Orientador: Prof. Dr. Luciano Puzer / Tese (doutorado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biossistemas, 2018. / Serpinas sao proteinas inibidoras de serino-proteases, responsaveis pelo controle dos mais diversos processos fisiologicos e que cujo mecanismo de inibicao consite em formar um complexo covalente com a enzima alvo, em um processo de inibicao irreversivel. A alca de centro reativo (RCL) e responsavel por interagir com a protease, mimetizando um substrato, e quando clivada se insere como uma ¿À-fita no interior da serpina, trazendo a protease e causando uma distorcao no seu sitio ativo. Como as serpinas forma ligacoes covalentes com seus alvos durante a inibicao, essas proteinas tem sido utilizadas para o estudo do mecanismo de hidrolise das serino-proteases. No entanto, elas tambem oferecem a possibilidade do desenvolvimento de novas drogas contra enzimas relacionadas com patologias, como pode ser o caso da Vioserpina, uma serpina bacteriana capaz de inibir serino-proteases do tipo tripsina-like como a calicreina tecidual humana 5. Encontrar uma maneira de produzir uma Vioserpina fluorescente pode resultar no desenvolvimento de uma poderosa ferramenta para moniotramento e controle dessa e outras enzimas envolvidas com processos patologicos, como o antigeno prostatico especifico (PSA). Dessa maneira, realizamos mutacoes pontuais no gene da Vioserpina para a incorporacao do aminoacido cumarinico via par ortogonal tRNA/aaRS por supressao do codon ambar de parada. O aminoacido cumarinico e um aminoacido nao-canonico capaz de emitir fluorescencia na comprimento de onda de 450 nm quando excitado a 363 nm, permitindo o facil monitoramento e deteccao de uma proteina. Tres residuo distintos da Vioserpina foram escolhidos para a incorporacao do aminoacido cumarinico: Trp 208, Ile 342 (P4 da RCL) e Val 343 (P3 da RCL). A incorporacao nas posicoes Trp 208 e Ile 342 resultou em proteina fluorescentes, mas truncadas apos a insercao do aminoacido. Foi possivel obter uma Vioserpina completa com o aminoacido cumarinico na posicao Ile 342, embora com rendimento muito baixo. Tal mutante apresentou capacidade de inibicao e especificidade diferentes da Vioserpina wild type, em ensaios de inibicao enzimatica contra Tripsina e Quimotripsina, indicando que o aminoacido cumarinico em P4 parece causar diferentes interacoes no momento de inibicao da serpina. Para averiguar as melhores sequencias resultantes da incorporacao do aminoacido cumarinico, foi gerada uma biblioteca de genes da Vioserpina variando aleatoriamente as posicoes P4, P2, P1 e P1f da RCL, com incosporacao do aminoacido cumarinico na posicao P3 (Val 343). A biblioteca de Vioserpina foi apresentada por Phage Display no capsideo do fago M13 fusionada a proteina PIII, utilizando Biopanning para selecao das melhores sequencias com incorporacao do aminoacido nao-canonico, contra a serino-protease quimotripsina. A biblioteca de fagos gerou cinco sequencias com melhor inibicao que da Vioserpina, e mostrou que a insercao do aminoacido cumarinico parece acontecer com maior frequencia quando flanqueado por aminoacidos hidrofobicos ou sem cargas. A incorporacao do aminoacido cumarinico em sequencias da Vioserpina foi bem sucedida, sendo possivel avaliar a insercao de tal aminoacido na capacidade inibitoria dessa serpina. A investigacao da insercao de aminoacido nao-canonicos por Phage Display e Biopanning representa um grande passo para entender melhor como ocorre a incorporacao de tais aminoacidos, e quais residuos podem ocupar com maior naturalidade suas posicoes laterais. / Serpins are serine protease inhibitor proteins, responsible for the control of the most diverse physiological processes and whose mechanism of inhibition consists in forming a covalent complex with the target enzyme, in an irreversible inhibition process. The reactive center loop (RCL) acts as a bait for the protease, and when cleaved it inserts as a â-strand inside the molecule, distorting the protease active site. As serpins form covalent bonds with their targets, these proteins have been used to study the hydrolysis mechanism of serine proteases. However, they also offer the possibility of developing new drugs against disease-related enzymes, as is the case of Vioserpin, a bacterial serpin capable of inhibiting trypsin-like serine proteases such as human tissue kallikrein. Finding a way of producing fluorescent Vioserpin may result in the development of a powerful tool for monitoring and controlling this and other enzymes involved in pathological processes, such as prostate specific antigen (PSA). Thus, we performed point mutations in the Vioserpin gene for incorporation of the coumarin amino acid through tRNA/aaRS orthogonal pair by suppression of the amber stop codon. The coumarin amino acid is a non-canonical amino acid capable of emitting fluorescence at 450 nm when excited at 363 nm, allowing for easy detection of a protein. Three different residues of Vioserpin were chosen for incorporation of the coumarin amino acid: Trp 208, Ile 342 (P4 in RCL) and Val 343 (P3 in RCL). Incorporation at positions Trp 208 and Ile 342 resulted in fluorescent but truncated proteins following amino acid insertion. A complete Vioserpin bearing the coumarin amino acid at the Ile 342 position was possible, although at very low yield. Such a mutant exhibited different inhibition and specificity compared to Vioserpin wild type in enzymatic inhibition assays against trypsin and chymotrypsin, indicating that the coumarin amino acid at P4 appears to cause different interactions during serpin inhibition. To ascertain the best sequences resulting from coumarin amino acid incorporation, a Vioserpin gene library was generated by randomly varying the P4, P2, P1 and P1' positions in RCL, with coumarin amino acid incorporated at the P3 (Val 343) position. The Vioserpin library was exhibited by Phage Display in the M13 phage capsid fused to the PIII protein, using Biopanning against chymotrypsin to select the best sequences with incorporation of the non-canonical amino acid. The phage library generated five sequences with better inhibition than Vioserpin, and pointed to coumarin amino acid insertion appearing to occur more frequently when flanked by hydrophobic or uncharged amino acids. The incorporation of the coumarin amino acid into Vioserpin sequences was successful, and it is possible to evaluate the insertion of such amino acid in the inhibitory capacity of this serpin. The investigation of non-canonical amino acid insertion by Phage Display and Biopanning represents a great step to better understand how the incorporation of such amino acids occurs, and which residues may more naturally occupy their lateral positions

