A leishmaniose é uma doença negligenciada causada por protozoários parasitos do gênero Leishmania sp. e transmitida por vetores. Esta doença pode apresentar formas clínicas que variam de lesões cutâneas simples que podem desaparecer espontaneamente até a forma visceral, a qual acomete órgãos como baço, fígado, medula óssea e linfonodos, e pode levar a morte se não tratada corretamente. Além disso, de acordo com a Organização Mundial da Saúde as leishmanioses são endêmicas em 98 países. O tratamento ainda é feita principalmente com dois medicamentos, os antimoniais pentavalentes e anfotericina B, os quais causam uma série de efeitos secundários, além disso, relatos de resistência a esses fármacos têm sido publicados. Além disso, medicamentos alternativos aprovados para uso, como a miltefosina e pentamidina, também possuem sérios efeitos colaterais e nem sempre são efetivos para todas as espécies do parasito e/ou formas clínicas. Estes fatos demonstram que é necessário o desenvolvimento de fármacos alternativos para a quimioterapia das leishmanioses. Nesse sentido, o reposicionamento de fármacos se mostra como uma importante estratégia para o desenvolvimento de novas alternativas terapêuticas para a leishmaniose, pois fármacos já liberados para o uso em humanos podem ser reutilizados, diminuindo o tempo de desenvolvimento e custos empregados para o desenvolvimento de novos fármacos. Leishmania sp. possui como um dos principais lipídios o ergosterol, cuja rota metabólica é complexa e envolve uma série de enzimas, as quais, se corretamente bloqueadas poderão suprimir a produção do ergosterol e, portanto, a viabilidade de parasitos. Considerando estes aspectos, o presente estudo objetivou investigar a ação leishmanicida de fármacos que possuem ação inibitória em enzimas da via de esteróis como o fármaco anti-hiperlipidêmico rosuvastatina (inibidor da enzima 3-hidroxi-3-metil-glutaril-CoA redutase) e, os antifúngicos voriconazol, tiaconazol, fenticonazol (inibidores da enzima 14 alfa-metilesterol 14-demetilase), naftifina e tolnaftato (inibidores da enzima esqualeno epoxidase), e por fim a nistatina que age diretamente sobre ergosterol. O potencial contra formas promastigotas e amastigotas intracelulares de L. (L.) amazonensis, L. (L.) infantum e L. (V.) braziliensis foram avaliados, e então foram investigadas possíveis alterações ultraestruturais, fisiológicas em promastigotas de L. (L.) amazonensis (formação de poros de membrana, e alteração do potencial de membrana mitocondrial) ou nas células hospedeiras (produção de óxido nítrico, peróxido de hidrogênio, e mudanças no pH intracelular). O fenticonazol, tioconazol, nistatina e o tolnaftato foram capazes de eliminar as formas promastigotas e amastigotas intracelulares, sendo a nistatina, o tolnaftato e o fenticonazol os mais seletivos para amastigotas das três espécies de parasitos estudados. Por outro lado, rosuvastatina, voriconazol e a naftifina não apresentaram ação contra formas amastigotas intracelulares. Além disso, os fármacos com atividade leishmanicida alteraram morfologicamente e fisiologicamente a mitocôndria do parasito. Apesar de não haver estímulo da produção de H2O2 ou NO por parte dos fármacos analisados, o fenticonazol foi capaz de alcalinizar macrófagos hospedeiros infectados. Considerando que estes fármacos foram capazes de inibir o crescimento de multi-espécies do parasito no interior dos macrófagos, esses resultados sugerem que medicamentos antifúngicos podem ser interessantes alvos para reposicionamento da quimioterapia das leishmanioses tegumentar e visceral / Leishmaniosis is a neglected disease caused by parasitic protozoa belonging to the genus Leishmania sp. and transmitted by vectors. This disease presents different clinical forms ranging from single lesion, that can heal spontaneously, to the visceral form, that affects the spleen, liver, bone marrow and lymph nodes, and may lead to death if not properly treated. Additionally, according to the World Health Organization, leishmaniosis is endemic to 98 countries. The