Activated neutrophils release a neutrophil serine proteinase (NSP) called Proteinase 3 (PR3). In granulomatosis with polyangiitis (GPA), an autoimmune vasculitis, enhanced PR3 release results in endothelial damage. Serine proteinase inhibitors (serpins) such as α-1 proteinase inhibitor (API) inhibit NSPs through the serpin’s reactive center loop (RCL). However, API is known to bind PR3 with a low specificity, compared to its main inhibitory target Human Neutrophil Elastase (HNE). The current treatment for GPA is immunosuppression, which leaves patients immunocompromised. Thus, the overall aim of this study was to engineer an API variant with a higher specificity to PR3 than HNE, which could serve as a possible novel therapeutic strategy for GPA. We created an API expression library, hypervariable at RCL residues A355-I356-P357-M358-S359, and expressed it in a T7 bacteriophage display system. This phage library was then biopanned for PR3 binding. Two conditions were used for each round of biopanning: experimental, with PR3, and the negative control, without PR3. The library was biopanned for a total of five consecutive rounds, with the product of one screen serving as the starting material for the next. A bacterial mass lysate screen was also employed to further probe the library with PR3. The phage-display and bacterial lysate screens resulted in the selection of two novel variants API-DA (D357/A358) and API-N (N359). Serpin-proteinase gel complexing assays indicated that API-N formed complex with PR3 similar to API-WT (wild-type), while API-DA was mainly cleaved as a substrate. There was no significant difference between the second order rate constants of API-N and API-WT reactions with PR3. Rate constants for API-DA binding to PR3 or for API-HNE reactions were not completed due to novel coronavirus (COVID-19) restrictions. However, this project successfully demonstrated the ability to screen a hypervariable API phage library with PR3, yielding two new novel API variants. / Thesis / Master of Science in Medical Sciences (MSMS) / When harmful substances enter our body such as bacteria or viruses, we have ways of protecting ourselves from them. One of those ways is through a cell called the neutrophil. This is an immune cell that can release “fighting tools” into our blood to combat the harm. Some of these tools are called proteins. One of those proteins is Proteinase 3. However, sometimes our neutrophils can be activated without the presence of viruses or bacteria by products made in our bodies called autoantibodies. When this happens, too many of the “fighting tool” Proteinase 3 is released leading to damage to the tubes or vessels that our blood flows through. This project aimed to find a new possible way to stop these extra fighting tools from doing harm to our body. We did this by creating a library of different proteins that can stop Proteinase 3 once it is released by the neutrophil.

