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Opioid analgesics have been a major contribution to pain therapy with opioids being used as an effective treatment for various recalcitrant pain conditions. The drug class has come under increased scrutiny due to the raising concerns about the public health crisis of opioid misuse and addiction, thereby increasing the need for alternative and safer analgesics. The exploration of alternative pharmacotherapy for pain management has led to an increasing paradigm shift towards the development of a single-drug-multiple-target approach that takes inspiration from numerous naturally occurring drugs. The mu-opioid receptor has been the primary target for the management of pain; however, the voltage-gated sodium channel Nav1.7 is gaining attention as a putative antinociceptive target based on human genetic evidence. The proposed research aims to develop multi-target directed ligands (MTDL) that modulates two key targets for pain perception, the MOR, and Nav1.7 to generate analgesics with reduced side effects and enhanced analgesia. This will be achieved by exploiting polypharmacology to develop hybrid analgesia in two ways: (i) performing structure-activity relationship (SAR) studies to design a single drug with two pharmacophores that specifically interacts with both the targets (ii) exploiting in silico techniques by performing structure-based virtual ligand screening (VLS) of a chemical library. In our work, we report that through SAR studies and molecular docking studies that the designed compounds having in combination the pharmacophore of PZM21 and aryl sulfonamide demonstrate significant interactions between the active compounds and both the MOR and Nav1.7 proteins. This study also reports the first ever bifunctional virtual ligand screening where a library consisting of over a million compounds was screened for bifunctional activity at the MOR and the Nav1.7 ion channel. We also report the development of a novel mechanism-specific membrane potential assay to that can be used to screen for subtype selective Nav1.7 inhibitors. The research performed in this thesis will serve as a platform to explore the possibility of MTDL as potential therapeutic solutions to diseases of complex etiologies such as chronic pain. It will also serve as a starting point to exploring bifunctional VLS as a way to screen large chemical libraries for MTDLs.

Worldwide, malaria is one of the deadliest diseases. In 2016 it sickened 216 million people and caused 445,000 deaths. In order to control the spread of this deadly diseases to human, we can either target the mosquito vector (Anopheles gambiae) or the parasite (Plasmodium falciparum). Due to recent emergence of resistance to current insecticides and antimalarial drugs there is a pressing need to discover and develop new agents that engage new targets in these organisms. To circumvent the effect of resistance to pyrethroid insecticides on the efficacy of insecticide treated nets (ITNs), the use of acetylcholinesterase (AChE) inhibitors on ITNs has drawn attention. In the first project, we explored a small library of γ- substituted oxoisoxazole- 2(3H)-carboxamides and isoxazol-3-yl carbamates, and nitriles as AChE inhibitors targeting wild- type (G3) and resistant (Akron) An. gambiae mosquito. In total 23 compounds were synthesized and evaluated. Both carbamates and carboximides with a 2-cyclopropylethyl side chain (1-87a and 1-88a) were extremely toxic to Akron mosquitos, yet these compounds did not exhibit appreciable selectivity between human and An. gambiae AChE. Unfortunately, none of the nitriles showed appreciable toxicity to G3 strain of the mosquitoes, nor did they inhibit An. gambiae AChE. In the second project, conducted in collaboration with Professor Michael Klemba, we focused on the mode of action of an established antimalarial drug, Mefloquine (MQ). Dr. Klemba's recently developed amino acid efflux assay was used to determine the effect of MQ and its open-ring analogs on hemoglobin endocytosis and catabolism in P. falciparum-infected erythrocytes. In total 26 MQ analogs were synthesized and 18 were studied in depth to determine their potency to inhibit leucine (Leu) efflux and parasite growth (SYBR Green). An excellent correlation (R² = 0.98) over nearly 4 log units was seen for these 18 compounds in the two assays. These data are consistent with the hypothesis that the antimalarial action of these compounds principally derives from inhibition of hemoglobin endocytosis. After this observation, a number of photo-affinity probes were designed and synthesized in hopes of isolating the molecular target of MQ. These analogs are currently being used by Dr. Klemba in pull-down experiments. In the third project, conducted in