Drug resistance is a global health threat costing society billions of dollars and impacting millions of lives each year. Current drug design strategies are inadequate because they focus on disrupting target activity and not restricting the evolutionary pathways to resistance. Improved strategies would exploit the structural and dynamic changes in the enzyme–inhibitor system integrating data from many inhibitors and variants. Using HIV-1 protease as a model system, I aimed to elucidate the underlying resistance mechanisms, characterize conserved protease-inhibitor interactions, and generate more robust inhibitors by applying these insights. For primary mechanisms of resistance, comparing interactions at the protease–inhibitor interface showed how specific modifications affected potency. For mutations distal to the active site, molecular dynamics simulations were necessary to elucidate how changes propagated to reduce inhibitor binding. These insights informed inhibitor design to improve potency against highly resistant variants by optimizing hydrogen bonding. A series of hybrid inhibitors was also designed that showed excellent potency by combining key moieties of multiple FDA-approved inhibitors. I characterized the structural basis for alterations in binding affinity in HIV-1 protease both from mutations and inhibitors. I applied these strategies to HTLV-1 protease, a potential drug target. I identified the HIV-1 inhibitor darunavir as a viable scaffold and evaluated analogues, leading to a low-nanomolar compound with potential for optimization. Hopefully, insights from this thesis will lead to the development of potent HTLV-1 protease inhibitors. More broadly, these inhibitor design strategies are applicable to other rapidly evolving targets, thereby reducing drug resistance rates in the future.

Philosophiae Doctor - PhD / The continued success of antiretroviral programmes in the treatment of HIV is dependent on access to a cost-effective HIV drug resistance test (HIV-DRT). HIVDRT involves sequencing a fragment of the HIV genome and characterising the presence/absence of mutations that confer resistance to one or more drugs. HIV-DRT using conventional DNA sequencing is prohibitively expensive (~US$150 per patient) for routine use in resource-limited settings such as many African countries. While the advent of ultra deep pyrosequencing (UDPS) approaches have considerably reduced (3-5 fold reduction) the cost of generating the sequence data, there has been an even more significant increase in the volume of data generated and the complexity involved in its analysis. In order to address this issue we have developed Seq2Res, a computational pipeline for HIV drug resistance test from UDPS genotypic data. We have developed QTrim, software that undertakes high throughput quality trimming of UDPS sequencing data to ensure that subsequently analyzed data is of high quality. The comparison of QTrim to other widely used tools showed that it is equivalent to the next best method at trimming good quality data but outperforms all methods at trimming poor quality data. Further, we have developed, and evaluated, a computational approach for the analysis of UDPS sequence data generated using the novel Primer ID that enables the generation of a consensus sequence from all sequence reads originating from the same viral template, thus reducing the presence of PCR and sequencing induced errors in the dataset as well as reducing. We see that while the Primer ID approach does undoubtedly reduce the prevalence of PCR and sequencing induced errors, it artificially reduces the diversity of the subsequently analysed data due to the large volume of data that is discarded as a result of there being an insufficient number of sequences for consensus sequence generation. We validated the sensitivity of the Seq2Res pipeline using two real biological datasets from the Stanford HIV Database and five simulated datasets The Seq2Res results correlated fully with that of the Stanford database as well as identifying a drug resistance mutations (DRM) that had been incorrectly interpreted by the Stanford approach. Further, the analysis of the simulated datasets showed that Seq2Res is capable of accurately identifying DRMs at all prevalence levels down to at least 1% of the sequence data generated from a viral population. Finally, we applied Seq2Res to UDPS resistance data generated from as many as 641 individuals as part of the CIPRA-SA study to evaluate the effectiveness of UDPS HIV drug resistance genotyping in resource limited settings with a high burden of HIV infections. We find that, despite the FLX coverage being almost three times as much as that of the Junior platform, resistance genotyping results are directly comparable between both of the approaches at a range of prevalence levels to as low as 1%. Further, we find no significant difference between UDPS sequencing and the "gold standard" Sanger based approach, thus indicating that pooling as many as 48 patient's data and sequencing using the Roche/454 Junior platform is a viable approach for HIV drug resistance genotyping. Further, we explored the presence of resistant minor variants in individual's viral populations and find that the identification of minor resistant variants in individuals exposed to nevirapine through PMTCT correlates with the time since exposure. We conclude that HIV resistance genotyping is now a viable prospect for resource limited setting with a high burden of HIV infections and that UDPS approaches are at least as sensitive as the currently used Sanger-based sequencing approaches. Further, the development of Seq2Res has provided a sensitive, easy to use and scalable technology that facilitates the routine use of UDPS for HIV drug resistance genotyping.

