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Universidade Estadual De Campinas Instituto De Biologia Thalita Camêlo Da Silva Ferreira Relevance of Multi-Species Phenotypic

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Universidade Estadual De Campinas Instituto De Biologia Thalita Camêlo Da Silva Ferreira Relevance of Multi-Species Phenotypic UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA THALITA CAMÊLO DA SILVA FERREIRA RELEVANCE OF MULTI-SPECIES PHENOTYPIC ASSAYS IN LEISHMANIA EARLY DRUG DISCOVERY RELEVÂNCIA DE ENSAIOS FENOTÍPICOS COM DIVERSAS ESPÉCIES DE LEISHMANIA NA DESCOBERTA INICIAL DE FÁRMACOS CAMPINAS 2019 THALITA CAMÊLO DA SILVA FERREIRA RELEVANCE OF MULTI-SPECIES PHENOTYPIC ASSAYS IN LEISHMANIA EARLY DRUG DISCOVERY RELEVÂNCIA DE ENSAIOS FENOTÍPICOS COM DIVERSAS ESPÉCIES DE LEISHMANIA NA DESCOBERTA INICIAL DE FÁRMACOS Thesis presented to the Biology Institute of the State University of Campinas in partial fulfillment of the requirements for the degree of Doctor in Genetics and Molecular Biology in the area of Microbiology Tese apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do título de Doutora em Genética e Biologia Molecular, na área de Microbiologia. Supervisor: Dr. Lucio Holanda Gondim de Freitas Junior ESTE EXEMPLAR CORRESPONDE À VERSÃO FINAL DA TESE, DEFENDIDA PELA ALUNA THALITA CAMÊLO DA SILVA FERREIRA E ORIENTADA PELO DR. LUCIO HOLANDA GONDIM DE FREITAS JUNIOR CAMPINAS 2019 Agência (s) de fomento e n°(s) de processo(s): CNPq, 870370/1997-9; FAPESP, 2015/10436-6 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 -Informações para Biblioteca Digital Título em outro idioma: Relevância de ensaios fenotípicos com diversas espécies de Leishmania na descoberta inicial de fármacos Palavras-chave em inglês: Leishmania Leishmaniasis Drug discovery High-throughput screening assays Área de concentração: Microbiologia Titulação: Doutora em Genética e Biologia Molecular Banca examinadora: Lucio Holanda Gondim de Freitas Junior [Orientador] Elizabeth Bilsland André Gustavo Tempone Cardoso Jadel Muller Kratz Rafael Lemos Miguez Couñago Data de defesa: 27-02-2019 Programa de Pós-Graduação: Genética e Biologia Molecular Identificação e informações acadêmicas do(a) aluno(a) -ORCID do autor: https://orcid.org/0000-0001-8282-5708 -Currículo Lattes do autor: http://lattes.cnpq.br/9465460141211530 EXAMINATION COMMITTEE Dr. Lucio Holanda Gondim de Freitas Junior (supervisor) Profa. Dra. Elizabeth Bilsland Prof. Dr. André Gustavo Tempone Cardoso Prof. Dr. Jadel Muller Kratz Dr. Rafael Lemos Miguez Couñago The members of the Examination Committee signed the Defense Act, which is in the student's academic life record. Os membros da Comissão Examinadora acima assinaram a Ata de Defesa, que se encontra no processo de vida acadêmica do aluno. ACKNOWLEDGMENTS First and foremost, I praise God for giving me the opportunity, knowledge, ability, and strength to undertake this research study and to persevere and complete it. Dedicated to my eternal cheerleader, my mom: because I owe all to you. Many Thanks! I would like to express my sincere gratitude to my supervisors, Lucio Freitas-Junior and Carolina Borsoi, for accepting me as a doctoral student and for all their support. This accomplishment would not have been possible without them. Thank you. I have great pleasure in acknowledging my gratitude to the past and present members of our lab: Adalberto Araújo, Bruno Pascoalino, Caio Haddad, Claudia Bertolacini, Denise Pilger, Giovana Cintra, Luisa Naves, Nicolli Bellotti, Rafaela Bonotto, Vanessa Fontana and Valber Florêncio. Their support, encouragement and credible ideas have been great contributors in the completion of this work. It was great sharing laboratory with all of you! With a special mention to my leishmaniac colleague, Laura Alcântara, thanks for your patience, insightful discussions, and your always solicitous support. I want to express my deep thanks to professors Danilo Ciccone and Mauro Cortez for kindly allowing me to use their facilities and teaching me so much during this period. This thesis appears in its current form due to the support and assistance of several institutions. I would therefore like to offer my sincere thanks to all of them This project was partially carried out in the Brazilian Center for Research in Energy and Materials (CNPEM). Partial results were also obtained in the following organizations: (i) Butantan Institute; (ii) Immunobiology of the Leishmania-macrophage Interaction lab (Lab head: Prof. Mauro Cortez), in the Institute of Biomedical Sciences (ICB) of the University of São Paulo (USP); and (iii) Leishmania Infection Biology Studies lab _ LEBIL (Lab head: Prof. Danilo Ciccone), in the Institute of Biology of the University of Campinas (UNICAMP). The CEFAP-USP (Centro de Facilidades de Apoio à Pesquisa) and FMRP-USP (Faculdade de Medicina de Ribeirão Preto) provided service to the use