Milk is provided to new borns as their first food source and it contains essential nutrients, vitamins and other beneficial components, such as enzymes and antibodies that are required for rapid growth and development of the new born and for sustained growth over time. Milk contains two main types of proteins; casein proteins and whey proteins. Although casein proteins account for up to 80% of the proteins found in bovine milk, it is the whey protein that has become of high interest because of its bioactive content. Whey, a very watery mixture of lactose, proteins, minerals and trace amounts of fat, is formed from milk when the milk is coagulated and/or the casein proteins are removed from the milk. Bovine whey protein, including both the acidic and basic fractions (low and high isoelectric point, respectively), has previously been studied in vitro (cell based) and in vivo (using rats) for its impact on bone to determine if it can help improve bone mineral density and help reduce the risk of developing bone diseases, such as osteoporosis. Bone is constantly undergoing a remodelling process of being dissolved and reformed and the two main cell types responsible for this bone remodelling process are mature osteoclasts, which dissolve (resorb) bone, and osteoblasts, which reform the bone. Prior work has shown that acidic protein fractions derived from different sources of whey protein concentrate (WPC) have both in vivo and in vitro activity on bone, particularly anti-resorptive properties. However, the component(s) which confer activity have not yet been identified. In this thesis, work was undertaken to better understand the analytical composition of three types of WPC (cheese, mineral acid and lactic acid) and their associated acidic protein fractions and relate this to bone activity in the hope of identifying where the activity lies. Bone activity was assessed using in vitro screening with osteoblast cells (MC3T3-E1) and osteoclast cells (RAW 264.7). Comparison of the cell-based bone activity of the parent WPCs and corresponding acidic fractions indicated that the acidic fractions derived from both mineral acid and lactic WPC were superior in their ability to inhibit osteoclast development. Although compositional data was complex and definitive correlations with both bone bioactivities could not be made, it appeared that elements common to both the acidic fractions were a higher proportion of GLYCAM-1 and bone sialoprotein-1 (osteopontin). Further studies to more closely investigate the bone bioactivity of the acidic fractions are warranted.

The immune system often recognises tumour cells and infectious agents from the unique peptides found on their surfaces therefore, synthetic peptides of similar structure can be used as vaccines to stimulate the immune system. Despite the problems associated with proteolysis and delivery to the immune system, peptide-based vaccines have enormous potential due to their ease of synthesis and purification. The aim of this research was to synthesise ligands for mannose receptors (MRs) that are found on human Antigen Presenting Cells (APCs), for use in synthetic vaccines. Carbohydrate bearing antigens are recognised by MRs which play an important role in binding antigens, migration of dendritic cells (DCs) and interaction of DCs with lymphocytes. Hence, incorporation of a sugar residue into a peptide chain can be used to enhance antigen presentation. This thesis describes the synthesis of fluorescein labelled O-mannosylated peptides using either manual or microwave assisted solid phase glycopeptide synthesis (SPGS) on pre-loaded WANG resin. The mannosylated peptides thus prepared can be tested for their ability to bind mannose receptors on human APCs in vitro. In order to prepare compounds that could be analysed in biological screens, a fluorescent label (5(6)-carboxyfluorescein) was introduced into the glycopeptides via the Nα- or the Nε-amino group of the lysine residue. It was found that preparation of the glycopeptide was more facile when the peptide chain was built onto the Nε of Lys (label into Nα) rather than onto the Nα of Lys (label into Nε). In order to overcome problems experienced when introducing more than one glycosylated building block into the peptide chain, a polyethylene glycol (PEG) linker was employed as a sugar carrier. It was found that mono- and dimannosylated building blocks attached to PEG carrier were incorporated more easily into the peptide chain compared to mono- and dimannosylated serine units. Importantly, microwave technology (CEM Liberty microwave peptide synthesiser) was used for SPGS which resulted in improved purity and yields of the glycopeptides thus prepared with a significant reduction in reaction times. The first fifteen glycopeptides prepared in the present study were tested for binding to mannose receptors. Several compounds have shown improved binding to monocytes (bear MRs) in comparison to lymphocytes (do not bear MRs), in the presence of calcium ions. Calcium dependent binding is specific for C type lectin receptor family that MRs belong to. Five remaining glycopeptides are currently undergoing biological evaluation.