Le tissu adipeux (TA) est réparti dans tout le corps en différents dépôts. Il existe deux types distincts aux fonctions biens spécifiques : le tissu adipeux blanc sert de réservoir énergétique et stocke les lipides et le tissu adipeux brun permet la thermogénèse. Par ses fonctionnalités et son pouvoir endocrine, le TA assure le maintien de l’homéostasie énergétique. De graves désordres métaboliques résultent d’une surabondance retrouvée au cours de l’obésité ou lors d’un remodelage dans les lipodystrophies. Certaines ont une origine génétique, d’autres sont induites par des médicaments comme les inhibiteurs de la protéase (IP) du VIH administrés dans la thérapie antirétrovirale. Le pool de progéniteur adipeux (PA) présent dans chaque dépôt est essentiel au maintien de ce tissu car il permet de renouveler le stock d’adipocytes. Nous avons caractérisé et identifié de nouveaux gènes impliqués dans la boucle autocrine/paracrine de l’activineA qui est responsable de l’auto-renouvellement du pool de PA dont IER3. Son expression augmente chez les patients obèses et diminue sous traitement par les IP. La modélisation des différents dépôts montre que les IP inhibent préférentiellement l’auto-renouvellement ou la différenciation adipocytaire des PA en fonction de leur localisation. Les lipodystrophies induites par la thérapie antirétrovirale auraient des causes multifactorielles. Enfin, nos résultats révèlent que les IP diminuent drastiquement et sélectivement la production d’adipocytes bruns. Ces effets doivent être considérés dans un contexte de développement inopportun du tissu adipeux brun afin de corriger des désordres métaboliques associés à certaines pathologies. / The adipose tissue (AT) is distributed throughout the body in different depots. There are two distinct types with specific functions: the white adipose tissue is used as an energetic reservoir and stores the lipids whereas the brown adipose tissue allows the thermogenesis. By its functionalities and its endocrinal capacity, the AT ensures the energetic homeostasis maintenance. Severe metabolic disorders result from an excess found during obesity or a remodelling in the lipodystrophies. Some of them have a genetic origin, the others are induced by drugs such as the HIV-protease inhibitors (PI) administered in the antiretroviral therapy against HIV. The adipose progenitor (AP) pool present in each depot is necessary for the maintenance of this tissue because it allows to renew the adipocyte stock. We characterized and identified new genes involved in the autocrine/paracrine Activin A loop which is responsible for AP pool self-renewal of whom is IER3. Its expression increases in obese patients and decreases under PI treatment. The modelling of the different depots shows that PI inhibit preferentially PA self-renewal or adipose differentiation depending on their localisation. Thus, lipodystrophies induced by antiretroviral therapy would have multifactorial causes. Finally, our results reveal PI dramatically and selectively reduce the brown adipocyte production. These effects should be considered in the context of inappropriate brown adipose tissue development in order to correct metabolic disorders associated to some pathologies.

Drug resistance is a major problem in quickly evolving diseases, including the human immunodeficiency (HIV) and hepatitis C viral (HCV) infections. The viral proteases (HIV protease and HCV NS3/4A protease) are primary drug targets. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition; the drug resistant protease variants are no longer effectively inhibited by the competitive drug molecules but can process the natural substrates with enough efficiency for viral survival. Therefore, the inhibitors that better mimic the natural substrate binding features should result in more robust inhibitors with flat drug resistance profiles. The native substrates adopt a consensus volume when bound to the enzyme, the substrate envelope. The most severe resistance mutations occur at protease residues that are contacted by the inhibitors outside the substrate envelope. To guide the design of robust inhibitors, we investigate the shared and varied properties of substrates with the protein dynamics taken into account to define the dynamic substrate envelope of both viral proteases. The NS3/4A dynamic substrate envelope is compared with inhibitors to detect the structural and dynamic basis of resistance mutation patterns. Comparative analyses of substrates and inhibitors result in a solid list of structural and dynamic features of substrates that are not shared by inhibitors. This study can help guiding the development of novel inhibitors by paying attention to the subtle differences between the binding properties of substrates versus inhibitors.

