In this work, we examine the structure and function of two important human proteins. The first is human kallikrein 6 (hK6), which is a newly identified enzyme in the serine proteinase family that is expressed in the central nervous system. In chapter 2, the X-ray crystal structure of mature, active recombinant human kallikrein 6 at 1.75 Å is presented. This high resolution model provides the first three-dimensional view of one of the human kallikreins and one of only a few structures of serine proteinases predominantly expressed in the central nervous system. Enzymatic and X-ray data provide support for the characterization of human kallikrein 6 as a degradative proteinase with structural features more similar to trypsin than the regulatory kallikreins. In chapter 3, we have re-solved the structure of hK6 to a resolution of 1.56 Å. In addition, a detailed analysis of the preferred substrate specificity of hK6 at the positions P3, P2, P1′, P2′, and P3′ is undertaken using internally quenched fluorescent substrates based on a peptide background sequence of the identified autolysis region. Furthermore, the identified optimized substrate sequence is modeled into the 1.56 Å structure of human kallikrein 6 using docking in order to identify structural aspects of the protein responsible for this preference. The substrate specificity data show that human kallikrein 6 displays little discrimination for particular amino acids at the tested positions with the exception of P2′, where there is a pronounced preference for proline. The second protein studied in this work is human fibroblast growth factor-1 which is a member of the β-trefoil superfold. In chapter 4, a 1.10 Å atomic-resolution x-ray structure of human fibroblast growth factor 1, a member of the β-trefoil superfold, is reported. The FGF-1 structure exhibits numerous core packing defects detectable using a 1.0Å radius probe. In addition to contributing to the relatively low thermal stability of FGF-1, these defects may also permit domain motions within the structure. The availability of refined ADP's permits a translation/libration/ screw (TLS) analysis of putative rigid body domains. The observed rigid body motion in FGF-1 appears related to the ligand-binding functionalities. / Dissertation / PhD

<p>It is well established that mast cells (MC) are key players in airway pathologies such as allergic asthma, but they are also known to contribute to host defense and tissue remodeling. MC serine proteases are the major protein components of mast cell granules and accordingly, are most likely involved in many aspects of MC function. Two major groups of MC serine proteases have been described; chymases, which cleave a target preferentially after aromatic amino acids, and tryptases, which cleave preferentially after positively charged residues. Biochemical characterization of these proteases is a first step towards understanding their contribution to MC function. One of the issues addressed in this thesis is the target specificity of two rodent MC chymases, rat mast cell protease (rMCP)-4 and rMCP-5. The substrate specificity was analyzed using a substrate phage display technique, in which a large library of peptide substrates is screened simultaneously in a single reaction. The substrate analysis revealed that rMCP-4 displays very stringent substrate specificity, with striking preference for two subsequent aromatic amino acids N-terminal of the cleavage site. This chymase therefore holds a substrate recognition profile clearly distinct from other chymases. Database searches using the generated peptide sequence identified several interesting potential targets for rMCP-4, such as the FcγRIII and the TGFβ receptor. The phage display technique was also used to analyze the substrate specificity of rMCP-5. rMCP-5 is the rat chymase most closely related in sequence to human chymase. Interestingly, rMCP-5, unlike human chymase, was shown to hydrolyze substrates after small aliphatic amino acids, but not after aromatic residues. rMCP-5 and human chymase might therefore have different biological functions. Thus, studies of cleavage specificity can be a successful approach both to elucidate subtle differences in specificity of closely related proteases, as well as to identify new biological targets for a protease.</p><p>The MC tryptases contribute to the pro-inflammatory activities of the MC. To assess the requirements for activation and stability of a mouse tryptase, mMCP-6, recombinant mMCP-6 protein was produced in mammalian cells. A low pH (<6.5), as well as a negatively charged proteoglycan, e.g. heparin, were shown to be necessary both to obtain and maintain activity. With this in mind, heparin antagonists were studied for their potential to inhibit mMCP-6 and human tryptase. Indeed, the heparin antagonists were shown to be highly efficient tryptase inhibitors. Thus, heparin antagonists might be promising candidates to attenuate inflammatory disorders, such as allergic asthma. </p>