of High Content Image Screening equipment. I would like to thank FAPESP (#15/10436-6) and CNPq (#870370/1997-9) for awarding me a doctoral fellowship. I also wish to express gratitude to the Drugs for Neglected Diseases initiative (DNDi) and the Medicines for Malaria Venture (MMV) for partially funding this research project. I would still like to thank the Graduate Program in Genetics and Molecular Biology for all the assistance. I am grateful to my family and friends for their prayers throughout my years of study. I warmly thank my father and my friend Danilo Ferreira for their material and moral support. Emerson, Thais, Ingrid Ester, and Milena Rosa, my beloved siblings, thank you for your love! My little nephew, Kauã, who always brings so much joy and happiness to my life, thank you! Finally, I must express my very profound gratitude to my friend, Luiz Gustavo dos Santos, for providing me with unfailing support and continuous encouragement throughout the writing process of this thesis. ABSTRACT The leishmaniasis are a group of poverty-associated diseases caused by the protozoan Leishmania spp. The complexity of this kinetoplastid parasite is highlighted by biological, ecological, and epidemiological aspects. It is endemic in more than 98 countries affecting around 12 million people. Approximately 20 species can be transmitted to humans by 78 species of the phlebotomine sandfly vector. Infected people can develop one of the several pathologies from which the most common are: cutaneous lesions, the disfiguring mucocutaneous disorder, and the life-threatening visceral disease. The final outcome is multifactorial, depending on intricate host-parasite interactions and environmental factors. The few chemotherapeutic options available are mostly unsatisfactory due to low efficacy, poor safety, emergence of parasite resistance, and other factors related to treatment (such as administration route, length of treatment or high costs) that are not suitable for the socioeconomic reality of affected populations. The current scenario demands research focused on the identification of novel effective therapeutics. Modern technologies enable the screening of millions of compounds, but a more predictive in vitro assays is still lacking. It is a common practice for a research group to target a single species, usually L. dovovani, the causative agent of visceral disease. Addressing a representative sample of viscerotropic and dermotropic species/strains of Leishmania can be useful to prioritize compounds based on their spectrum of activity. This work focused on the discovery of starting points for the development of new antileishmanials using an image-based methodology. Careful standardization was carried out aiming to achieve robustness and reproducibility, based on: (i) the biological model, determining the best condition for parasite and host cell culture, infection and drug exposure, and (ii) the image analysis algorithm. The multi-species high content assay was successfully established and validated to assess compound activity against some of the most clinically relevant dermotropic (L. amazonensis and L. braziliensis) and viscerotropic agents (L. donovani and L. infantum). This semi-automated assay is based on THP-1 macrophages infected with stationary phase promastigotes and can be virtually adapted to any in vitro infective species, providing the basis for the discovery of broad-spectrum antileishmanial molecules. A species-specific profile was observed in the general activity of libraries screenings, and a reduced number of compounds were active for all species. The simultaneous screening of the Pathogen Box library against four Leishmania species along with literature data analysis resulted in the identification of 12 pan-antileishmanial compounds. Although these molecules have been reported as anti-kinetoplastid agents, their activity against different Leishmania species had not been explored yet. The results obtained from this study demonstrate the potential value of including a panel of species in early steps of the drug discovery process, which can facilitate the prospection, validation and progression of more promising compounds. The species panel, together with other reported secondary assays, is suggested as part of a cell-based assay pipeline for Leishmania spp. aiming to empower the prioritization of compounds based on crucial aspects besides the physico-chemical and toxicity filters traditionally applied. RESUMO As leishmanioses são um grupo de doenças associadas à pobreza causadas por protozoários do gênero Leishmania. A complexidade desse kinetoplastídeo é evidenciada por aspectos biológicos, ecológicos e epidemiológicos. Essas doenças são endêmicas em mais de 98 países e acometem em torno de 12 milhões de pessoas. Aproximadamente 20 espécies de Leishmania infectam humanos e são transmitidas
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