The immune system often recognises tumour cells and infectious agents from the unique peptides found on their surfaces therefore, synthetic peptides of similar structure can be used as vaccines to stimulate the immune system. Despite the problems associated with proteolysis and delivery to the immune system, peptide-based vaccines have enormous potential due to their ease of synthesis and purification. The aim of this research was to synthesise ligands for mannose receptors (MRs) that are found on human Antigen Presenting Cells (APCs), for use in synthetic vaccines. Carbohydrate bearing antigens are recognised by MRs which play an important role in binding antigens, migration of dendritic cells (DCs) and interaction of DCs with lymphocytes. Hence, incorporation of a sugar residue into a peptide chain can be used to enhance antigen presentation. This thesis describes the synthesis of fluorescein labelled O-mannosylated peptides using either manual or microwave assisted solid phase glycopeptide synthesis (SPGS) on pre-loaded WANG resin. The mannosylated peptides thus prepared can be tested for their ability to bind mannose receptors on human APCs in vitro. In order to prepare compounds that could be analysed in biological screens, a fluorescent label (5(6)-carboxyfluorescein) was introduced into the glycopeptides via the Nα- or the Nε-amino group of the lysine residue. It was found that preparation of the glycopeptide was more facile when the peptide chain was built onto the Nε of Lys (label into Nα) rather than onto the Nα of Lys (label into Nε). In order to overcome problems experienced when introducing more than one glycosylated building block into the peptide chain, a polyethylene glycol (PEG) linker was employed as a sugar carrier. It was found that mono- and dimannosylated building blocks attached to PEG carrier were incorporated more easily into the peptide chain compared to mono- and dimannosylated serine units. Importantly, microwave technology (CEM Liberty microwave peptide synthesiser) was used for SPGS which resulted in improved purity and yields of the glycopeptides thus prepared with a significant reduction in reaction times. The first fifteen glycopeptides prepared in the present study were tested for binding to mannose receptors. Several compounds have shown improved binding to monocytes (bear MRs) in comparison to lymphocytes (do not bear MRs), in the presence of calcium ions. Calcium dependent binding is specific for C type lectin receptor family that MRs belong to. Five remaining glycopeptides are currently undergoing biological evaluation.

The immune system often recognises tumour cells and infectious agents from the unique peptides found on their surfaces therefore, synthetic peptides of similar structure can be used as vaccines to stimulate the immune system. Despite the problems associated with proteolysis and delivery to the immune system, peptide-based vaccines have enormous potential due to their ease of synthesis and purification. The aim of this research was to synthesise ligands for mannose receptors (MRs) that are found on human Antigen Presenting Cells (APCs), for use in synthetic vaccines. Carbohydrate bearing antigens are recognised by MRs which play an important role in binding antigens, migration of dendritic cells (DCs) and interaction of DCs with lymphocytes. Hence, incorporation of a sugar residue into a peptide chain can be used to enhance antigen presentation. This thesis describes the synthesis of fluorescein labelled O-mannosylated peptides using either manual or microwave assisted solid phase glycopeptide synthesis (SPGS) on pre-loaded WANG resin. The mannosylated peptides thus prepared can be tested for their ability to bind mannose receptors on human APCs in vitro. In order to prepare compounds that could be analysed in biological screens, a fluorescent label (5(6)-carboxyfluorescein) was introduced into the glycopeptides via the Nα- or the Nε-amino group of the lysine residue. It was found that preparation of the glycopeptide was more facile when the peptide chain was built onto the Nε of Lys (label into Nα) rather than onto the Nα of Lys (label into Nε). In order to overcome problems experienced when introducing more than one glycosylated building block into the peptide chain, a polyethylene glycol (PEG) linker was employed as a sugar carrier. It was found that mono- and dimannosylated building blocks attached to PEG carrier were incorporated more easily into the peptide chain compared to mono- and dimannosylated serine units. Importantly, microwave technology (CEM Liberty microwave peptide synthesiser) was used for SPGS which resulted in improved purity and yields of the glycopeptides thus prepared with a significant reduction in reaction times. The first fifteen glycopeptides prepared in the present study were tested for binding to mannose receptors. Several compounds have shown improved binding to monocytes (bear MRs) in comparison to lymphocytes (do not bear MRs), in the presence of calcium ions. Calcium dependent binding is specific for C type lectin receptor family that MRs belong to. Five remaining glycopeptides are currently undergoing biological evaluation.

