylases (HDACs), with substituted stilbene or terphenyl derivatives able to block cell cycle, to induce apoptosis and cell differentiation and with Sorafenib derivative, a multikinase inhibitor. The new chimeric derivatives were characterized with respect to their cytotoxic activity and their effects on cell cycle progression on leukemia Bcr-Abl-expressing K562 cell lines, as well as their HDACs inhibition. Preliminary results confirmed that one of the hybrid compounds has the desired chimeric profile. A distinct project was developed in the laboratory of Dr Spring, regarding the synthesis of a diversity-oriented synthesis (DOS) library of macrocyclic peptidomimetics. From a biological point of view, this class of molecules is extremely interesting but underrepresented in drug discovery due to the poor synthetic accessibility. Therefore it represents a valid challenge for DOS to take on. A build/couple/pair (B/C/P) approach provided, in an efficient manner and in few steps, the structural diversity and complexity required for such compounds.

In the past years, genome biology had disclosed an ever-growing kind of biological targets that emerged as ideal points for therapeutic intervention. Nevertheless, the number of new chemical entities (NCEs) translated into effective therapies employed in the clinic, still not observed. Innovative strategies in drug discovery combined with different approaches to drug design should be searched for bridge this gap. In this context organic synthetic chemistry had to provide for effective strategies to achieve biologically active small molecules to consider not only as potentially drug candidates, but also as chemical tools to dissect biological systems. In this scenario, during my PhD, inspired by the Biology-oriented Synthesis approach, a small library of hybrid molecules endowed with privileged scaffolds, able to block cell cycle and to induce apoptosis and cell differentiation, merged with natural-like cores were synthesized. A synthetic platform which joined a Domino Knoevenagel-Diels Alder reaction with a Suzuki coupling was performed in order to reach the hybrid compounds. These molecules can represent either antitumor lead candidates, or valuable chemical tools to study molecular pathways in cancer cells. The biological profile expressed by some of these derivatives showed a well defined antiproliferative activity on leukemia Bcr-Abl expressing K562 cell lines. A parallel project regarded the rational design and synthesis of minimally structurally hERG blockers with the purpose of enhancing the SAR studies of a previously synthesized collection. A Target-Oriented Synthesis approach was applied. Combining conventional and microwave heating, the desired final compounds were achieved in good yields and reaction rates. The preliminary biological results of the compounds, showed a potent blocking activity. The obtained small set of hERG blockers, was able to gain more insight the minimal structural requirements for hERG liability, which is mandatory to investigate in order to reduce the risk of potential side effects of new drug candidates.

La dernière classe de matériaux poreux, les solides hybrides inorganiques-organiques cristallisés aussi communément appelés Metal-Organic Frameworks (MOFs) présente de nombreux avantages pour des applications biomedicales, tels que grandes tailles de pores, biodégradabilité et propriétés d’imagerie médicale. Cependant, on a proposé d’évaluer la citotoxicité des MOFs avec différent composition et structure chez deux différent lignes cellulaire. Nous avons observé que les MOFs présent nul ou très faible citotoxicité et que cela dépend de la ligne cellulaire, du métal et de la taille de particule. Concernant MOFs comment systèmes de libération contrôle de médicaments, nous avons entrepris une étude systématique de l'encapsulation et la libération de molécules modèles telles que la caféine (cosmetique), à partir d’une série de MOFs peu toxiques, possédant des compositions et topologies différentes. Les résultats montrent que l’encapsulation et la cinétique de libération de caféine peuvent être modulées en jouant avec la composition et la structure des MOFs. La dernière approche de ce travail a consisté en la mise en forme de patchs constitués de mélanges hybrides organiques-inorganiques avec le MIL-100 chargé avec la caféine et les polymères biocompatibles pour administration transdermique de médicament. Les études de libération in vitro ont montré que les patchs hybrides sont plus efficaces pour ralentir la libération de la caféine. Les études ex vitro réalisées en chambre d’Ussing ont démontré une plus grande absorption de la caféine sur la peau dans le patch Gel-CAF et légèrement similaire dans le cas de MIL-100-CAF-Gel en comparaison avec la crème commerciale caféine
The last class of porous materials, organic-inorganic hybrid solids crystalline also commonly called Metal-Organic Frameworks (MOFs) has many advantages for biomedical applications, such as large pore sizes, biodegradability and properties of medical imaging. However, it was proposed to evaluate the cytotoxicity of MOFs with different composition and structure in two different cell lines. We found that MOFs present no or very low cytotoxicity and that depends on the cell line, metal and particle size. Regarding MOFs as controlled drugs release systems, we perfomed a systematic study of the encapsulation and release of model compounds such as caffeine (cosmetics), from a series of MOFs with low toxicity, compositions and topologies different. Results showed that encapsulation and kinetics release of caffeine can be modulated by changing the composition and structure of MOFs. The last approach of this work consisted in forming patches consisting of organic-inorganic hybrid mixtures with the MIL-100 loaded with caffeine and biocompatible polymers for transdermal drug delivery. In vitro release studies showed that the hybrid patches are more effective for slow release caffeine. Studies ex vitro carried out in Ussing chamber showed a greater absorption of caffeine on the skin patch and Gel-CAF somewhat similar in the case of MIL-100-CAF-Gel compared with commercial cream caffeine