Drug resistance is the most important factor that influences the successful treatment of individuals infected with the human immunodeficiency virus type 1 (HIV-1), the causative organism of the acquired immunodeficiency syndrome (AIDS). Tremendous advances in our understanding of HIV and AIDS have led to the development of Highly Active Antiretroviral Therapy (HAART), a combination of drugs that includes HIV-1 reverse transcriptase, protease, and more recently, integrase and entry inhibitors, to combat the virus. Though HAART has been successful in reducing AIDS-related morbidity and mortality, HIV rapidly evolves resistance leading to therapy failure. Thus, a better understanding of the mechanisms of resistance will lead to improved drugs and treatment regimens. Protease inhibitors (PIs) play an important role in anti-retroviral therapy. The development of resistance mutations within the active site of the protease greatly reduces its affinity for the protease inhibitors. Frequently, these mutations reduce catalytic efficiency of the protease leading to an overall reduction in viral fitness. In order to overcome this loss in fitness the virus evolves compensatory mutations within the protease cleavage sites that allow the protease to continue to recognize and cleave its substrates while lowering affinity for the PIs. Improved knowledge of this substrate co-evolution would help better understand how HIV-1 evolves resistance and thus, lead to improved therapeutic strategies. Sequence analyses and structural studies were performed to investigate co-evolution of HIV-1 protease and its cleavage sites. Though a few studies reported the co-evolution within Gag, including the protease cleavage sites, a more extensive study was lacking, especially as drug resistance was becoming increasingly severe. In Chapter II, a small set of viral sequences from infected individuals were analyzed for mutations within the Gag cleavage sites that co-occurred with primary drug resistance mutations within the protease. These studies revealed that mutations within the p1p6 cleavage site coevolved with the nelfinavir-resistant protease mutations. As a result of increasing number of infected individuals being treated with PIs leading to the accumulation of PI resistant protease mutations, and with increasing efforts at genotypic and phenotypic resistance testing, access to a larger database of resistance information has been made possible. Thus in Chapter III, over 39,000 sequences were analyzed for mutations within NC-p1, p1-6, Autoproteolysis, and PR-RT cleavage sites and several instances of substrate co-evolution were identified. Mutations in both the NC-p1 and the p1-p6 cleavage sites were associated with at least one, if not more, primary resistance mutations in the protease. Previous studies have demonstrated that mutations within the Gag cleavage sites enhance viral fitness and/or resistance when they occur in combination with primary drug resistance mutations within the protease. In Chapter III viral fitness in the presence and absence of cleavage site mutations in combination with primary drug resistant protease mutations was analyzed to investigate the impact of the observed co-evolution. These studies showed no significant changes in viral fitness. Additionally in Chapter III, the impact of these correlating mutations on phenotypic susceptibilities to various PIs was also analyzed. Phenotypic susceptibilities to various PIs were altered significantly when cleavage site mutations occurred in combination with primary protease mutations. In order to probe the underlying mechanisms for substrate co-evolution, in Chapter IV, X-ray crystallographic studies were performed to investigate structural changes in complexes of WT and D30N/N88D protease variants and the p1p6 peptide variants. Peptide variants corresponding to p1p6 cleavage site were designed, and included mutations observed in combination with the D30N/N88D protease mutation. Structural analyses of these complexes revealed several correlating changes in van der Waals contacts and hydrogen bonding as a result of the mutations. These changes in interactions suggest a mechanism for improving viral fitness as a result of co-evolution. This thesis research successfully identified several instance of co-evolution between primary drug resistant mutations in the protease and mutations within NC-p1 and p1p6 cleavage sites. Additionally, phenotypic susceptibilities to various PIs were significantly altered as a result of these correlated mutations. The structural studies also provided insights into the mechanism underlying substrate co-evolution. These data advance our understanding of substrate co-evolution and drug resistance, and will facilitate future studies to improve therapeutic strategies.