Orientador: Prof. Dr. Luciano Puzer / Tese (doutorado) - Universidade Federal do ABC, Programa de Pós-Graduação em Ciência & Tecnologia - Química, 2014. / Serpina é o nome dado a uma superfamília de proteínas com grande diversidade de funções biológicas, e que tem como principal característica a inibição de serino proteases. Até meados do ano de 2002, acreditava-se que as serpinas eram exclusivas de organismos eucarióticos. No entanto, com o desenvolvimento das técnicas de sequenciamento de genomas, essas proteínas passaram a ser identificadas também em organismos procariotos. Assim com o objetivo de avaliar a capacidade de duas serpinas bacterianas (G. violaceus e M. xanthus) em inibir serino proteases foi realizado nesse trabalho a clonagem, expressão e caracterização bioquímica da atividade inibitória de duas serpinas bacterianas descritas no banco de dados de genoma "genbank". As serpinas que foram alvo de nosso estudo possuem diferentes sequências de aminoácidos na sua RCL (alça do centro reativo), visando produzir serpinas com diferentes especificidades para serino proteases. Os genes codificadores das duas serpinas foram clonados em vetor de expressão pET-28a(+). As serpinas S1 (Gloeobacter violaceus) e S2 (Myxococcus xanthus) foram expressas na cepa bacteriana E. coli Bl21 (D3), purificadas pela técnica de cromatografia de afinidade em resina de níquel Ni-NTA e obtidas na forma solúvel. Foram realizados ensaios para determinar a atividade inibitória das serpinas S1 (G. violaceus) e S2 (M. xanthus) contra as enzimas tripsina, quimotripsina, elastase, subtilisina, NS3 (dengue) e ainda da serpina S1 frente as calicreínas teciduais humanas 1, 3 e 5. A eficiência da reação de inibição da serpina S1 contra essas enzimas também foi testada na presença de glicosaminoglicanos (GAG¿s): heparina, sulfato de dermatan e sulfato de condroitina. A serpina S1 (G. violaceus) apresentou atividade inibitória frente à tripsina na ausência e também na presença dos GAG¿s heparina, sulfato de dermatan e sulfato de condroitina, sendo que na presença de heparina foi possível observar o menor valor de constante de velocidade de segunda ordem (k¿) em relação aos demais GAG¿s testados, sugerindo que a heparina atua de alguma forma na diminuição da velocidade na reação de inibição da tripsina pela serpina S1. Foi possível visualizar a formação do complexo covalente entre a serpina S1 (G. violaceus) e a tripsina por análise em SDS-PAGE 10%. Também analisamos a ação inibitória de compostos sintéticos derivados do isomanídeo frente às calicreínas teciduais humanas 1, 3, 5, 6 e 7. Nesse estudo foi possível obter inibidores seletivos para as calicreínas humanas teciduais 5 e 7, a partir dos compostos sintéticos derivados do isomanídeo e através dos estudos de docking, juntamente com a análise das estruturas das KLK5 e KLK7, foram fornecidas informações sobre as diferenças observadas entre as afinidades de ligação dos diferentes compostos derivados do isomanídeo refletidos nos resultados dos testes de inibição. / Serpin is the name given to the superfamily of proteins with wide range of biological functions, and that has as main feature the inhibition of serine proteases. Until mid-year 2002 it was believed that the serpins were unique to eukaryotic organisms. However, with the development of genome sequencing techniques, these proteins are now also been identified in prokaryotic organisms. Thus, with the objective of evaluate the ability of two bacterial serpins (G. violaceus and M. xanthus) to inhibit serine proteases was performed in this work the cloning, expression and biochemical characterization of the inhibitory activity of two bacterial serpins described in the database of genome "genbank". Serpins that have been the target of our study have different sequences of amino acids in RCL (the reactive center loop), to produce serpins with different specificities for serine proteases. The genes encoding the two serpins were cloned into the expression vector pET-28a (+). S1 (Gloeobacter violaceus) and S2 (Myxococcus xanthus) serpins were expressed in the bacterial strain E. coli BL21 (D3), purified by the technique of affinity chromatography on nickel Ni-NTA resin and obtained in soluble form. Assays were performed to determine the inhibitory activity of serpins S1 (G. violaceus) and S2 (M. xanthus) against the enzymes trypsin, chymotrypsin, elastase, subtilisin, NS3 (dengue) and also the serpin S1 against human tissue kallikrein 1, 3 and 5. The efficiency of the inhibition reaction against these enzymes serpin S1 was also tested in the presence of glycosaminoglycans (GAG's) heparin, dermatan sulfate and chondroitin sulfate. S1 serpin (G. violaceus) had inhibitory activity against trypsin in the absence and presence of GAGs heparin, dermatan sulfate and chondroitin sulfate, and in the presence of heparin was observed the lowest value of the rate constant of the second order (k') compared to the other GAG's tested, suggesting that heparin acts in some way in reducing the speed in inhibiting reaction of trypsin by serpin S1. It was possible to visualize the formation of a covalent complex between S1 (G. violaceus) serpin and trypsin by SDS-PAGE 10% analysis. We also analyzed the inhibitory activity of synthetic compounds derived from isomannide against human tissue kallikrein 1, 3, 5, 6 and 7. In this study it was possible to obtain specific inhibitors for human tissue kallikrein 5 and 7 from synthetic compound derived from the isomannide and through docking studies, together with the analysis of the structures of KLK5 and KLK7, were provided information about the differences between the various binding affinities of compounds derived from isomannide and reflected in the results of the inhibition tests.

Dissertation (Ph.D.)--University of South Florida, 2008. / Includes vita. Also available online. Includes bibliographical references (leaves 93-111).

published_or_final_version / abstract / toc / Zoology / Master / Master of Philosophy