The foci of this dissertation are on advanced liquid chromatography (LC) separation and mass spectrometry (MS) techniques for the analysis of small bioactive molecules. In addition to discussing general aspects of such techniques the results from analyses of polyphenols (PPs), alkaloids and amino acids published in five appended studies are presented and discussed. High efficiency and well understood principles make LC the method of choice for separating analytes in many kinds of scientific investigations. Moreover, when LC is coupled to an MS instrument, analytes are separated in two stages: firstly they are separated and pre-concentrated in narrow bands using LC and then separated according to their mass-to-charge (m/z) ratios in the MS instrument. Some MS instruments can provide highly accurate molecular weight measurements and mass resolution allowing identification of unknown compounds based purely on MS data, thus making prior separation unnecessary. However, prior separation is essential for analyzing substances in most complex matrices – especially useful is the ultra-high performance LC (UHPLC). The advantages of using UHPLC rather than HPLC for the analysis of PPs in tea and wine were evaluated in one of the studies this thesis is based upon. The phenolic composition of red wine was also examined, using a novel LDI technique, following solid phase extraction (SPE). A class of small aromatic molecules (medicinally important alkaloids) also proved to be amenable to straightforward analysis, by thin layer chromatography (TLC) work-up followed by LDI-MS. Finally, a LC-MS method for monitoring neurotoxins (β-N-methyl-amino-L-alanine and 2,3-diaminobutyric acid) in complex biological matrices was developed and applied. Overall, the studies show that careful attention to the physicochemical properties of analytes can provide insights that can greatly facilitate the development of alternative methods to analyze them, e.g. by LDI.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In press. Paper 5: Manuscript.

Diss. (sammanfattning) Stockholm : Stockholms universitet, 2010.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: In press. Paper 5: Manuscript. Härtill 5 uppsatser.

The metal-catalysed allylic oxidation of alkenes has emerged as a powerful method for the functionalisation of Sp3 C-H bonds. This transformation has allowed for the expedient preparation of synthetically useful materials from hydrocarbon building blocks. With the development of air stable and environmentally benign copper(I)-NHC catalysts from readily available materials, it has been shown that these catalysts can participate in the allylic oxidation of alkenes in an effective manner. We have developed a powerful protocol for the functionalisation of alkenes into allylic alcohols and enones, by the use of different terminal oxidants in a divergent fashion. The highly regio- and chemoselective copper(I)-NHC-catalysed allylic oxidation has been examined in the syntheses of functionalised cyclopentenones and cyclohexenones, which has provided mechanistic insights into the oxidation. The system displays excellent tolerance of a plethora of sensitive functional groups and provides a general approach with high efficiency. It has been shown that high regioselectivity is not necessary straightforward and can depend on many factors, including stereoelectronic interactions. The studies towards the enantioselective variant via the desyrnrnetrisation of the proposed prochiral intermediate utilising a range of chiral copper(I)-NHC catalysts was unsuccessful. The synthetic utility of this transformation has been validated by the total synthesis of (±)-untenone A in the shortest and most efficient approach to date. Studies towards the total synthesis of cephalimysin A are currently ongoing, which would employ the late stage copper(I)-NHC-catalysed allylic oxidation on a densely functionalised intermediate.