The immune system often recognises tumour cells and infectious agents from the unique peptides found on their surfaces therefore, synthetic peptides of similar structure can be used as vaccines to stimulate the immune system. Despite the problems associated with proteolysis and delivery to the immune system, peptide-based vaccines have enormous potential due to their ease of synthesis and purification. The aim of this research was to synthesise ligands for mannose receptors (MRs) that are found on human Antigen Presenting Cells (APCs), for use in synthetic vaccines. Carbohydrate bearing antigens are recognised by MRs which play an important role in binding antigens, migration of dendritic cells (DCs) and interaction of DCs with lymphocytes. Hence, incorporation of a sugar residue into a peptide chain can be used to enhance antigen presentation. This thesis describes the synthesis of fluorescein labelled O-mannosylated peptides using either manual or microwave assisted solid phase glycopeptide synthesis (SPGS) on pre-loaded WANG resin. The mannosylated peptides thus prepared can be tested for their ability to bind mannose receptors on human APCs in vitro. In order to prepare compounds that could be analysed in biological screens, a fluorescent label (5(6)-carboxyfluorescein) was introduced into the glycopeptides via the Nα- or the Nε-amino group of the lysine residue. It was found that preparation of the glycopeptide was more facile when the peptide chain was built onto the Nε of Lys (label into Nα) rather than onto the Nα of Lys (label into Nε). In order to overcome problems experienced when introducing more than one glycosylated building block into the peptide chain, a polyethylene glycol (PEG) linker was employed as a sugar carrier. It was found that mono- and dimannosylated building blocks attached to PEG carrier were incorporated more easily into the peptide chain compared to mono- and dimannosylated serine units. Importantly, microwave technology (CEM Liberty microwave peptide synthesiser) was used for SPGS which resulted in improved purity and yields of the glycopeptides thus prepared with a significant reduction in reaction times. The first fifteen glycopeptides prepared in the present study were tested for binding to mannose receptors. Several compounds have shown improved binding to monocytes (bear MRs) in comparison to lymphocytes (do not bear MRs), in the presence of calcium ions. Calcium dependent binding is specific for C type lectin receptor family that MRs belong to. Five remaining glycopeptides are currently undergoing biological evaluation.