The Hepatitis C Virus (HCV) is a global health problem as it afflicts an estimated 170 million people worldwide and is the major cause of viral hepatitis, cirrhosis and liver cancer. HCV is a rapidly evolving virus, with 6 major genotypes and multiple subtypes. Over the past 20 years, HCV therapeutic efforts have focused on identifying the best-in-class direct acting antiviral (DAA) targeting crucial components of the viral lifecycle, The NS3/4A protease is responsible for processing the viral polyprotein, a crucial step in viral maturation, and for cleaving host factors involved in activating immunity. Thus targeting the NS3/4A constitutes a dual strategy of restoring the immune response and halting viral maturation. This high priority target has 4 FDA approved inhibitors as well as several others in clinical development. Unfortunately, the heterogeneity of the virus causes seriously therapeutic challenges, particularly the NS3/4A protease inhibitors (PIs), which suffer from both the rapid emergence of drug resistant mutants as well as a lack of pan-genotypic activity. My thesis research focused on filling two critical gaps in our structural understanding of inhibitor binding modes. The first gap in knowledge is the molecular basis by which macrocyclization of PIs improves antiviral activity. Macrocycles are hydrophobic chains used to link neighboring chemical moieties within an inhibitor and create a structurally pre-organized ligand. In HCV PIs, macrocycle come in two forms: a P1 - P3 and P2 - P4 strategy. I investigated the structural and thermodynamic basis of the role of macrocyclization in reducing resistance susceptibility. For a rigorous comparison, we designed and synthesized both a P1 - P3 and a linear analog of grazoprevir, a P2 - P4 inhibitor. I found that, while the P2 - P4 strategy is more favorable for achieving potency, it does not allow the inhibitor sufficient flexibility to accommodate resistance mutations. On the other hand, the P1 - P3 strategy strikes a better balance between potency and resistance barrier. The second gap my thesis addresses is elucidating the structural basis by which highly potent protease inhibitors function in genotype 1 but not in genotype 3, despite having an 87% sequence similarity. After mapping the amino acids responsible for this differential efficacy in genotypes 1 and 3, I engineered a 1a3a chimeric protease for crystallographic studies. My structural characterization of three PIs in complex with both the 1a3a and genotype 1 protease revealed that the loss of inhibitor efficacy in the 1a3a and GT-3 proteases is a consequence of disrupted electrostatic interactions between amino acids 168 and 155, which is critical for potent binding of quinoline and isoindoline based PIs. Here, I have revealed details of molecular and structural basis for the lack of PI efficacy against GT-3, which are needed for design of pan-genotypic inhibitors.

The human immunodeficiency virus type-1 (HIV-1) is the leading cause of acquired immunodeficiency syndrome (AIDS) in the world. As there is no cure currently available to treat HIV-1 infections or AIDS, the major focus of drug development efforts has been to target viral replication in an effort to slow down the progression of the infection to AIDS. The aspartyl protease of HIV-1 is an important component in the viral replication cycle and thus, has been an important anti-HIV-1 drug target. Currently there are nine protease inhibitors (PIs) that are being used successfully as a part of highly active antiretroviral therapy (HAART). However, as is with all HIV-1 drug targets, the emergence of drug resistance substitutions within protease is a major obstacle in the use of PIs. Understanding how amino acid substitutions within protease confer drug resistance is key to develop new PIs that are not influenced by resistance mutations. Thus, the primary focus of my dissertation research was to understand the molecular basis for drug resistance caused by some of these resistance substitutions. Until recently, the genetic diversity of the HIV-1 genome was not considered to be important in formulating treatment strategies. However, as the prevalence of HIV-1 continues, the variability of the HIV-1 genome has now been identified as an important factor in how the virus spreads as well as how fast the infection progresses to AIDS. Clinical studies have also revealed that the pathway to protease inhibitor resistance can vary between HIV-1 