A interação de várias substancias bioativas com monocamadas de fosfolipídios foi investigada usando isotermas de pressão e potencial de superfície, incluindo as drogas farmacológicas dipiridamol (DIP), clopromazina (CPZ) e trifluoperazina (TFP), além da melatonina (MEL) e o colesterol (COL). Os fosfolipídios empregados foram o zwiteriônico dipalmitoil fosfatidil colina (DPPC) e o aniônico dipalmitoil fosfatidil glicerol (DPPG) espalhados na superfície de água ultrapura, sendo que as monocamadas servem como modelo simples de membranas. A cooperatividade na interação entre fosfolipídios e moléculas com atividade biológica foi essencial para entender os acentuados efeitos na expansão (ou condensação) das monocamadas e as mudanças no momento de dipolo (até 10% de aumento na expansão em relação à monocamada do fosfolipídio puro para as misturas DIP/DPPC) que ocorreram a concentrações molares muito baixas entre 0,2-0,4% do DIP. Tais efeitos foram observados para todas as cinco substâncias investigadas, em todos os regimes de pressão. Nas altas concentrações, o comportamento da interação depende do tipo de mólecula e também de se a monocamada é de DPPC ou DPPG. Para o DPPC, as drogas farmacológicas foram expelidas da interface em vários graus a altas pressões, e existia um máximo de concentração da droga acima do qual ocorria a saturação, provavelmente porque as moléculas em excesso foram para a subfase. Essas concentrações críticas foram de 2% em mol para o DIP e a CPZ e de 5% em mol para a TFP. Para o DIP, em particular, os resultados das isotermas foram correlacionados com experimentos de espectroscopia de FTIR e microscopia de fluorescência \"in situ\", realizados por colaboradores, os quais permitiram a determinação de uma localização precisa da droga estudada. Não existe inserção do DIP na região da cauda hidrofóbica da monocamada do DPPC, com a interação ocorrendo com o grupo fosfato no zwiteríon, cujas pequenas mudanças na orientação induzidas pelo DIP levam a grandes mudanças no momento de dipolo. Como o DPPG está carregado negativamente sobre a superfície da água pura, não existe saturação nos efeitos de expansão com o aumento da concentração das drogas. O aumento do momento de dipolo efetivo na monocamada mista é atribuído a alterações na densidade de carga superficial pela adsorção da droga catiônica, que reduz a contribuição negativa do potencial da dupla camada, quando comparado com o da monocamada de DPPG puro. Os resultados do COL e a MEL devem ser considerados separadamente devido a sua natureza distinta, embora um comportamento cooperativo também tenha observado com grandes efeitos nas baixas concentrações. Tanto o COL como o MEL induzem mudanças na expansão das monocamadas de DPPC até a máxima concentração empregada, 20% molar. Para o COL foi observado um efeito de condensação a baixas concentrações, o qual foi seguido por uma expansão a altas concentrações, confirmando assim resultados prévios da literatura. Todas as monocamadas mistas COL/DPPG apresentavam-se expandidas, também confirmando alguns resultados da literatura para lipídios (diferentes do DPPC) quando misturados com o COL. A interação da MEL com o DPPC foi essencialmente similar à do COL, apesar do fato de a MEL pura não formar monocamadas estáveis. Sua interação com o DPPG foi peculiar já que o efeito que esta induz satura a 5% em mol. Isto também difere do comportamento das drogas farmacológicas. A MEL é neutra em todos os pHs, portanto, sua intenção com as membranas modelo de DPPG e DPPC só pode ocorrer via dipolo. O mesmo se aplica ao colesterol, o que justifica as diferenças no comportameto destas duas moléculas quando comparadas com as drogas (DIP, CPZ, TFP), que são carregadas sobre a água pura, nas misturas com os dois fosfolipídios (DPPG e DPPC).