Com o objetivo de buscar e identificar novo(s) inibidor(es) da cruzaína uma cisteíno-protease do Trypanosoma cruzi, o agente etiológico da doença de Chagas foram propostos, validados e, a seguir, aplicados sobre a biblioteca de compostos ZINC (3.294.714 compostos), dois modelos de virtual screening (Modelos I e II). Os modelos de virtual screening propostos, contendo seqüências de filtros físicoquímicos, farmacofóricos, de docking e de seleção por inspeção visual, foram construídos a partir de informações de 13 complexos da cruzaína e de 20 complexos de outras cisteínoprotease, cujas estruturas estão disponíveis no PDB. Numa primeira etapa, o reconhecimento detalhado das características estruturais da cruzaína foi realizado por inspeção visual; pelos campos de interação molecular, gerados pelo programa GRID; pela identificação das propriedades de interação molecular na superfície da cavidade, geradas pelo programa CA VBASE e; por simulações de dinâmica molecular. O Modelo I de virtual screeníng - obtido a partir do reconhecimento das estruturas dos 13 complexos da cruzaína depositadas no PDB - foi aplicado sobre o ZINC, selecionando 10 compostos, dos quais 6 compostos foram adquiridos e submetidos ao teste de inibição enzimática da cruzaína, para a validação experimental do modelo. Observou-se que 3 destes compostos (ZINC02470662, ZINC02682879 e ZINC03192044, respectivamente) não mostraram inibição significativa da cruzaína, nas condições experimentais utilizadas, até a concentração de 7 mM, enquanto que os 3 restantes (ZINC02663001, ZINC01936854 e ZINC03326243, respectivamente) apresentaram inibição enzimática inespecífica, sugerindo que estes últimos agem pelo mecanismo promíscuo. O mecanismo promíscuo de inibição enzimática, foi verificado pela adição de 0,1% Triton X-100 no ensaio enzimático, observando-se a correspondente perda de inibição da cruzaína. Para estes compostos, a confirmação do mecanismo promíscuo foi feita observando-se a perda de inibição da enzima, após o aumento em dez vezes da concentração da cruzaína no ensaio enzimático. O Modelo II - obtido a partir do reconhecimento das estruturas dos 13 complexos da cruzaína e dos 20 complexos de outras cisteíno-proteases, identificadas na busca por cavidades similares à cruzaína - foi aplicado sobre o banco de dados ZINC,selecionando 55 compostos dos quais 19 foram adquiridos e submetidos ao teste de inibição enzimática da cruzaína, para validação experimental do modelo. Observou-se que o composto ZINC01794422 apresentou inibição específica da enzima com constante de inibição no valor de Ki = 21 µM, enquanto que os demais 18 compostos não mostraram inibição significativa, nas condições experimentais utilizadas, até a concentração de 592 µM. O mecanismo promíscuo de inibição enzimática não foi observado, uma vez que todos os testes foram realizados com 0,1% de Triton X-100. O Modelo II identificou, ainda, mais dois inibidores da cruzaína (ZINC04899534 e ZINC01547017) que, por serem estruturalmente semelhantes aos utilizados na construção do modelo e já terem sido descritos na literatura, não foram adquiridos ou testados nos ensaios enzimáticos. Considerando apenas o novo inibidor identificado, o Modelo II apresentou uma taxa de acerto de 5,3%. Este valor esta de acordo com as taxas de acerto encontradas na literatura que variam entre 1 a 50% . / In order to search and identify new cruzain inhibitor(s) - a cysteine-protease of Trypanosoma cruzi, the etiologic agent of Chagas disease - two virtual screening schemes(Models I and II) were proposed, validated- and applied to the ZINC database (3.294.714 compounds). The proposed virtual screening models, bearing a sequence of different physicalchemical, pharmacophore and docking filters, as well as a visual inspection filter, were built from information taken from 13 cruzain complexes and from 20 complexes of other cysteine proteases, having their structures available in PDB. In a first step, a detailed recognition of the cruzain structural features and characteristics was performed through visual inspection of the enzyme environment; followed by the analysis of GRID generated molecular interaction fields; through the identification of molecular interaction properties exposed at the enzyme cavity surface, generated by the CAVBASE program; and by molecular dynamics simulations. The virtual screening Model I, - generated