<p>Immune cells like NK cells, T cells, neutrophils and mast cells store high amounts of <u>gr</u>anule <u>s</u>erine <u>p</u>rote<u>ases</u>, graspases. Graspases are encoded from the mast cell chymase locus. The human locus holds four genes: α-chymase, cathepsin G, and granzymes H and B. In contrast, the mouse locus contains at least 14 genes. Many of these belong to subfamilies not found in human, e.g. the Mcpt8-family. These differences hamper functional comparisons of graspases and of immune cells in the two species. Studies of the mast cell chymase locus are therefore important to better understand the mammalian immune system. </p><p>In this thesis, the evolution of the mast cell chymase locus was analysed by mapping the locus in all available mammalian genome sequences. It was revealed that one single ancestral gene founded this locus probably over 215 million years ago. This ancestor was duplicated more than 185 million years ago. One copy evolved into the α-chymases, whereas the second copy founded the families of granzymes B and H, cathepsin G, Mcpt8 and duodenases. Different subfamilies were later remarkably expanded in particular mammalian lineages, e.g. the Mcpt8- and Mcpt2-subfamilies in the rat. Four novel members of these families were identified in rat mucosal mast cells. Rat and mouse mast cells express numerous different graspases, whereas human and dog mast cells express only one graspase, chymase. To better understand mast cell functions in these species, one member of the mouse Mcpt8-family, mMCP-8, and human and dog chymase were studied. The preferred substrate sequence was analysed by substrate phage display. mMCP-8 remains yet enigmatic, although it is probably proteolytically active. Dog and human chymase, interestingly, have common preferences in certain substrate positions, but differ in others. These two chymases may have coevolved with an <i>in vivo</i> substrate that is conserved only in the positions with a common preference. We also obtained evidence that substrate positions on either side of the scissile bond influence each other. This kind of interactions can only be detected with a method investigating both sides simultaneously, such as substrate phage display.</p>

It is well established that mast cells (MC) are key players in airway pathologies such as allergic asthma, but they are also known to contribute to host defense and tissue remodeling. MC serine proteases are the major protein components of mast cell granules and accordingly, are most likely involved in many aspects of MC function. Two major groups of MC serine proteases have been described; chymases, which cleave a target preferentially after aromatic amino acids, and tryptases, which cleave preferentially after positively charged residues. Biochemical characterization of these proteases is a first step towards understanding their contribution to MC function. One of the issues addressed in this thesis is the target specificity of two rodent MC chymases, rat mast cell protease (rMCP)-4 and rMCP-5. The substrate specificity was analyzed using a substrate phage display technique, in which a large library of peptide substrates is screened simultaneously in a single reaction. The substrate analysis revealed that rMCP-4 displays very stringent substrate specificity, with striking preference for two subsequent aromatic amino acids N-terminal of the cleavage site. This chymase therefore holds a substrate recognition profile clearly distinct from other chymases. Database searches using the generated peptide sequence identified several interesting potential targets for rMCP-4, such as the FcγRIII and the TGFβ receptor. The phage display technique was also used to analyze the substrate specificity of rMCP-5. rMCP-5 is the rat chymase most closely related in sequence to human chymase. Interestingly, rMCP-5, unlike human chymase, was shown to hydrolyze substrates after small aliphatic amino acids, but not after aromatic residues. rMCP-5 and human chymase might therefore have different biological functions. Thus, studies of cleavage specificity can be a successful approach both to elucidate subtle differences in specificity of closely related proteases, as well as to identify new biological targets for a protease. The MC tryptases contribute to the pro-inflammatory activities of the MC. To assess the requirements for activation and stability of a mouse tryptase, mMCP-6, recombinant mMCP-6 protein was produced in mammalian cells. A low pH (&lt;6.5), as well as a negatively charged proteoglycan, e.g. heparin, were shown to be necessary both to obtain and maintain activity. With this in mind, heparin antagonists were studied for their potential to inhibit mMCP-6 and human tryptase. Indeed, the heparin antagonists were shown to be highly efficient tryptase inhibitors. Thus, heparin antagonists might be promising candidates to attenuate inflammatory disorders, such as allergic asthma.