The interaction of various bioactive substances with phospholipids monolayers has been investigated using surface pressure and surface potential isotherms, which include the pharmaceutical drugs dipyridamole (DIP), chlorpromazine (CPZ) and trifluoperazine (TFP), in addition to melatonin (MEL) and cholesterol (COL). The phospholipids employed were the zwitterionic dipalmitoyl phosphatidyl choline (DPPC) and the anionic dipalmitoyl phosphatidyl glycerol (DPPG) spread onto ultra pure water surfaces, where the monolayers served as simple model membrane systems. Cooperativity in the interaction between phospholipid and bioactive molecules was essential to account for the large effects of expansion (up to 10% increase in area in relation to the pure phospholipid monolayer for the DIP/DPPC mixture) of the monolayers and changes in dipole moment, which occurred at very low concentrations, e.g. 0.2 - 0.4 mol% of the substance. Such large effects were observed for all 5 substances investigated, at all surface pressure regimes. At higher concentrations, the interaction behavior depended on the type of molecule and also on whether the host monolayer was DPPC or DPPG. For DPPC, the pharmaceutical drugs were expelled at varying degrees from the interface at high surface pressures, and there was a maximum drug concentration above which the effects saturated, probably because the molecules in excess were lost to the subphase. These critical concentrations were 2mol% for DIP and CPZ and 5mol% for TFP. For DIP, in particular, the results from isotherm were correlated with in situ FTIR spectroscopy and fluorescent microscopy experiments, carried out by collaborators, which allowed the precise location of the drug to be determined. There is no insertion of DIP into the hydrophobic tail region of the DPPC monolayer, with interaction taking place with the phosphate group in the zwitterion, whose small changes in orientation induced by DIP lead to the large changes in dipole moment. Because DPPG is negatively charged on a pure water surface monolayer, there is no saturation of the expansion effects with the increase in drug concentration. The increase in the effective dipole moment of the mixed monolayers are attributed to alterations in the surface charge density by adsorption of the cationic drugs, which then reduces the negative contribution of the double-layer potential as compared to the pure DPPG monolayer. The results for COL and MEL must be considered separately owing to their distinct nature, even though a cooperative behavior was also observed with large effects at low concentrations. Both COL and MEL induce changes in the DPPC monolayers up to the highest concentration employed, viz. 20mol%. For COL, a condensation effect was observed at low concentrations, which was followed by monolayer expansion at high concentrations, thus confirming previous results in the literature. All COL/DPPG monolayers were more expanded than pure DPPG, also confirming previous results from the literature. While the interaction of MEL with DPPC was essentially similar to that of COL, in spite of the fact that MEL does not form stable monolayers on its own, its interaction with DPPG was somewhat peculiar in that the effects it induced saturate at 5mol%. This also differs from the behavior of the pharmaceutical drugs. MEL is neutral over a wide range of pHs, and therefore its interaction with DPPC and DPPG monolayers must occur via dipole interaction. The same applies to COL, and this explains why the behavior of these two substances is different from the drugs (DIP, CPZ and TFP) that are charged on the water surface, in the interaction with DPPC and DPPG.