clades. Therefore, in studying the molecular basis of drug resistance in HIV-1 protease, I have also attempted to understand how genetic variability in HIV-1 protease contributes to PI resistance. In Chapters II, III and Appendix 1, I have examined how clade specific amino acid variations within HIV-1 CRF01_AE and clade C protease affect enzyme structure and activity. Furthermore, I have examined how these sequence variations, which are predominantly outside the active site, contribute to inhibitor resistance in comparison to clade B protease. With the results presented in Chapter II, I was able to show that sequence variations within CRF01_AE protease resulted in structural changes within the protease that might influence enzyme activity. In Chapter III, I focused on how sequence variations in CRF01_AE influence protease activity and inhibitor binding in comparison to clade B protease. Enzyme kinetics data showed that the CRF01-AE had reduced catalytic turnover rates when compared to clade B protease. Binding data also indicated that CRF01_AE protease had an inherent weaker affinity for the PIs nelfinavir (NFV) and darunavir (DRV). In work described in Chapter III, I have also examined the different pathways to NFV resistance seen in CRF01_AE and clade B protease. Using x-ray crystallographic studies I have shown the molecular mechanism by which the two different pathways confer NFV resistance. Furthermore, I provide a rational for why different resistance pathways might emerge in the two clades. In Appendix I, I present results from a parallel study carried out on clade C protease. In Chapter IV, I have examined the role of residue 50 in HIV-1 protease in modulating inhibitor binding. Patients failing amprevavir (APV) and DRV therapy often develop the I50V substitution while the I50L substitution is often observed in patients failing atazanavir (ATV) therapy. This indicates that by making subtle changes at residue 50 the protease is able to confer differential PI resistance. With binding data presented in this chapter I have shown that substitutions at residue 50 change the susceptibility profiles of APV, DRV and ATV. Furthermore, from analyses of protease-inhibitor complexes, I have described structural insights into how substitutions at residue 50 can modulate inhibitor binding. This thesis presents results that reveal mechanistic insights into how a number of resistance substitutions within protease confer drug resistance. The results on non-B clade proteases demonstrate that clade specific sequence variations play a role in modulating enzyme activity and influence the pathway taken to confer PI resistance. Furthermore, the results provide structural insights into how amino acid substitutions outside the active site effectively alter inhibitor binding.

Glycosidases are carbohydrate processing essential enzymes necessary for the growth and development of all organisms such as intestinal digestion, post-translational processing of glycoproteins and the lysosomal catabolism of glycoconjugates. The function of these glycosidases is limited and studies are still in progress to understand their function at cellular level. In recent years, biological role of carbohydrates has resulted in various carbohydrate-based therapeutics2. These carbohydrates serve as a tool to study the function of glycosidases by inhibiting their active site. The concept of inhibition is yet another approach for the discovery of drugs. Glycosidase inhibitors studied are often sugar analogs and a wide range of such inhibitors are reported in the literature.3, 4 Thiosugars, in particular, have gained new perspectives owing to their electronic, geometric, conformational and flexibility differences, as sulfide moiety being less electronegative and more polarizable than the oxygen counter-part.5 These differences make the thiosugars distinct from their oxygen analogs and hence can mimic the active site of the enzyme. Many molecules are reported to be promising glycosidase inhibitors but are not easily accessible due to difficulties in their synthesis. Hence, the chemical synthesis of thio-analogs of carbohydrates, by synthetic routes, remains a major challenge. To address the complexity of synthesis and to make available new strategies, we envisioned the use of benzyltriethylammonium tetrathiomolybdate [BnEt3N]2MoS4, a versatile and efficient sulfur transfer reagent. Objectives of the study: a. Design novel thiosugars as glycosidase inhibitors. b. Devise