Within the immune system, Y-shaped proteins known as antibodies play crucial roles in detecting and blocking the harmful effects of foreign pathogens. Antibodies are naturally synthesized in our bodies by plasma B-cells, but they can also be synthesized and manufactured in labs through methods of recombinant antibody technology. Today, the field of antibody research and development is a competitive area of study due to the great promise it carries. In this study, 4 clones were developed as phage linked and soluble scFv proteins in order to be tested for their specificity against an RTK antigen, T1. T1 was of interest due to its hypothesized involvement in a breast cancer causing pathway. Subsequent selection assays in the form of ELISA and Western Blot were performed in order to identify a promising antibody candidate both robust in expression and specific in binding. The ELISA results pointed to Clone A1 as having the greatest potency and specificity for the T1 target antigen when it was presented as a phage linked and soluble scFv protein. Evaluation of the expression profiles for the 4 soluble and phage linked clones also pointed to clone A1 as being the most robust and potent. In conclusion, clone A1 exhibited the greatest ability in expression and detection of the T1 antigen and was thereby determined to be the most promising candidate in further development and optimization procedures. A1’s results in the preliminary tests also suggests strong performance in its translation into a successful therapeutic drug.

In this study, we demonstrated that the CSKSSDYQC-peptide ligand which was identified from a random phage-peptide library through an in vivo phage display technique with rats could prominently improve the transport efficiency of macromolecules, such as large filamentous phage particles (M13 bacteriophage), across the intestinal mucosal barrier. Synthetic CSKSSDYQC-peptide ligands significantly inhibited the binding of phage P1 encoding CSKSSDYQC-peptide ligands to the intestinal mucosal tissue and immunohistochemical analysis showed that the CSKSSDYQC-peptide ligands could be transported across the intestinal mucosal barrier via goblet cells as their specific gateway. Thus, we inferred that CSKSSDYQC-peptide ligand might have a specific receptor on the goblet cells and transported from intestinal lumen to systemic circulation by transcytosis mechanism. These results suggest that CSKSSDYQC-ligand could be a promising tool for development of an efficient oral delivery system for macromolecular therapeutics in the carrier-drug conjugate strategy.