碩士
東海大學
化學系
103
This thesis describes the application of multi-component reactions (MCRs) to the synthesis of potentially biologically active molecules. The first part discusses microwave-assisted synthesis of a series of pyrano[2,3-b]pyridines derivatives using pipecolic acid, aldehyde, and coumarin as the three substrates. The second part again describes the MCR synthesis of a series of pyrrolizidine derivatives through the combinations of different proline, aldehyde, and ,-unsaturated 1,3-indenedione under microwave irradiation conditions. The third part focuses on a pseudo three component reaction of 4-chloro-3-nitrocoumarin and acetophenone to afford azepine derivatives.

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006.
Source: Dissertation Abstracts International, Volume: 68-02, Section: B, page: 0981. Adviser: Paul J. Hergenrother. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Bismuth(III) has been used in the medicinal industry for many years, but its mechanism of action is not fully understood and there is very little information on thermodynamic and kinetic parameters for complex formation. Amino acids are the building blocks of life and so, by initially simply determining the complexing ability of various amino acids with bismuth, an indication of how bismuth could interact in the body can slowly be developed and could assist in the eventual development and design of more effective bismuth containing drugs.

Small molecules have played an important role in defining the functions and identities of numerous proteins involved in fundamental biological processes as well as pathways involved in disease. Chemical genetics represents the formalization of this process into a defined field desiring to achieve the breadth and specificity of classical genetics. In order to gain full advantage of a small molecule's ability to perturb the cell for novel or desired phenotypes, a complete understanding of the molecule's mechanism of action must be achieved. Identification of the biological targets of a molecule represents the most direct approach to attaining this knowledge. In our strategy to find novel mechanisms to target cancers with oncogenic RAS mutations, we have used small molecules to probe specific weaknesses of this cancerous network through synthetic lethal screening. One molecule identified in these screens, RSL3, attracted interest as a candidate for target identification studies because of its potent lethality and potentially unique mechanism of action. We used an affinity chromatography approach to directly isolate binding partners of RSL3 by modifying the molecules structure to incorporate various affinity tags. Through these experiments we ultimately identified a number of interesting candidate targets. Investigations validating these targets suggest that multi-targeted modulation of antioxidant and prostaglandin networks may be a mechanism for selectively killing cancers with oncogenic RAS. The identification of biological targets of small molecules poses a difficult challenge to the field of forward chemical genetics. Thus, we attempted to optimize a unique method for target identification, the yeast three-hybrid system (Y3H), which detects small molecule-protein interactions through a transcriptional assay in vivo. We created a version of our Y3H system that incorporated a covalent anchor and compared it with the existing state-of-the-art, which uses a high affinity non-covalent anchor. Transcriptional assays indicated our new system was functional, but surprisingly could not improve upon the original Y3H system. These results highlight the complexities of manipulating ligand-receptor interactions in vivo.

Simulations of various hydration levels of lamellar phase 23:2 Diyne PC were performed, and subsequent, serial docking simulations of a tyrosine monomer were replicated for each system in both hydrated and dehydrated states.
The goal was to evaluate how hydration impacts self-assembly and crystallization on the surface, and
whether or not these simulations, when run sequentially, could determine the answer. It was discovered that hydrated and dehydrated surfaces behave differently, and that
headgroup orientation plays a role in the initial docking and self-assembly process of the tyrosine monomer. It was also determined that potential energy as a sole metric
for determining whether or not a specific conformation of intermolecular orientation is not entirely useful, and docking scores are likely useful metrics in discriminating between conformations with identical potential energy values.

Cyclobutane pyrimidine dimers (CPD) are the predominant DNA lesions formed upon exposure of this biopolymer to sunlight. Given the potentially dire biological consequences of DNA lesions, there is a need to fully characterize their behaviour, with an eye towards understanding their complete reactivity and as a possible means to detect and quantify their presence in the genome. The work described in this dissertation describes studies of the alkaline reactivity of CPD lesions generated within dinucleotide & polynucleotide strands. It was found that CPD-TpT is generally inert under alkaline conditions at room temperature, which is in agreement with earlier studies on alkaline hydrolysis of CPD-thymine and CPD-thymidine. However, a re-evaluation of the same reaction in the presence of ¹⁸O labelled water demonstrated that, similar to other UV-induced DNA lesions containing a saturated pyrimidine ring, CPD undergoes a water addition at the C4=O group of the nucleobase leading to the formation of a hemiaminal intermediate. This intermediate, however, does not lead to hydrolysis products and completely reverts to starting material under those same conditions. Moreover, the two C4=O groups present on 3′ and 5′-thymines in a CPD molecule show different chemical reactivities, with the 3′ C4=O group having greater affinity towards water addition as compared to the one on 5′ end, a fact reflected in different rates of exchange with the incoming nucleophile leading to the hemiaminal intermediate. The ¹⁸O labelling reaction was also investigated in CPD lesions generated within oligonucleotides to probe the cause of asymmetry between the 3′ vs 5′ C4=O groups; ultimately, it was determined that the asymmetric reactivity observed to occur between the two C4=O groups was an intrinsic property of the CPD molecule and did not arise as a result of asymmetry in a dinucleotide setting.

In addition to the above studies, during the course of the investigation of the nucleophilic reactivity of CPD, a chemical reaction was observed leading to what appeared to be the rapid and total chemical reversal of CPD lesions to the original TpT (thymine-thymine dinucleotide)! This “repair” reaction occurred when CPD reacted with hydrazine, and appears facilitated by an inert atmosphere under which it rapidly proceeds to completion at room temperature.

Pathogenic bacteria present a critical threat to modern medicine. Therapeutic strategies to target and eliminate resilient bacteria are not advancing at the same rate as the emergence of bacterial resistance. An associated urgent concern regarding antibiotic resistance is the existence and proliferation of intracellular bacteria, which find refuge from bactericidal mechanisms by hiding within mammalian cells. Therefore, many once-successful antibiotics become ineffective through the development of resistance, or through failure to reach intracellular locations in therapeutic concentration. To overcome these challenges, the covalent combination of a conventional antibiotic with an antibiotic, cell-penetrating peptide was explored to develop dual-action antibiotic conjugates.