treatment is still carried out with two main drugs, antimonials and amphotericin B that induce side effects; in addition, reports about the emergence of parasite resistance have been published. Besides, alternative drugs such as miltefosine and pentamidine still have serious side effects and are not always effective to treat all Leishmania species and/or clinical form. In this regard, drug repurposing has been considered an important strategy to develop new therapeutic alternatives to leishmaniasis chemotherapy, since drugs already approved to human use may be reused, decreasing time and costs needed for the research of new drugs. Leishmania sp. possesses ergosterol as the main membrane lipid, and the metabolic pathway to produce this lipid is complex and involves different enzymes, which if correctly inhibited may suppress ergosterol production and, therefore, parasite viability. Considering these aspects, the aims of this study is to investigate the leishmanicidal potential of drugs who inhibit enzymes of the ergosterol pathway, such as the anti-hyperlipidemic drug rosuvastatin (inhibitor of the 3-hydroxy-3-methyl-glutaryl-CoA reductase), the antifungals voriconazole, tioconazole, fenticonazole, (inhibitors of the 14 Alpha-methylsterol 14-demethylase), naftifine and tolnaftate (inhibitors of squalene epoxidase), and nystatin, that acts directly on ergosterol. The anti-promastigote and anti-amastigote potentials of drugs against L. (L.) amazonensis, L. (L.) infantum and L. (V.) braziliensis were evaluated; ultrastructural and physiological alterations of L. (L.) amazonensis promastigotes (membrane pore formation and mitochondrion membrane potential alterations) and host macrophages (nitric oxide and hydrogen peroxide productions and changes to intracellular pH) were investigated. Fenticonazole, tioconazole, nystatin and tolnaftate were capable to eliminate promastigote and amastigotes, being the most selective drugs nystatin, tolnaftate and fenticonazole to all studied species amastigotes. Rosuvastatin, voriconazole and naftifine were unable to eliminate amastigote forms. Furthermore, the drugs that possess leishmanicidal effects affected parasite mitochondrion. Although these drugs did not trigger the production of H2O2 or NO, fenticonazole was able to alkalinize host infected macrophages. Considering these drugs were able to inhibit multiple species of the parasite growth in macrophages, these results suggest that antifungal drugs can be interesting targets to be repurposed in the cutaneous and visceral leishmaniasis

Drug repositioning can save considerable time and resources and significantly speed up the drug development process. The increasing availability of drug action and disease-associated transcriptome data makes it an attractive source for repositioning studies. Here, we have developed a transcriptome-guided approach for drug/biologics repositioning based on multi-layer self-organizing maps (ml-SOM). It allows for analyzing multiple transcriptome datasets by segmenting them into layers of drug action- and disease-associated transcriptome data. A comparison of expression changes in clusters of functionally related genes across the layers identifies “drug target” spots in disease layers and evaluates the repositioning possibility of a drug. The repositioning potential for two approved biologics drugs (infliximab and brodalumab) confirmed the drugs’ action for approved diseases (ulcerative colitis and Crohn’s disease for infliximab and psoriasis for brodalumab). We showed the potential efficacy of infliximab for the treatment of sarcoidosis, but not chronic obstructive pulmonary disease (COPD). Brodalumab failed to affect dysregulated functional gene clusters in Crohn’s disease (CD) and systemic juvenile idiopathic arthritis (SJIA), clearly indicating that it may not be effective in the treatment of these diseases. In conclusion, ml-SOM offers a novel approach for transcriptome-guided drug repositioning that could be particularly useful for biologics drugs.

No description available.