from the structural characteristics recognized from 13 PDB cruzain complexes - when applied to the ZINC database selected 10 compounds. For the experimental validation ofthe model, six ofthese compounds have been acquired and were tested as cruzain inhibitors. It was observed that three of the tested compounds (ZINC02470662, ZINC02682879 and ZINC03192044, respectively) did not show any significant cruzain inhibition, up to 7 mM. Meanwhile the other three tested compounds (ZINC02663001, ZINC01936854 and ZINC03326243, respectively) showed an unspecific cruzain inhibition, suggesting that an enzyme inhibition by promiscuous mechanism occurred. This mechanism was verified by the addition of 0.1% Triton X-100 on the enzymatic assay with a concomitant loss of cruzain inhibition activity. For these compounds, the confirmation of the promiscuous mechanism was also done, observing the loss of enzyme inhibition, after a ten times increase in the cruzain concentration on the enzymatic assay. The virtual screenmg Model II - generated from the structural characteristics recognized from 13 cruzain complexes and 20 complexes of other cysteine proteases, that have been identified on a search for cavities similar to cruzain - selected 55 compounds, when applied to the ZINC database. In order to experimentally validate the model, nineteen compounds have been acquired and were tested as cruzain inhibitors. It has been observed that one compound, ZINC01794422, showed a specific cruzain inhibition (Ki = 21 µM), while the other eighteen showed no significant inhibition, up to 592 µM concentration. The promiscuous mechanism of enzymatic inhibition was not observed, since 0.1% of Triton X-100 was added in ali assays. Additionally, Model II identified two other cruzain inhibitors (ZINC04899534 and ZINC01547017). However, these compounds have not been acquired or tested, since they are known cruzain inhibitors - already described in the literature and are structurally similar to the inhibitors used in the construction of the mode!. Referring to new inhibitors found, Model II showed a hit rate of 5,3%. This value is in agreement with those found in the literature, which ranges from 1 to 50%.

Com o objetivo de buscar e identificar novo(s) inibidor(es) da cruzaína uma cisteíno-protease do Trypanosoma cruzi, o agente etiológico da doença de Chagas foram propostos, validados e, a seguir, aplicados sobre a biblioteca de compostos ZINC (3.294.714 compostos), dois modelos de virtual screening (Modelos I e II). Os modelos de virtual screening propostos, contendo seqüências de filtros físicoquímicos, farmacofóricos, de docking e de seleção por inspeção visual, foram construídos a partir de informações de 13 complexos da cruzaína e de 20 complexos de outras cisteínoprotease, cujas estruturas estão disponíveis no PDB. Numa primeira etapa, o reconhecimento detalhado das características estruturais da cruzaína foi realizado por inspeção visual; pelos campos de interação molecular, gerados pelo programa GRID; pela identificação das propriedades de interação molecular na superfície da cavidade, geradas pelo programa CA VBASE e; por simulações de dinâmica molecular. O Modelo I de virtual screeníng - obtido a partir do reconhecimento das estruturas dos 13 complexos da cruzaína depositadas no PDB - foi aplicado sobre o ZINC, selecionando 10 compostos, dos quais 6 compostos foram adquiridos e submetidos ao teste de inibição enzimática da cruzaína, para a validação experimental do modelo. Observou-se que 3 destes compostos (ZINC02470662, ZINC02682879 e ZINC03192044, respectivamente) não mostraram inibição significativa da cruzaína, nas condições experimentais utilizadas, até a concentração de 7 mM, enquanto que os 3 restantes (ZINC02663001, ZINC01936854 e ZINC03326243, respectivamente) apresentaram inibição enzimática inespecífica, sugerindo que estes últimos agem pelo mecanismo promíscuo. O mecanismo promíscuo de inibição enzimática, foi verificado pela adição de 0,1% Triton X-100 no ensaio enzimático, observando-se a correspondente perda de inibição da cruzaína. Para estes compostos, a confirmação do mecanismo promíscuo foi feita observando-se a perda de inibição da enzima, após o aumento em dez vezes da concentração da cruzaína no ensaio enzimático. O Modelo II - obtido a partir do reconhecimento das estruturas dos 13 complexos da cruzaína e dos 20 complexos de outras