Herein, we utilized a strategy in conjugating the antibiotics by a cleavable linkage to cationic amphiphilic polyproline helices (CAPHs) to improve vancomycin and linezolid antibiotics. This approach enables the conjugate to penetrate cells and deliver two potent monomeric antimicrobial drugs. The vancomycin-CAPH conjugate, VanP14S, showed enhanced mammalian cell uptake compared to vancomycin, a poor mammalian cell-penetrating agent; and VanP14S was capable of cleaving and releasing two antibiotics under mimicked physiological conditions. Enhanced antibacterial activity was observed against a spectrum of Gram-positive and Gram-negative pathogens, including drug-resistant strains. Further investigation revealed that this conjugate’s bactericidal activity was not entirely the result of significant membrane perturbation such as a lytic mode of action. Mammalian cell toxicity and red blood cell lysis were insignificant at relevant bactericidal concentrations below 20 µM. The current results suggest an enhanced binding to the peptidoglycan of bacteria, the target of vancomycin, although more work is needed to justify this claim. Preliminary results on VanP14GAPS, a conjugate with a more rigid CAPH, convey similar activity to VanP14S; however, moderate increases in red blood cell lysis and cytotoxicity were observed.

Regarding the LnzP14 conjugate, preliminary data reveal that the conjugate has Gram-negative activity against Escherichia coli, whereas linezolid is ineffective in killing Gram-negative bacteria. This conjugate showed significant enhancement in cellular uptake compared to the CAPH, and the release of linezolid and CAPH in physiological conditions was confirmed. Overall, arming a conventional antibiotic with an antimicrobial, cell-penetrating peptide appears to be a powerful strategy in providing novel antibiotic conjugates with the propensity to overcome the limitations in treating challenging pathogens.

Decytospolides A and B are natural products isolated from Cytospora sp. No ZW02 that show mild anticancer properties. The interest in synthesizing these compound lies not in their activities, but rather the simplicity of the structure which could easily be modified to provide more potent derivatives. Previous syntheses of these compounds relied on transition metals to install the tetrahydropyran core or extensive use of protecting groups. Our first generation synthesis made use of the Achmatowicz rearrangement to synthesize the tetrahydropyran moiety. Based on this, a concise, protecting group free synthesis has been accomplished utilizing the Achmatowicz rearrangement of an optically active furanyl alcohol followed by diastereoselective Kishi reduction of the resulting dihydropyranone hemiacetal.

Carambolaflavone A is a natural product isolated from A. carambola with antidiabetic properties. Notably, these compound promote both insulin secretion and glucose uptake by muscle cells in hyperglycemic rats. A previous synthesis has been reported by Wang and coworkers, however this synthesis does not offer much potential for the formation of derivatives and relies on a C-glycosylation that requires heating for regio- and diastereoselectivity. Progress towards a concise synthesis has been made featuring a Lewis acid promoted highly diastereoselective substrate controlled C-glycosylation that does not require heating and a one pot oxidation of chroman to chromone utilizing DDQ. Further research is underway to complete the synthesis of this molecule by an oxidative addition to the chromone and subsequent removal of protecting groups.