Orientador: Prof. Dr. Luciano Puzer / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biossistemas, São Bernardo do Campo, 2017. / Serpina é o nome dado à superfamília de proteínas com uma vasta diversidade de funções biológicas, que tem como principal característica a inibição irreversível de serino proteases. A característica estrutural mais marcante das serpinas é a presença de uma alça na sua porção C-terminal, composta por 20 aminoácidos denominados alça do centro reativo (RCL). A RCL é a região da serpina que se liga covalentemente ao sítio ativo da serino protease, promovendo a inibição irreversível da enzima pela desarticulação de estruturas funcionais essenciais para a catálise enzimática. As calicreínas teciduais humanas (KLKs) são um grupo de 15 serino proteases (KLK1-KLK15) expressas em uma gama de tecidos. A rKLK5, estudada neste trabalho, é expressa abundantemente na pele humana, e parece que exerce importante papel no processo de descamação epidermal, podendo estar relacionada à patologias, como a psoríase e dermatite atópica. Assim, nesse trabalho foi realizada subclonagem, expressão e caracterização bioquímica da atividade inibitória dos mutantes (VSR344G e VSA345G) da serpina oriunda da cianobactéria Gloeobacter violaceus, identificada pelo nosso grupo e nomeada vioserpina. Os genes codificadores da vioserpina foram previamente clonados no vetor de expressão pET-28a e por meio da técnica de mutação sítio-dirigida foram produzidos dois mutantes substituindo os resíduos de aminoácidos arginina e alanina nas posições P1 e P2 da alça do centro reativo (RCL) da vioserpina, respectivamente, por um resíduo de aminoácido glicina (VSR344G e VSA345G). O sucesso das mutações foi avaliado através de sequenciamento de DNA. As vioserpinas mutantes foram expressas na cepa bacteriana E. coli BL21(D3), purificadas pela técnica de cromatografia de afinidade em resina de níquel (Ni-NTA) e obtidas na forma solúvel. Foi possível visualizar a formação do complexo covalente entre a vioserpina e a KLK5 por análise em SDS-PAGE 10% confirmados pela espectrometria de massas. Também foi analisada a ação inibitória dos mutantes (VSR344G e VSA345G) frente a KLK5. Os valores de SI (estequiometria de inibição) apresentaram valores altos o que indica que é preciso uma concentração grande de inibidor, no caso os mutantes da vioserpina, para que a enzima tenha sua atividade inibida, apresentando-se desta forma uma inibição ineficiente frente a rKLK5. Nesse estudo foi possível obter um inibidor específico (vioserpina) para a rKLK5, podendo assim contribuir para o desenvolvimento de novos procedimentos terapêuticos para patologias envolvidas com o processo de descamação epidermal. / Serpin is the name given to the superfamily of proteins with wide range of biological functions, and that has as main feature the irreversible inhibition of serine proteases. The most striking structural feature of serpins is the presence of a loop in the C-terminal portion of the protein, composed by 20 aminoacids called Reative Center Loop (RCL). The RCL is the region of the serpin that binds covalently to the serine protease active site, which causes the irreversible inhibition of the enzyme by the disarticulation of functional structures essencial for the enzymatic catalysis. Human tissue kalikreins (KLKs) are a group of 15 serine proteases (KLK1-KLK15) expressed in a plethora of tissues. The rKLK5, studied in this work, is abundantly expressed in human skin, and seems to play an important role in the epidermal desquamation process, and may be related to pathologies such as psoriasis and atopic dermatitis. Therefore, in this work the subcloning, expression and biochemical characterization of the inhibitory activity of serpin mutants (VSR344G e VSA345G) of the cyanobacteria Gloeobacter violaceus, recently described by our group and named vioserpin, was proposed. The genes coding for vioserpin were previously cloned into the pET-28a expression vector and through the site-directed mutation technique two mutants were produced by substituting the arginine and alanine amino acid residues at the P1 and P2 positions of the serine reactive center loop (RCL), respectively, by a glycine amino acid residue (VSR344G e VSA345G). The success of the mutations was assessed by DNA sequencing. The mutant vioserpin was expressed in the bacterial strain E. coli BL21 (D3), purified by the nickel resin affinity chromatography technique (Ni-NTA) and obtained in the soluble form. Covalent complex formation between vioserpin and rKLK5 could be visualized by 10% SDS-PAGE analysis confirmed by mass spectrometry. We also analyzed the inhibitory action of mutants (VSR344G and VSA345G) against rKLK5. The SI values (inhibition stoichiometry) presented high values indicating that a large inhibitor concentration is required in the case of the vioserpin mutants, so that the enzyme has its inhibited activity, thus presenting an inefficient inhibition in front To rKLK5. In this study it was possible to obtain a specific inhibitor (vioserpin) for rKLK5, thus contributing to the development of new therapeutic procedures for pathologies involved with the epidermal desquamation process.

Dissertation (Ph.D.)--University of South Florida, 2008. / Title from PDF of title page. Document formatted into pages; contains 111 pages. Includes vita. Includes bibliographical references.