collaboration with Professor Belen Cassera, we sought to optimize a new antimalarial drug lead that would circumvent current resistance mechanisms. In Plasmodium parasites, the methylerythritol phosphate (MEP) pathway is known to be essential for its growth. This pathway is absent in humans, presenting the opportunity to develop potentially safe and effective therapeutic candidates. Previous work in the Cassera and Carlier lab had established that MMV008138 was the only compound in the Malaria Box that targeted the MEP pathway and that it was (1R,3S)-configured. My research expanded previous efforts in the Carlier group and produced synthesis of 73 analogs of MMV008138 (3-21a'1) that were tested for growth inhibition. These analogs featured variation at the A-, B-, C- and D-ring. In the process, a novel Pictet-Spengler ring expansion reaction of ortho-substituted acetphenones was discovered. The ring-expanded products were identified by means of 1D and 2D NMR experiments, HRMS, and X-ray crystallography. Among the 73 analogs prepared, four compounds showed similar growth inhibition potency to the lead 3-21a'1. In particular, the methoxyamide 3-80a, and the fluorinated A-ring analogs 3-124a, 3-124c and 3-124d all showed excellent (500-700 nM) growth IC₅₀ values against P. falciparum. All four showed full rescue upon co-application of IPP (200 μM), confirming that they target the MEP pathway. ADME-Tox evaluation of these new analogs will soon be underway. / PHD

The asymmetric reduction of ketones to chiral hydroxyl compounds by alcohol dehydrogenases (ADHs) is an established strategy for the provision of valuable precursors for fine chemicals and pharmaceutics. However, most ADHs favor linear aliphatic and aromatic carbonyl compounds, and suitable biocatalysts with preference for cyclic ketones and diketones are still scarce. Among the few candidates, the alcohol dehydrogenase from Thauera aromatica (ThaADH) stands out with a high activity for the reduction of the cyclic α-diketone 1,2-cyclohexanedione to the corresponding α-hydroxy ketone. This study elucidates catalytic and structural features of the enzyme. ThaADH showed a remarkable thermal and pH stability as well as stability in the presence of polar solvents. A thorough description of the substrate scope combined with the resolution and description of the crystal structure, demonstrated a strong preference of ThaADH for cyclic α-substituted cyclohexanones, and indicated structural determinants responsible for the unique substrate acceptance.

Yes / The antitumor prodrug temozolomide is compromised by its dependence for activity on DNA mismatch repair (MMR) and the repair of the chemosensitive DNA lesion, O6-methylguanine (O6-MeG), by O6-methylguanine-DNA-methyltransferase (E.C. 2.1.1.63, MGMT). Tumor response is also dependent on wild-type p53. Novel 3-(2-anilinoethyl)-substituted imidazotetrazines are reported that have activity independent of MGMT, MMR, and p53. This is achieved through a switch of mechanism so that bioactivity derives from imidazotetrazine-generated arylaziridinium ions that principally modify guanine-N7 sites on DNA. Mono- and bifunctional analogues are reported, and a quantitative structure-activity relationship (QSAR) study identified the p-tolyl-substituted bifunctional congener as optimized for potency, MGMT-independence, and MMR-independence. NCI60 data show the tumor cell response is distinct from other imidazotetrazines and DNA-guanine-N7 active agents such as nitrogen mustards and cisplatin. The new imidazotetrazine compounds are promising agents for further development, and their improved in vitro activity validates the principles on which they were designed.

Chapter 1 gives background information on proteases and discusses the concept of protease inhibition as a therapeutic strategy for humans. It introduces the key concept that conformation defines biological activity. It also outlines how proteases almost universally bind their substrate/inhibitors in an extended β-strand conformation. The use of calpain as a prototype protease for the testing of β-strand mimics synthesised later in the thesis is also discussed. Chapter 2 describes how molecular modeling was used to rationalise the structure based activity relationships (SAR) of known calpain inhibitors. Molecular modeling was then used to successfully design a number of acyclic β-strand mimics. The synthesis and testing of eight such inhibitors is described. The most potent β-strand mimic prepared was 2.13. This was determined to have an IC₅₀ of 30 nM against calpain II. Chapter 3 outlines the history and application of ring closing metathesis (RCM) to the synthesis of cyclic compounds. The attempted synthesis of an eight membered cyclic nitrogen to nitrogen conformationally