Microglia are a population of specialized, tissue-resident immune cells that make up around 10% of total cells in our brain. They actively prune neuronal synapses, engulf cellular debris, and misfolded protein aggregates such as the Alzheimer’s Disease (AD)-associated amyloid-beta (Aβ) by the process of phagocytosis. During AD, microglia are unable to phagocytose Aβ, perhaps due to the several disease-associated changes affecting their normal function. Functional molecules such as lipids and metabolites also influence microglial behavior but have primarily remained uncharacterized to date. The overarching question of this work is, How do microglia become dysfunctional in chronic inflammation? To this end, we developed new chemical tools to better understand and investigate the microglial response to Aβ in vitro and in vivo. Specifically, we introduce three new tools. (1) Recombinant human Aβ was developed via a rapid, refined, and robust method for expressing, purifying, and characterizing the protein. (2) A pH-sensitive fluorophore conjugate of Aβ (called Aβ^pH) was developed to identify and separate Aβ-specific phagocytic and non-phagocytic glial cells ex vivo and in vivo. (3) New lysosomal, mitochondrial, and nuclei-targeting pH-activable fluorescent probes (called LysoShine, MitoShine, and NucShine, respectively) to visualize subcellular organelles in live microglia. Next, we asked, What changes occur to the global lipid and metabolite profiles of microglia in the presence of Aβ in vitro and in vivo? We screened 1500 lipids comprising 10 lipid classes and 700 metabolites in microglia exposed to Aβ. We found significant changes in specific lipid classes with acute and prolonged Aβ exposure. We also identified a lipid-related protein that was differentially regulated due to Aβ in vivo. This new lipid reprogramming mechanism “turned on” in the presence of cellular stress was also present in microglia in the brains of the 5xFAD mouse model, suggesting a generic response to inflammation and toxicity. It is well known that activated microglia induce reactive astrocytes during inflammation. Therefore, we asked, What changes in proteins, lipids, and metabolites occur in astrocytes due to their reactive state? We provide a comprehensive characterization of reactive astrocytes comprising 3660 proteins, 1500 lipids, and 700 metabolites. These microglia and astrocytes datasets will be available to the scientific community as a web application. We propose a final model wherein the molecules secreted by reactive astrocytes may also induce lipid-related changes to the microglial cell state in inflammation. In conclusion, this thesis highlights chemical neuroimmunology as the new frontier of neuroscience propelled by the development of new chemical tools and techniques to characterize glial cell states and function in neurodegeneration.

New experimental strategies and algorithmic approaches were devised and tested to improve the analysis of pharmaceutically relevant materials. These new methods were developed to address key bottlenecks in the design of amorphous solid dispersions for the delivery of low-solubility active pharmaceutical ingredients in the final dosage forms exhibiting high bioavailability.

Infectious diseases caused by bacteria, fungi, and plasmodium parasites are a huge global health problem which ultimately leads to millions of deaths annually. The emergence of strains that exhibit resistance to nearly every class of antimicrobial agents, and the inability to keep up with these resistance trends has brought to the fore the need for new therapeutic agents (antibacterial, antifungal, and antimalarial) with novel scaffolds and functionalities capable of targeting microbial resistance. A novel class of compounds featuring an aryl isonitrile moiety has been discovered that exhibits potent inhibitory activity against several clinically relevant strains of methicillin-resistant Staphylococcus aureus (MRSA). Synthesis, structure-activity relationship (SAR) studies, and biological investigations have led to lead molecules that exhibit anti-MRSA inhibitory activity as low as 1 – 2 µM. The most potent compounds have also been shown to have low toxicity against mammalian cells and exhibit in vivo efficacy in MRSA skin and thigh infection mouse models.

The novel aryl isonitriles have also been evaluated for antifungal activity. This study examines the SAR of aryl isonitrile compounds and showed the isonitriles as compounds that exhibit broad spectrum antifungal activity against species of Candida and Cryptococcus. The most potent derivatives are capable of inhibiting growth of these pathogens at concentrations as low as 0.5 µM. Notably, the most active compounds exhibit excellent safety profile and are non-toxic to mammalian cells up to 256 µM.

Beyond the antibacterial and antifungal activities, structure-antimalarial relationship analysis of over 40 novel aryl isonitrile compounds has established the importance of the isonitrile functionality as an important moiety for antimalarial activity. Of the many isonitrile compounds exhibiting potent antimalarial activity, two have emerged as leads with activity comparable to that of Artemisinin. The SAR details presented in this study will prove essential for the development new aryl isonitrile analogues to advance them to the next step in the antimalarial drug discovery process.

17-nor-Excelsinidine, a zwitterion monoterpene indole alkaloid isolated from Alstonia scholaris is a subject of synthetic scrutiny. This is primarily due to its intriguing chemical structure which includes a bridged bicyclic ammonium moiety, and its anti-adenovirus and anti-HSV activity. Herein we describe a six-step total synthesis of (±)-17-nor-Excelsinidine from tryptamine. Key to the success of this synthesis is the use of palladium-catalyzed carbonylative heck lactamization methodology which built the 6, 7-membered ring lactam in one step. The resulting pentacyclic product, beyond facilitating the easy access to (±)-17-nor-Excelsinidine, could also serve as a precursor to other related indole alkaloids.