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Thesis advisor: Jianmin Gao / Covalent drugs present a unique situation in the clinical world. Formation of a covalent bond between a drug molecule and its target protein can lead to significant increases in a number of desirable traits such as residence time, potency, and efficacy of a drug. From a kinetic perspective, the formation of a covalent bond between a drug and its target functionally eliminates the dissociation rate (koff) of the compound, ensuring that the compound will stay engaged with its target. However, development of covalent drugs has been met with caution and concern, as an irreversible covalent bond forming on the wrong target can have disastrous results, so specificity is of the utmost importance. One option for increasing specificity is by linking a covalent binding electrophile, or warhead, to a peptide. Peptide-based therapeutics have already been shown to serve as effective protein-targeting modalities with high specificity, a specificity that would greatly benefit covalent drugs. Phage display is a powerful technique for the discovery of selective peptides which utilizes the screening of vast libraries of randomized peptides to identify strong binders. This technology has been used to discover a large number of protein-targeting peptides, but also a smaller number of cyclic, covalent binding peptides that function as enzymatic inhibitors. Herein, this study aimed to explore the idea of adding covalent-binding functionality to phage libraries in novel ways and expand upon the scope of proteins that can be targeted with phage libraries containing covalent libraries. We sought to develop a mechanistic and chemical understanding of the interactions between bacteriophage and chemical warheads to best understand both the limits and the potential of this technology. In order to best understand the relationship between chemical warhead and phage particle, a model system was developed based on the M13KE pIII protein. It was found that the extracellular N-terminal domains of this protein could be expressed and purified in low yields in bacterial cells and that these domains would behave similarly in solution as in the membrane of the M13KE bacteriophage. With this protein in hand, experiments previously performed using small, cysteine containing peptides, could be performed on a full protein to mimic the phage labeling environment. This protein was used to identify efficient cysteine crosslinkers, most notably dichloroacetone (DCA) and bis-chlorooxime (BCO). The pIII protein system was then used to study the viability of bifunctional warhead molecules containing a covalent warhead and a cysteine crosslinker. Based on preliminary analyses with the pIII protein, aryl sulfonyl fluoride was chosen as a novel warhead candidate that warranted further pursuit. Kinetic NMR studies verified that aryl sulfonyl fluoride was capable of forming covalent bonds with phenols under phage labeling conditions. Labeling experiments analyzed with LC/MS seemed to indicate a degradation of the warhead. However, as the source of the degradation was not able to be determined, it was decided that various affinity assays would be used to identify if phage could be labeled with an aryl sulfonyl fluoride-DCA conjugate. Both streptavidin-bead pulldown assays and ELISA assays were used, however both assays yielded results that could not conclusively verify the integrity of the warhead. During phage labeling experiments, a phenomenon was noted that phage titers after modification showed a 2-3 order of magnitude drop in phage count. Covalent modification of phage beyond what is intended could have troubling consequences for all covalent phage libraries, and so a more in-depth approach was taken to identify and better understand phage toxicity as it relates to covalent warheads. As a model, a well-studied diazaborine-mediated warhead with a slow dissociation rate was selected and used in a range of phage toxicity screenings. Despite statistical fluctuations between trials, toxicity screenings using this warhead served to highlight a unique concern for bifunctional covalent warheads. A concentration-dependent toxicity can be seen in phage incubated with bifunctional small molecules that is not present when incubated with the monofunctional equivalents. The presence of this toxicity even towards a phage with no free thiols highlights a unique challenge of off-target labeling within phage particles that, if solved, could provide the next significant step towards developing novel covalent phage libraries. / Thesis (MS) — Boston College, 2022. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

CAR T-cellbehandling är en immunterapi som har visat lovande resultat vid behandling av cancer. Trots det riktade immunsvaret som kan uppnås, betonar komplexiteten i tillverkningsprocessen och behandlingsproceduren det utrymme somm finns för förbättringar. Omprogrammerade T-celler har illustrerat en hög persistens hos patienter, som utsätter dem för risken för systemisk toxicitet. In-vivo transienta CAR T-celler som använder självförstärkande mRNA leverade genom affinitetsproteinbelagda LNP, föreslås som ett standardiserat alternativ som möjligör dosering av terapin vid behov.  Med hjälp av fagdisplay utfördes ett urval av affibody molekyler mot de tre immunonkologiska målproteinerna CD5, CD8 och CD19, i fyra cykler. Monoklonal fag-ELISA och DNA-sekvensering identifierade sju förmodade kandidater mot CD5, en förmodad kandidat mot CD8 och tre mot CD19. SPR analys visade specifik binding från CD5 kandidaterna, medan binding till målprotein inte kunde påvisas för CD8- och CD19 kandidaterna. De identifierade CD5-bindarna kan konjugeras till LNP för T-cell inriktad leverans av själv-amplififerande mRNA, med genetisk kod för en valfri CAR. / Chimeric antigen receptor (CAR) T-cell therapy is an immunotherapy which has shown promising results in treating patients suffering from oncological malignancies. Despite the targeted immune response that can be achieved, elaborate manufacturing and procedure processes emphasise room for improvement. Engineered T-cells have illustrated a high persistence in patients, exposing them to the risk of systemic toxicity. In-vivo transient CAR T-cells using self-amplifying mRNA by delivery through affinity protein coated lipid nanoparticles (LNP) is proposed as a standardised and reversible alternative, allowing for dosing when needed. Using phage display technology, selection of affibody molecules toward the three immune oncology proteins CD5, CD8 and CD19 was performed in four cycles. Monoclonal phage enzyme-linked immunosorbent assay (ELISA) and DNA sequencing identified seven putative candidates toward CD5, one putative candidate was isolated toward CD8, and three toward CD19. Surface plasmon resonance analysis (SPR) showed specific target binding of the CD5 candidate binders, while target binding could not be demonstrated for the CD8 and CD19 candidates. The identified CD5 binders could be conjugated to LNP for T-cell targeted delivery of self-amplifying mRNA encoding any CAR of interest.

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No description available.

No description available.