A artrite reumatoide (AR) é uma doença autoimune, inflamatória, crônica, sistêmica e de etiologia desconhecida que pode ser induzida experimentalmente em animais por administração de colágeno e adjuvante (CIA). Os medicamentos biológicos contra o fator de necrose tumoral (TNF)-α são indicações terapêuticas atualmente consolidadas para os casos mais severos de AR. As limitações ao uso dessa classe de medicamentos têm sido o alto custo e a dificuldade em fabricar genéricos ou similares com composição, qualidade e desempenho equivalentes na mesma dose e via de administração. O presente estudo avaliou a hipótese de que drogas sintéticas que inibam a produção de TNF-α e / ou fatores relacionados teriam potencial para tornarem-se terapias complementares ou alternativas eficientes para esta doença. Para isso, foram utilizados ratos submetidos ao modelo CIA e tratados cronicamente com pentoxifilina (PTX), rolipram (ROL), talidomida (TAL) e rupatadina (RUP). Um tratamento com prednisolona (PRED) foi também efetuado para avaliar sua influência na eventual ação antiartrítica de PTX, ROL, TAL e RUP, de modo a mimetizar seu efeito imunossupressor, quando administrada agudamente (AG) antes de medicamentos biológicos, bem como pelo seu conhecido efeito anti-inflamatório, quando administrada cronicamente (CR) no tratamento da AR. O desenvolvimento da AR e a efetividade dessas drogas sobre a AR foram avaliadas, de forma seletiva e sequencial, por meio da detecção de eritema e cianose, bem como medidas de edema, massa corporal, hemograma, TNF-α no plasma, fator reumatoide (FR) e anticorpo antinuclear (ANA) no soro, interleucina (IL)-1β e IL-6 no soro e líquido sinovial, atividade de aminopeptidase básica (APB) na fração solúvel (FS) do tecido sinovial (TS) e de células mononucleares do sangue periférico (PBMCs), densitometria óssea e análise histológica. A hepatotoxicidade dessas drogas foi avaliada pelas medidas de alanina-transaminase (ALT) e aspartato-transaminase (AST) no plasma. A AR caracterizou-se pelo aumento de TNF-α plasmático e de IL-1β e IL-6 no líquido sinovial, alterações histológicas na articulação tíbio-tarsal, bem como edema, cianose, eritema, diminuição de linfócitos e atividade APB de FS aumentada no TS e diminuída em PBMCs. A AR aumentou ALT e AST. O tratamento com PRED crônico promoveu um efeito antiedematogênico. O coquetel (MIX de PTX+ROL+RUP+TAL) também apresentou efeito antiedematogênico. A administração concomitante de PRED AG ou PRED CR com MIX não produziu sinergismo ou potenciação do efeito antiedematogênico da administração isolada do MIX ou da PRED crônica. Além do MIX, ROL e TAL diminuíram o edema. MIX, ROL e TAL melhoraram TNF-α no plasma e APB na FS do TS e não causaram hepatotoxicidade, tal como refletido nos níveis de ALT e AST. TAL recuperou ALT e AST, sem alteração do hemograma. Uma vez que PTX e RUP não apresentaram efeito antiedematogênico, ROL e TAL foram hipotetizados como os prováveis responsáveis pela atividade antiartrítica do MIX. Então, os tratamentos com ROL, TAL e ROL+TAL foram selecionados para avaliação da histologia óssea e medidas de parâmetros diferenciais entre animais controles sadios e artríticos. Esta avaliação mostrou que o tratamento isolado da AR com ROL ou TAL não alterou IL-6, mas recuperou IL-1β no líquido sinovial, efeitos esses que não se diferenciaram do tratamento combinado de ROL+TAL, exceto pelo fato de que essa combinação também diminuiu a massa corporal. TAL se destacou por seu efeito hepatoprotetor nos animais AR. Considerando os efeitos conhecidos de RUP, PTX, TAL e ROL é possível hipotetizar que a ação antiartrítica de TAL e ROL deve-se à inibição da síntese de TNF-α decorrente da inibição de PDE4 em suas principais fontes celulares. Os dados deste estudo prospectivo fornecem subsídios adicionais que estimulam a realização de novos ensaios clínicos, mais amplos e sistematizados, sobre os efeitos antiartríticos de ROL e TAL. Conclui-se que o uso isolado de TAL emerge como uma alternativa terapêutica econômica, simples e eficaz para a AR, enquanto a combinação de ROL+TAL pode ser uma opção viável para portadores de AR com sobrepeso ou obesidade / Rheumatoid arthritis (RA) is an autoimmune, inflammatory, chronic and systemic disease with unknown etiology that can be experimentally induced in animals by