strategy for the synthesis of novel thiosugars through a simple, practical approach. c. Evaluate the synthesized molecules as glycosidase and HIV-1 protease inhibitors, in silico. d. Study miscellaneous applications of the novel thiosugar-derived thialactones. The thesis is divided into five sections: Section A entitled “Synthesis of deoxythiosugars and thiosugar-based lactones” is divided into two parts, Part A and Part B. Part A – “An introduction and background on thiosugars and sulfur transfer reagents” has been provided. A brief discussion of sulfur transfer reagents in carbohydrate synthesis and earlier work related to the use of benzyltriethylammonium tetrathiomolybdate, [BnEt3N]2MoS4, as an efficient sulfur transfer reagent have been provided. Part B –“Design of inhibitors of glycosidases and HIV-1 protease” deals with the design of inhibitors of glycosidase and HIV-1 protease. The designed thiosugar molecules exhibit the characteristics of sugars and will act as planar molecules to mimic the active site conformation of a good inhibitor. Synthetic methodologies devised and adopted for the synthesis of constrained sugar-derived thialactones include: (a) Double displacement, (b) Displacement-cum-intramolecular thia-Michael addition, (c) Epoxide ring-opening-cum-intramolecular thia-Michael addition, and (d) Displacement-cum-epoxide ring opening in an intramolecular fashion. In all the above mentioned strategies, sulfur transfer step is the crucial step which was achieved by the use of benzyltriethylammonium tetrathiomolybdate [BnEt3N]2MoS46 as the key reagent. (a) Various constrained thialactones synthesized by double displacement strategy using tetrathiomolybdate as the sulfur transfer reagent are shown in Scheme – 1. (b) A number of constrained thialactones were synthesized following nucleophilic displacement-cum-intramolecular thia-Michael addition strategy as shown in Scheme – 2. (c) Synthesis of bicyclic thiolactones was achieved using the strategy of epoxide ring-opening-cum-intramolecular thia-Michael addition. (Scheme – 3) (d) A few bicyclic thialactones were synthesized through displacement-epoxide ring opening-cyclization as shown in Scheme – 4. The methodology was also utilized for the synthesis of thiosugar derivatives and azido-thialactones. (Fig. 1) Figure 1 Synthesis of deoxythiosugars: The bicyclic thialactones (designed as inhibitors) on reduction with borohydride exchange resin (BER) easily furnished the deoxythiosugars (Fig. 2). It is worth mentioning that the synthesis of these thiosugars as reported in the literature involved lengthy procedures whereas the present methodology turns out to be short and concise. Figure 2 Section B entitled “Synthesis of amines, β-amino acids and novel thiosugar-based dehydroamino acids” comprises a brief introduction on the importance of amines, β-amino acids and dehyroamino acids. In this section the effective utilization of benzyltriethylammonium tetrathiomolybdate as a key reagent for reductive transformations and its application in the synthesis of amines, β-amino acids and dehyroamino acids have been presented. A one pot reduction of azides to amines followed by intermolecular aza-Michael addition employing tetrathiomolybdate was achieved to furnish a number of different β-amino esters as shown in Scheme -4: Scheme 4 The study was further extended to the reduction of a few anomeric azides to afford the corresponding anomeric amines and derivatives. (Fig. 3) Figure 3 A one-pot thia-Michael addition-vinyl azide reduction in a tandem fashion employing benzyltriethylammonium tetrathiomolybdate was studied and was shown to be effective for the synthesis of thiosugar derived dehydroamino acid derivatives. (Scheme – 5) Scheme 5 Section C entitled “Molecular docking studies of deoxythiosugar probes” gives an overview of different glycosidases, HIV-1 protease and their inhibitors. This section also deals with a brief introduction on active site conformations of potent inhibitors. In this connection we have studied the crystal conformations of the synthesized molecules whose conformations were the same as that of the existing inhibitors in the active site. (Fig. 4) With this background in silico study of the synthesized deoxythiosugar probes was conducted on human glycosidases: α-mannosidase, α-galactosidase, β-glucosidase and HIV-1 protease, respectively. Figure 4 Molecular docking was carried out using Autodock suite, molecular modeling simulation. Separate docking