constrained dipeptide is described. The synthesis of a conformationally constrained β-amino acid calpain inhibitor (3.73) is also described. A novel calpain inhibitor motif was designed in Chapter 4. On the basis of this an in-silico combinatorial library of two hundred and eighty eight possible β-strand templates was prepared. Conformational analysis of this library was performed and from this a number of excellent β-strand templates were identified and selected for synthesis. The preparation of ten β-strand templates is described. New microwave irradiation methodology was developed to achieve this. vii The formation of a six-membered catalyst deactivating chelate is also proposed to explain why some dienes fail to undergo RCM. Two methods to circumvent the formation of such a chelate are outlined. The addition of Lewis acid chloro-dicyclohexyl borane to the RCM reaction mixture and chain length alteration are investigated. Chapter 5 describes the design of macrocyclic β-strand mimics using induced fit molecular modelling. The physicochemical properties of these were calculated in-silico. From this analysis a number of Tyr-XX-Gly based and Tyr-XX-Cys based macrocyclic calpain inhibitors were selected for synthesis. The preparation and testing of these are described. In the Tyr-XX-Gly macrocyclic system a number of variables were investigated and numerous SAR implications concluded. Aldehyde 5.14 was identified as the best electrophilic warhead macrocyclic calpain inhibitor with an IC₅₀ against calpain II of 27 nM. The best non-electrophilic warhead macrocycle (5.13) had an IC₅₀ against calpain II of 704 nM. Chapter 6 describes synthetic optimisation for the preparation of calpain inhibitors 2.13, 5.14 and 5.17. Multi-gram quantities of each were prepared. Aldehydes 2.13 and 5.14 were evaluated as anti-cataract agents using in-vivo cataract sheep model. Both of these β-strand mimics were demonstrated to retard cataract development. Macrocycle 5.14 was found to be the most effective, decreasing the rate of cataract development between forty four and forty nine per cent relative to control. Chapter 7 outlines the attempted development of RCM methodology for the chiral synthesis of α-α disubstituted amino acid lactams. In addition, methodology for the stereoselective incorporation of a C-N constrained β-amino acid carbocycle into a peptide or peptidomimetic is described.

Les résistances aux traitements actuels contre le cancer imposent de trouver de nouvelles cibles thérapeutiques. Une de ces cibles est le réseau vasculaire assurant un apport suffisant en nutriments et en oxygène à la tumeur, et permettant l’apparition de métastases. Détruire la vascularisation de la tumeur par l’utilisation d’agents antivasculaires (VDA)revient à l’asphyxier et à l’affamer, inhibant ainsi la prolifération des cellules tumorales et empêchant le processus métastatique. L’objectif de ce travail de thèse a été d’étudier des analogues contraints de l’isocombrétastatine A-4 (isoCA-4), une molécule phare du laboratoire, ayant un excellent pouvoir d’inhibition de la polymérisation de la tubuline et présentant une activité antivasculaire. Ces structures dont la double liaison est incluse dans différents types de cycles C,ont été étudiées également afin d’évaluer l’influence de l’angle dièdre formé par les noyaux A et B sur les activités biologiques des divers types de structures. Préalablement sélectionnés par modélisation moléculaire, ces analogues contraints sont de type 1-arylnaphtalène, 5-arylbenzoxépine ou 4-arylchromène et ont été préparés par des voies d’ accès originales développées dans le cadre de cette thèse. Parmi les composés synthétisés, l’analogue de type benzoxépine 3-53est aussi cytotoxique que l’isoCA-4 et possède un pouvoir d’inhibition de la polymérisation de la tubuline équivalent. Une évaluation plus poussée de son profil biologique, ainsi que celle des meilleurs représentants de chaque série chimique est actuellement en cours. / Most tumor cells rely on an efficient vascular supply for their survival, making the tumor vasculature an attractive target for anti-cancer therapy. This thesis aimed at the design and synthesis of constrained analogues of isocombretastatin A-4(isoCA-4), an antivascular agent developed in the laboratory, which exerts excellent cytotoxicities against a large panel ofcancer cell lines, and strongly inhibits tubulin polymerization. Conformationally restricted analogues of isoCA-4,featuring 1-arylnaphthalene, 5-arylbenzoxepine or 4-arylchromene skeletons were designed by computational studies andprepared by novel synthetic strategies. Of all synthesized compounds, benzoxepine analogue 3-53 strongly inhibits tubulinpolymerization and shows excellent cytotoxicities against several human cancer cell lines.