Les tiques sont des arthropodes ectoparasites obligatoires qui se nourrissent sur une grande variété de vertébrés sur une large partie du globe. Au cours de leur repas, les tiques sécrètent dans leur salive de nombreux facteurs leur permettant de contourner bon nombre des défenses de l’hôte. Bien que la littérature rapporte beaucoup d’informations au sujet des effets du repas de la tique sur l’hôte, la nature des facteurs actifs exprimés par les glandes salivaires de la tique est peu connue. Au cours d’anciens travaux au sein du laboratoire, le crible de deux banques d’ADN complémentaires - issues de la rétro-transcription des ARN messagers synthétisés par les glandes salivaires de la tique Ixodes ricinus – a permis l’identification de 27 protéines dont l'expression est spécifiquement induite ou régulée positivement pendant le repas sanguin de la tique I. ricinus. Parmi ces protéines, la protéine Seq24, induite au cours du repas sanguin, présente la capacité de moduler les immunités innée et acquise de l’hôte. En conséquence, la protéine Seq24 a été nommée Iris pour « Ixodes ricinus Immunosuppressor ». Au cours de la présente étude, notre but fût de caractériser le rôle d’Iris et de déterminer son importance dans le repas sanguin de la tique I. ricinus.<p>La protéine Iris appartient à la famille des inhibiteurs de sérine protéases et présente une homologie significative avec l’inhibiteur d’élastase de leucocytes. Une analyse in silico a confirmé qu’Iris présentait la structure des serpines, et notamment le RCL (Reactive Center Loop), boucle responsable de l’activité anti-protéasique. Comme attendu (sur base de l’analyse in silico), Iris inhibe de manière spécifique l’activité de plusieurs sérine protéases, et en particulier l’élastase de leucocyte. Ces tests effectués, nous avons essayé de comprendre quel(s) pouvai(en)t être le(s) rôle(s) d’Iris dans l’accomplissement du repas sanguin de la tique, c’est à dire dans la lutte contre les différents systèmes de défenses de l’hôte.<p>Tout d’abord, des tests ont démontré la capacité d’Iris à inhiber les mécanismes de l’hémostase. Des tests sur du plasma et du sang complet ont montré qu’Iris allonge le temps de fibrinolyse, la voie intrinsèque de la coagulation et l’adhésion plaquettaire. L’utilisation de mutants a également démontré que si les deux premières activités sont dépendantes du RCL, et donc d’un mode de fonctionnement anti-protéolytique, l’adhésion plaquettaire est indépendante de ce système. Ce résultat met en évidence l’existence d’autres sites actifs, isolés par analyse in silico, nommés Receptor Binding Domain (RBD).<p>Un travail antérieur du laboratoire avait permis d’indiquer la capacité de la protéine recombinante Iris semi-purifiée à inhiber la production de TNF-a, d’IL-6, et d’IL-8 (cytokines pro-inflammatoires) ainsi que l’IFN-g par des PBMCs (Peripherical Blood Mononuclear Cells) humaines. Ces résultats ont été confirmés avec de la protéine purifiée. Des analyses complémentaires ont démontré qu’un mutant d’Iris - dépourvu d’activité anti-protéasique - conserve l’activité pro-inflammatoire. Là encore, ce mécanisme semble impliquer un ou plusieurs RBD. L’utilisation d’anticorps dirigés contre ces zones a permis de déterminer le domaine d’interaction (aa :105-120) impliqué dans cette fonction. D’autre part, une analyse par FACS a permis de démontrer qu’Iris interagit uniquement avec les cellules d’origine monocytaire.<p>Enfin, nous avons également analysé l’importance d’Iris au cours du repas sanguin de la tique par une approche vaccinale. Les résultats observés indiquent que 30 % des tiques nourries sur des lapins immunisés par la protéine rIris ne survivent pas au repas. / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished

Tick saliva contains a lot of biological active substances helping them to succesfully complete their feeding which is neccesary for their next development. Both proteinaceous and non-proteinaceous molecules including protease inhibitors are present in tick saliva. The biggest family of these proteases are serpins. Serpins are involved in many biological processes as blood coagulation, fibrinolysis, apoptosis or inflammation. The aim of this diploma work was to determine expression profiles of 10 serpins from nymphs of Ixodes ricinus fed for different times using quantitative real time PCR. For chosen genes (IRS 10, IRS 20) dsRNA for silencing of the gene was prepared and using RNA interference the role of these genes during tick (I. ricinus nymphs) feeding and transmission of Borrelia afzelii spirochetes, a vector of Lyme borreliosis, was evaluated.Tick saliva contains a lot of biological active substances helping them to succesfully complete their feeding which is neccesary for their next development. Both proteinaceous and non-proteinaceous molecules including protease inhibitors are present in tick saliva. The biggest family of these proteases are serpins. Serpins are involved in many biological processes as blood coagulation, fibrinolysis, apoptosis or inflammation. The aim of this diploma work was to determine expression profiles of 10 serpins from nymphs of Ixodes ricinus fed for different times using quantitative real time PCR. For chosen genes (IRS 10, IRS 20) dsRNA for silencing of the gene was prepared and using RNA interference the role of these genes during tick (I. ricinus nymphs) feeding and transmission of Borrelia afzelii spirochetes, a vector of Lyme borreliosis, was evaluated.