cisteíno-proteases, identificadas na busca por cavidades similares à cruzaína - foi aplicado sobre o banco de dados ZINC,selecionando 55 compostos dos quais 19 foram adquiridos e submetidos ao teste de inibição enzimática da cruzaína, para validação experimental do modelo. Observou-se que o composto ZINC01794422 apresentou inibição específica da enzima com constante de inibição no valor de Ki = 21 µM, enquanto que os demais 18 compostos não mostraram inibição significativa, nas condições experimentais utilizadas, até a concentração de 592 µM. O mecanismo promíscuo de inibição enzimática não foi observado, uma vez que todos os testes foram realizados com 0,1% de Triton X-100. O Modelo II identificou, ainda, mais dois inibidores da cruzaína (ZINC04899534 e ZINC01547017) que, por serem estruturalmente semelhantes aos utilizados na construção do modelo e já terem sido descritos na literatura, não foram adquiridos ou testados nos ensaios enzimáticos. Considerando apenas o novo inibidor identificado, o Modelo II apresentou uma taxa de acerto de 5,3%. Este valor esta de acordo com as taxas de acerto encontradas na literatura que variam entre 1 a 50% . / In order to search and identify new cruzain inhibitor(s) - a cysteine-protease of Trypanosoma cruzi, the etiologic agent of Chagas disease - two virtual screening schemes(Models I and II) were proposed, validated- and applied to the ZINC database (3.294.714 compounds). The proposed virtual screening models, bearing a sequence of different physicalchemical, pharmacophore and docking filters, as well as a visual inspection filter, were built from information taken from 13 cruzain complexes and from 20 complexes of other cysteine proteases, having their structures available in PDB. In a first step, a detailed recognition of the cruzain structural features and characteristics was performed through visual inspection of the enzyme environment; followed by the analysis of GRID generated molecular interaction fields; through the identification of molecular interaction properties exposed at the enzyme cavity surface, generated by the CAVBASE program; and by molecular dynamics simulations. The virtual screening Model I, - generated from the structural characteristics recognized from 13 PDB cruzain complexes - when applied to the ZINC database selected 10 compounds. For the experimental validation ofthe model, six ofthese compounds have been acquired and were tested as cruzain inhibitors. It was observed that three of the tested compounds (ZINC02470662, ZINC02682879 and ZINC03192044, respectively) did not show any significant cruzain inhibition, up to 7 mM. Meanwhile the other three tested compounds (ZINC02663001, ZINC01936854 and ZINC03326243, respectively) showed an unspecific cruzain inhibition, suggesting that an enzyme inhibition by promiscuous mechanism occurred. This mechanism was verified by the addition of 0.1% Triton X-100 on the enzymatic assay with a concomitant loss of cruzain inhibition activity. For these compounds, the confirmation of the promiscuous mechanism was also done, observing the loss of enzyme inhibition, after a ten times increase in the cruzain concentration on the enzymatic assay. The virtual screenmg Model II - generated from the structural characteristics recognized from 13 cruzain complexes and 20 complexes of other cysteine proteases, that have been identified on a search for cavities similar to cruzain - selected 55 compounds, when applied to the ZINC database. In order to experimentally validate the model, nineteen compounds have been acquired and were tested as cruzain inhibitors. It has been observed that one compound, ZINC01794422, showed a specific cruzain inhibition (Ki = 21 µM), while the other eighteen showed no significant inhibition, up to 592 µM concentration. The promiscuous mechanism of enzymatic inhibition was not observed, since 0.1% of Triton X-100 was added in ali assays. Additionally, Model II identified two other cruzain inhibitors (ZINC04899534 and ZINC01547017). However, these compounds have not been acquired or tested, since they are known cruzain inhibitors - already described in the literature and are structurally similar to the inhibitors used in the construction of the mode!. Referring to new inhibitors found, Model II showed a hit rate of 5,3%. This value is in agreement with those found in the literature, which ranges from 1 to 50%.