Immune cells like NK cells, T cells, neutrophils and mast cells store high amounts of <u>gr</u>anule <u>s</u>erine <u>p</u>rote<u>ases</u>, graspases. Graspases are encoded from the mast cell chymase locus. The human locus holds four genes: α-chymase, cathepsin G, and granzymes H and B. In contrast, the mouse locus contains at least 14 genes. Many of these belong to subfamilies not found in human, e.g. the Mcpt8-family. These differences hamper functional comparisons of graspases and of immune cells in the two species. Studies of the mast cell chymase locus are therefore important to better understand the mammalian immune system. In this thesis, the evolution of the mast cell chymase locus was analysed by mapping the locus in all available mammalian genome sequences. It was revealed that one single ancestral gene founded this locus probably over 215 million years ago. This ancestor was duplicated more than 185 million years ago. One copy evolved into the α-chymases, whereas the second copy founded the families of granzymes B and H, cathepsin G, Mcpt8 and duodenases. Different subfamilies were later remarkably expanded in particular mammalian lineages, e.g. the Mcpt8- and Mcpt2-subfamilies in the rat. Four novel members of these families were identified in rat mucosal mast cells. Rat and mouse mast cells express numerous different graspases, whereas human and dog mast cells express only one graspase, chymase. To better understand mast cell functions in these species, one member of the mouse Mcpt8-family, mMCP-8, and human and dog chymase were studied. The preferred substrate sequence was analysed by substrate phage display. mMCP-8 remains yet enigmatic, although it is probably proteolytically active. Dog and human chymase, interestingly, have common preferences in certain substrate positions, but differ in others. These two chymases may have coevolved with an in vivo substrate that is conserved only in the positions with a common preference. We also obtained evidence that substrate positions on either side of the scissile bond influence each other. This kind of interactions can only be detected with a method investigating both sides simultaneously, such as substrate phage display.

Mast cells (MC) are potent inflammatory cells that are known primarily for their prominent role in IgE mediated allergies. However, they also provide beneficial functions to the host, e.g. in bacterial and parasitic defence. MCs react rapidly upon stimulation by releasing potent granule-stored mediators, and serine proteases of the chymase or tryptase families are such major granule constituents. As a first step towards a better understanding of the biological function of these proteases, we have determined the extended cleavage specificities of four mammalian mast cell chymases, by utilizing a substrate phage display approach. The specificities of these enzymes have then been used to compare their functional characteristics. The major mucosal MC chymase in mice, mMCP-1, was found to possess a strict preference in four amino acid positions of the peptide substrate. Using this sequence to search the mouse proteome for potential in vivo substrates led to the identification of several very interesting potential novel substrates. Some of them may explain the increased epithelial permeability provided by this enzyme. Human MCs, express only one single α-chymase, and the rodent α-chymases have secondarily gained elastase-like primary cleavage specificity. However, rodents express additional chymases, the β-chymases, and rodent β-chymases may have adopted the function of the α-chymases. The cleavage specificities of the human chymase and two rodent β-chymases were therefore determined (rat rMCP-1 and mouse mMCP-4). N-terminal of the cleaved bond the three chymases showed similar preferences, but C-terminal the human chymase and mMCP-4 shared a high preference for acidic amino acids in the P2´ position and therefore seem to be functional homologues. The molecular interactions mediating the preference for acidic amino acids in position P2´ were further investigated. By site-directed mutagenesis of the human chymase, amino acids Arg143 and Lys192 were concluded to synergistically mediate this preference. Our data show that chymases, of different MC subpopulations, display quite different extended cleavage specificities. However mouse do possess a MC chymase with almost identical cleavage specificity as the human MC chymase indicating a strong evolutionary pressure to maintain this enzyme specificity.