procedures were employed for the four different receptors. The PDBs representing the four enzyme targets were 2V3D, 3H53, 1X9D and 3I8W for β–glucosidase, α–galactosidase, α–mannosidase and HIV–1 protease respectively. The control compounds used for α–mannosidase were mannostatin and kifunensine. NMB, THK, and BED were the positive controls for HIV–1 protease. Similarly, NBV and cyclophellitol were the controls used for β–glucosidase and NOJ, N–methyl calystegine B2 for α–galactosidase. (Fig. 5) Ligands TGSB68 and TGSB482 had the energy value of –6.49 kcal/mol comparable to that of the average reference value of the positive control, and thus, the potent candidate as identified by molecular docking to HIV-1 protease. (Fig. 6a) The control compounds used for α–mannosidase were mannostatin and kifunensine, which bind with mean binding energy of -9.11 and -5.56. In the case of α–mannosidase, the same compounds TGSB68 and TGSB482 were selected due to comparable energy and a good cluster size with that of positive control. (Fig. 6b) For β– glucosidase, ligands TGSC108 and TGSC236, which had comparable values to that of positive control was identified as the Figure 5 Figure 6 potent candidate. (Fig. 6c) In the case of α–galactosidase, again the ligands TGSB68 and TGSB482 were selected based on binding energies. (Fig. 6d) In conclusion, the concept analogy (deoxy nature, planarity, thiosugar framework, lactone moiety) for the design of inhibitors indeed worked positively. The results are really encouraging. An in vivo study of the synthesized novel thiosugar probes will certainly provide a potent inhibitor. Section D entitled “Research methodology” provides experimental procedures adopted with details of synthesis. Section E entitled “Bibliography” provides the references cited in this work.

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.

Buscou-se minimizar ou prevenir a degradação das fibrilas colágenas, tanto no controle da progressão do desgaste erosivo em dentina, quanto na preservação das interfaces adesivas aí estabelecidas, por meio do uso de agentes antiproteolíticos (clorexidina/CHX e epigalocatequina-3-galato/EGCG) ou, ao mesmo tempo, promotores de ligações cruzadas entre elas (proantocianidina/PAC). O papel de algumas dessas estratégias no estabelecimento, e conservação, de interfaces adesivas em dentina erodida, substrato adverso à interação com materiais adesivos, tem sido, porém, pouquíssimas vezes reportado. Este estudo in vitro propôs-se a avaliar, pois, o efeito de tais agentes, usados como estratégias para prevenção/controle do desgaste, na resistência de união (RU) do conjunto sistema adesivo condicione e lave simplificado-resina composta à dentina erodida, comparada à normal. A dentina superficial oclusal de terceiros molares foi apenas submetida à ação de uma lixa de SiC (granulação 600; 1 min; N: substrato normal) ou sequencialmente a desafio erosivo inicial (Coca-Cola®; 5 min). Recebeu, então, ou não (C: controle/sem aplicação), a aplicação de um dos géis com os seguintes princípios ativos - P: placebo/sem princípio ativo; CHX: digluconato de clorexidina a 0,12%; EGCG: epigalocatequina-3-galato a 400 ?m; PAC: proantocianidina a 10%. Aquela de início desmineralizada ainda foi submetida a ciclagem de pH (Coca-Cola®; imersões de 5 min, 3x/dia, 5 dias; E: substrato erodido). Após condicionamento (H3PO4 a 37%; 15 s; lavagem 30 s; secagem com papel absorvente), o adesivo AdperTM Single Bond 2® foi aplicado em todos os espécimes e a porção coronária, reconstruída com a resina FiltekTM Z350®. Transcorridas 24 h (água destilada/37?C), os espécimes foram seccionados em palitos e testados (?TBS; 0,5 mm/min). As superfícies fraturadas de cada palito foram avaliadas utilizando-se um microscópio digital (50x de aumento). Os valores de RU obtidos foram organizados considerando- se cada dente como unidade experimental e os testes de Análise de Variância a 2 critérios e de Tukey aplicados (?