O desenvolvimento de radioligantes para o sistema nervoso central (SNC) com características radiotraçadoras que justifiquem seu uso em diagnóstico por geração de imagens é esperado pela comunidade médica nuclear. Os benzodiazepínicos flumazenil-11C e iomazenil-123I são utilizados, com limitações, para investigações clínicas de densidade de sítios receptores benzodiazepínicos no cérebro em patologias como Alzheimer, epilepsia e depressão, entre outras. No Brasil, entretanto, estes traçadores ainda não estão disponíveis para uso clínico. Neste sentido, os flavonóides têm despertado interesses como perspectiva de nova classe de compostos com atividade no SNC podendo originar radiotraçadores com perspectivas para aplicação em imageamento cerebral. Baseado no exposto, a proposta deste estudo envolve o planejamento, a síntese e a marcação com radioiodo (131I e 123I) de flavona e análogos, o controle de qualidade radioquímico, os estudos de biodistribuição e o imageamento, para a avaliação do perfil de captação desses compostos e potencial aplicação em estudos cerebrais, frente a sítios receptores benzodiazepínicos. Os compostos estudados neste trabalho foram obtidos empregando-se a transformação de Baker-Venkataraman. A flavona e análogos foram identificados através de espectros de RMN-1H, RMN-13C e IV. O grau de pureza das substâncias obtidas foi confirmado através da medição da faixa de fusão. Os compostos radiomarcados foram obtidos com alta pureza radioquímica por substituição eletrofílica aromática direta. Esta marcação propiciou estabilidade in vitro após 24 horas e, para a flavona radiomarcada estabilidade in vivo, uma vez que a tireóide não apresentou captação significativa em tempos menores que 1 hora e excreção favorável no tempo de 24 horas. Os estudos de biodistribuição foram realizados em camundongos Swiss, verificando-se alta concentração de flavona-iodo-131 no cérebro, principalmente até 30 minutos após a injeção intravenosa e eliminação favorável após 24 horas de estudo. As imagens cerebrais foram realizadas em coelho New Zeland e em ratos Wistar adquiridas em gama câmara analógica sugerindo que a captação desse ligante no cérebro em tempos curtos, até 30 minutos, viabiliza a aquisição de imagens cintilográficas. Adicionalmente, foram desenvolvidos estudos de modelagem molecular da flavona e da flavona radiomarcada, utilizando-se mecânica quântica AM1 semi-empírico, corroborando a reatividade química desse composto frente à marcação com radioiodo por substituição eletrofílica, processo controlado predominantemente por interações eletrostáticas. Foram calculados os valores individuais de cargas para cada carbono da estrutura da flavona, incluindo cargas de Mulliken, Natural e Eletrostática, e foram gerados os mapas topográficos de distribuição de cargas de ambas as moléculas, evidenciando que as posições 6 e 8, na molécula de flavona, são as mais prováveis para a substituição por radioiodo. / The development of radioligands for the Central Nervous System (CNS) with adequate radiotracer characteristics for the use in imaging diagnostic has been long expected by the medical community. Benzodiazepines flumazenil-11C and iomazenil-123I are employed with limitations in clinical investigations of the density of receptor sites in the brain in pathologies such as Alzheimer, epilepsy, and depression. Nevertheless, in Brazil these radiotracers are not available in market, yet. In this respect, flavonoids has drawing attention as a perspective of a new class of compounds wit CNS activity and potential of originating radiotracers to be employed in brain imaging. Therefore, the goal of this work consisted in the planning, synthesis, and labeling with radioiodine (131I and 123I) of flavone and analogs, as well as to perform radiochemical quality control, biodistribuction, and imaging studies of the radiotracers obtained in order to evaluate the uptake profile and potential for use in cerebral studies of benzodiazepinic receptors sites. To obtain the compounds, we utilized the Baker-Venkataraman transformation, and NMR-1H, NMR-13C, and IR spectroscopy were employed for identification of the molecules. The purity of the compounds obtained was assessed by means of melting point determinations. The radiolabeled compounds were obtained by aromatic electrophilic substitution with a high degree of radiochemical purity. The labeling allowed in vitro stability after 24 hours and in vivo stability of the radiolabeled flavone, provided that the thyroid did not presented significant uptake in less than one hour and favorable excretion in 24 hours. Biodistribution studies were carried out employing Swiss mice. The results indicated high concentrations of flavone-I131 in the brain, especially in the first 30 minutes after intravenous injection, as well as favorable elimination after 24 hours. Brain images were obtained from New Zeland rabbit and Wistar rats in analogical gamma camera, suggesting that short-time brain uptake of the radioligand (up to 30 minutes) allows the acquisition of cynthilographic images. Additionally, molecular modeling studies of the flavone were performed employing the semi-empiric method of AM1. The results corroborate the chemical reactivity of the compound for labeling with radioiodine by aromatic electrophilic substitution, process that is governed mainly by electrostatic interactions. The individual values of Mulliken, Natural, and Electrostatic charges of each carbon atom in flavone structure were calculated and topographic maps of charge distribution were then generated. The analysis of the maps indicates that positions 6 and 8 in the flavone molecule are most likely to present the radioiodine substitution.