Introduction. The outermost layer of the epidermis, the stratum corneum (SC), plays a fundamental role in our defense against microorganisms, chemicals, and dehydration. The SC is composed of tightly packed keratinized skin cells, corneocytes. For a functioning skin it is essential that corneocytes are constantly shed (desquamated). Kallikrein-related peptidase (KLK) 5 and KLK7 may be important in the desquamation process through degradation of desmosomal proteins. Severe hereditary diseases, where inhibition of KLK5 and/or KLK7 is missing, points to the importance of regulation of protease activity. KLKs may be regulated in various ways: tissue expression, activation of proforms, specific inhibitors, and physico-chemical properties like pH. Besides their involvement in desquamation, KLKs may also be important in immune defense and inflammation by processing of mediators and via activation of proteinase-activated receptors (PARs). Aims. 1. To identify and characterize previously unknown proteases in the SC. 2. To further characterize KLK5 and KLK7 with special focus on activation mechanisms. 3. To identify new inhibitors of KLKs in human SC. 4. To further characterize KLKs regarding effects of various inhibitors and substrates. 5. To study possible functions of KLKs in inflammation, in particular via activation of PAR-2. Methods. Plantar SC was used as a source for purification of proteins. Recombinant proteins were produced in different expression systems (insect cells, yeast cells, and bacteria). Different activity assays and kinetic studies were performed. Tissue expression was studied by immunohistochemistry, immunoblot and PCR. PAR-2 activation was studied by measurement of intracellular [Ca2+] and immunofluorescense in KNRK-PAR2 cells. Results. Active KLK14 was purified from extracts of plantar SC. KLK14 showed a superior catalytic efficiency as compared to KLK5 when measuring trypsin-like activity. This indicated that KLK14, despite being present in low amounts in skin, may have great relevance for skin physiology. Among enzymes tested only KLK5 showed autocatalytic activity and is so far the only enzyme found in SC that can activate proKLK7. KLK5 could also activate proKLK14. This together with studies of pH dependence on activation placed KLK5 as a possible key activating enzyme in a proposed proteolytic cascade in the SC. In plantar SC extracts we have also identified the novel Kazal-type serine protease inhibitor 9 (SPINK9). Our results indicate that SPINK9 is preferentially expressed in palmo-plantar skin and specific for KLK5. Differences found regarding substrate specificity and inhibition profile can be useful in evaluating the contribution of individual KLKs to the proteolytic activity in crude SC extracts. One interesting finding was that KLK8, present at high protein levels in the epidermis, could not be inhibited by any protease inhibitor found in the extracts. PAR-2 activation studies showed that KLK5 and 14 but neither KLK7 nor 8 can activate PAR-2. Immunohistochemistry preferentially detected KLK14 in intraepidermal parts of the sweat ducts and in dermal sweat glands but we could also show coexpression of KLK14 and PAR-2 in the SC and stratum granulosum of the epidermis in inflammatory skin disorders. To summarize, KLK involvement in desquamation may be dependent on a proteolytic activation cascade regulated by an intrinsic pH gradient and specific inhibitors present in SC. Another possible function of KLKs is as mediators of inflammation through activation of PAR-2.

Mast cells are innate immune cells, historically involved in allergy responses involving IgE. Through this, they have earned a reputation as a fairly detrimental cell type. Their beneficial roles remain somewhat enigmatic although they clearly have the ability to modulate the immune system. This is due to their ability to synthesise many cytokines and chemokines as well as immediately release potent granule-stored mediators. One such mediator is a serine protease, chymase, which has been targeted by pharmaceutical companies developing inhibitors for use in inflammatory conditions. In order to address roles of the proteases, information regarding their cleavage specificity using substrate phage display can help find potential in vivo substrates.  The human chymase cleaves substrates with aromatic amino acids in the P1 position and has a preference for negatively charged amino acids in the P2’ position. The molecular interactions mediating this P2’ preference was investigated by site-directed mutagenesis, where Arg143 and Lys192 had a clear effect in this selectivity. As humans express one chymase and rodents express multiple chymases, extrapolating data between species is difficult. Here, the crab-eating macaque was characterised, which showed many similarities to the human chymase including a near identical extended cleavage specificity and effects of human chymase inhibitors.  Appropriate models are needed when developing human inhibitors for therapeutic use in inflammatory conditions. The effects of five specific chymase inhibitors in development were also tested. The selectivity of inhibitors was dependent on both Arg143 and Lys192, with a greater effect of Lys192. Identification of residues involved in specific inhibitor interactions is important for selective inhibitor development. Another innate cell type, the NK cell, is important in virus and tumour defence. In the channel catfish, a serine protease from an NK-like cell, granzyme-like I, was characterised. A strict preference for Met in the P1 position was seen, and caspase 6 was identified as a potential in vivo target. This may highlight a novel apoptosis-inducing mechanism from a similar cell type has been conserved for approximately 400 myr. Here, important residues mediating chymases’ specificity and interactions with inhibitors has been addressed, as well as finding a new animal model for providing ways to combat their roles in pathological settings.

SmSP1 is a chimerical serine protease consisted of three domains (cub, LDLa and trypsin-like) and found in Schistosoma mansoni. Its characterization was performed by molecular techniques such as PCR screen, qRT-PCR and RNA interference (RNAi) to gain information about expression profile, level expression and susceptibility to RNAi. Further, protein expression was carried out to gain an antigen for immunization and recombinant for biochemical studies. Results of PCR screen and qRT-PCR suggested possible function of SmSP1 in egg and adult stages but SmSP1 gene was not found susceptible to RNAi in NTS. Recombinant from E. coli was successfully used for immunization. Active recombinant was likely expressed in Pichia pastoris but expression conditions are unstable and expression optimization is necessary.