=0,05). Um dente extra para cada grupo foi tratado exatamente como os outros, mas o corante fluorescente rodamina B foi previamente adicionado (0,16 mg/mL) ao sistema adesivo para permitir a avaliação qualitativa da interface adesiva por meio de Microscopia Confocal de Varredura a Laser. Analisando-se os dados obtidos pôde-se observar que, diferentemente da variável aplicação de géis para prevenção/controle do desgaste erosivo (p=0,076), a variável condição do substrato dentinário exerceu influência significante sobre os resultados (p<0,001). Ademais, não houve interação entre elas (p=0,979). Os valores imediatos de RU ao substrato erodido foram, pois, sempre inferiores que aqueles ao substrato normal, independentemente da aplicação, ou não, de qualquer um dos géis para prevenção/controle do desgaste erosivo. Quanto ao padrão de fratura dos palitos testados, as falhas adesivas e mistas foram predominantes em relação às coesivas, independentemente se em dentina ou em resina. Menores porcentagens de falhas coesivas ainda puderam ser verificadas para o substrato erodido, com relação ao normal. No que se refere à análise qualitativa, observou-se, para o erodido, comparado ao normal, independetemente do tratamento para controle do desgaste, camada escura subjacente à de adesivo propriamente, representação da menor concentração de material marcado por rodamina B, bem como tags resinosos com maior comprimento e em maior quantidade. Assim sendo, conclui-se, por ora, que as estratégias estudadas não foram capazes de favorecer, tampouco de prejudicar, o estabelecimento de interface adesiva em dentina erodida. / In order to minimize the degradation of collagen fibrils, both to control the progression of the dentin erosive wear and to preserve adhesive interfaces established there, antiproteolytic (chlorhexidine/CHX and epigallocatechin-3-gallate/EGCG) or, at the same time, collagen cross-linking agents (grape seed proanthocyanidin extract/PAC) started to be successfully used. Some of these strategies in the establishment and preservation of adhesive interfaces on eroded dentin, a substrate adverse to the interaction with adhesive materials, has been seldom reported yet. This in vitro study aimed to evaluate, thus, the effect of such agents, used as strategies for wear preventing/controlling, on bond strength (BS) of a simplified etch-and-rinse adhesive system adhesive plus a resin composite to eroded, and normal (parameter for comparisons) dentin. Superficial occlusal dentin of third molars was only ground with a SiC paper (600-grit; 1 min; N: normal substrate), or subsequently submitted to an initial erosive challenge (Coca-Cola®; 5 min). It, then, received or not (C: control/without application), application of one of the gels with the following active principles - P: placebo/without active principle; CHX: 0.012% chlorhexidine digluconate; EGCG: epigallocatechin-3-gallate at 400 ?m; PAC: 10% proanthocyanidin. Initial demineralized dentin was still submitted to a pH cycling (Coca-Cola®, 5 min immersions, 3x/day, 5 days, E: eroded substrate). After acid-etched (37% H3PO4; 15 sec; 30 sec washing; drying with absorbent paper), the adhesive Adper(TM) Single Bond 2® was applied in all specimens and resin composite buildups were constructed with Filtek(TM)Z350®. After 24 h (distilled water/37?C), specimens were sectioned in beams and tested (?TBS; 0.5 mm/min). Obtained BS values were organized considering each tooth as an experimental unit and two-way ANOVA and Tukey tests were applied (?=0.05). An extra tooth for each group was treated just like the others, but the adhesive system was marked by the addition of rhodamine B (0.16 mg/mL) to allow qualitative evaluation of the adhesive interface by means of Confocal Laser Scanning Microscopy. As opposed to the variable application of gels for wear preventing/controlling (p=0.076), the condition of the dentin substrate had a significant influence on the results (p<0.001). In addition, there was no interaction between them (p=0.979). Immediate BS values to the eroded substrate were always lower than that to the normal substrate, regardless of the application or not of any of the gels for wear preventing/controlling. As for the fracture pattern of the tested beams, adhesive and mixed failures were predominant in relation to the cohesive failures, regardless of whether in dentin or in resin. Lower percentages of cohesive failures could still be verified for the eroded substrate, relative to the normal one. Concerning the qualitative analysis, it was observed, for the eroded substrate, compared to the normal, independently of the treatment for wear preventing/controlling, a dark layer underlying that of the adhesive itself, which represents a lower concentration of rhodamine B-labeled material, as well as resinous tags with greater length and in greater quantity. Therefore, studied strategies were not able either to improve, neither to impair, the establishment of adhesive interface on eroded dentin.