Submitted by Biblioteca da Faculdade de Farmácia (bff@ndc.uff.br) on 2017-03-17T18:50:12Z No. of bitstreams: 1 Portela, Aline Cordeiro [Dissertação, 2014].pdf: 9279752 bytes, checksum: 9172b58477a24ce8a80f3405e0759adb (MD5) / Made available in DSpace on 2017-03-17T18:50:12Z (GMT). No. of bitstreams: 1 Portela, Aline Cordeiro [Dissertação, 2014].pdf: 9279752 bytes, checksum: 9172b58477a24ce8a80f3405e0759adb (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A dengue é um problema de saúde pública mundial, acometendo cerca de 50 milhões de pessoas por ano. O HCV é a principal causa de hepatite crônica e estima-se que 200 milhões de pessoas estejam infectadas no mundo. A terapia atual contra o HCV apresenta eficácia limitada e baixa tolerância, enquanto que para a dengue não existe um tratamento antiviral específico. Com o objetivo de explorar essa demanda, o presente trabalho descreve a síntese para a obtenção de quinze compostos peptideomiméticos inéditos, contendo o cerne rígido proveniente do isosorbídeo, como potenciais agentes inibidores da enzima NS3 protease de ambos os vírus. A estratégia de síntese dos peptideomiméticos consistiu inicialmente na obtenção de dez compostos inéditos, das séries 28a-c (derivada de oxazolonas) e 29a-g (derivada de aminoácidos N-protegidos). Os compostos foram inicialmente testados frente à inibição da protease do DENV-2, os quais não apresentaram resultados significativos. Entretanto, os resultados de inibição enzimática dos compostos frente à NS3/4A do HCV-1b foram mais satisfatórios, sendo o composto 28a (1,4:3,6-dianidro-5-[[(2Z)-2-(benzoilamino)-1-oxo-3-(2-tienil)-2-propen-1-il]amino] -2-deoxi-2-O-(fenilmetil)-D-iditiol, o mais ativo, com IC50 = 88μm. Estudos de docking molecular foram realizados para avaliar o modo de interação dos ligantes com a serina protease NS3/4A do HCV. Dentre os compostos sintetizados, 28a foi considerado protótipo para o desenvolvimento de novos compostos com potencial de inibição da enzima em questão. A partir de 28a, a nova série de compostos inéditos 42a-e foi proposta e obtida. Os resultados dos ensaios farmacológicos frente à NS3/4A do HCV-1b permitiram-nos inferir que a substituição do tiofeno de 28a pelo furano e 3-metiltiofeno em 42b e 42c, respectivamente, resultou em um aumento de cerca de 30% no perfil de inibição enzimática, com inibição de 70% dessa enzima viral. Dessa forma, podemos identificar esses dois novos compostos como protótipos para o planejamento de futuras moléculas potencialmente inibidoras da enzima serina protease do vírus da Hepatite C / Dengue fever is a worldwide public health concern, affecting approximately 50 million people per year. HCV is the main cause of chronic hepatitis and it is estimated that 200 million people are infected worldwide. Current therapy against HCV has limited efficacy and low tolerance, and there is no specific antiviral treatment for dengue fever. In order to exploit this demand, this work describes the synthesis for obtaining fifteen novel peptidemimetic compounds, isosorbide derivatives as potential inhibitory agents of the NS3 protease enzyme of both viruses. Initially the synthetic strategy of peptidemimetics consisted in obtaining ten novel compounds: 28a-c (derived from oxazolones) and 29a-g (derived from N-protected amino acids) series. The compounds were initially tested on the inhibition of protease DENV-2 , which results were not significant. However, the results of enzymatic inhibition of the compounds against the NS3/4A HCV-1b was more satisfactory, and the compound 28a (1,4 : 3,6- dianhydro -5 - [[( 2Z ) -2- ( benzoylamino) -1 -oxo- 3- (2- thienyl) -2 - propen -1- yl] amino] -2- deoxy -2- O- ( phenylmethyl ) -D- iditiol) , the most active , presenting IC50 = 88μm. Molecular docking studies were performed to assess the compounds mode of interaction with the serine protease NS3 / 4A HCV. Among the compounds synthesized, 28a was considered a prototype for the development of new compounds with a potential inhibition of the enzyme in question. Staring from 28a as a prototype the 42a-e serie was proposed and obtained. The results of pharmacological tests against the NS3/ 4A HCV -1b allowed us to conclude that substitution of the 28a furan thiophene and 3- methylthiophene in 42b and 42c respectively resulted in an increase of 30 % in the profile enzyme inhibition , with inhibition of 70 % of the viral enzyme . Thus , we can identify these new compounds as prototypes for planning future potentially molecule inhibitors of serine protease enzyme of the Hepatitis C virus