administration of collagen and adjuvant (CIA). Biological drugs against tumor necrosis factor (TNF)- α are therapeutic indications currently consolidated for the most severe cases of RA. The limitations for the use of this class of drugs have been the high cost and the difficulty to manufacture a generic or similar ones with equivalent composition, quality and performance under the same dosage and route of administration. The present study evaluated the hypothesis that synthetic drugs that inhibit the production of TNF-α and/or related factors would have potential to become efficient complementary or alternative therapies for this disease. For this purpose, male rats submitted to the CIA model were chronically treated with pentoxifylline (PTX), rolipram (ROL), thalidomide (TAL) and rupatadine (RUP). The treatment with prednisolone (PRED) was also performed to evaluate its influence on the possible antiarthritic action of PTX, ROL, TAL and RUP, in order to mimic its immunosuppressive effect when acutely (AG) administered prior to biological drugs, as well as due to its known anti-inflammatory effect when administered chronically (CR) to treat RA. The development of RA and the efficacy of these drugs on RA were evaluated, by selective and sequential ways, through the detection of erythema and cyanosis, as well as measurements of edema, body mass, hemogram, plasma TNF-α, rheumatoid factor (FR) and anti-nuclear antibody (ANA) in serum, interleukin (IL)-1β and IL-6 in serum and synovial fluid, basic aminopeptidase activity (APB) in soluble fraction (FS) from synovial tissue (TS) and from peripheral blood mononuclear cells (PBMCs), bone densitometry and histological analysis. The hepatotoxicity of these drugs was evaluated by measurements of alanine-transaminase (ALT) and aspartate-transaminase (AST). RA was characterized by increased TNF-α in plasma and IL-1β and IL-6 in synovial fluid, histological alterations in the tibio-tarsal joint, as well as edema, cyanosis, erythema, decreased lymphocyte number and increased APB activity in TS and decreased APB activity in PBMCs. RA produced increased ALT and AST. As expected, the chronic treatment with PRED promoted an antiedematogenic effect. The cocktail (MIX of PTX+ROL+RUP+TAL) also presented antiedematogenic effect. Concomitant administration of acute or chronic PRED with MIX did not produce synergism or potentiation of the antiedematogenic effect due to the single administration of MIX or chronic PRED. In addition to MIX, ROL and TAL were also antiedematogenic. MIX, ROL and TAL ameliorated plasma TNF-α and APB in FS from TS without hepatotoxicity, as reflected by ALT and AST levels. TAL recovered ALT and AST, but it did not affect the hemogram. Since PTX and RUP did not present antiedematogenic effects, ROL and TAL were hypothesized as probable responsible for the antiarthritic activity of MIX. Thus, the treatments with ROL, TAL and ROL+TAL were selected for evaluation of bone histology and measurements of differential parameters between healthy control and arthritic animals. This evaluation showed that the treatment of RA with ROL or TAL alone did not alter IL-6 levels, but recovered IL-1β in the synovial fluid. Both these effects were not different from those of the concomitant treatment with ROL+TAL, except that this combination also decreases the body mass. TAL stands out for its hepatoprotective effect in RA animals. Considering the known effects of RUP, PTX, TAL and ROL it can be hypothesized that antiarthritic action of TAL and ROL is due to the inhibition of TNF-α synthesis as consequence of its inhibition in its main cellular sources by PDE4. Data from this prospective study provide additional subsidies that stimulate further and more comprehensive clinical trials on the antiarthritic effects of ROL and TAL. In conclusion, the treatment with TAL alone emerges as an economical, simple and effective therapeutical alternative for RA, while the combination of ROL+TAL can be a viable option for RA sufferers with overweight or obesity

A artrite reumatoide (AR) é uma doença autoimune, inflamatória, crônica, sistêmica e de etiologia desconhecida que pode ser induzida experimentalmente em animais por administração de colágeno e adjuvante (CIA). Os medicamentos biológicos contra o fator de necrose tumoral (TNF)-α são indicações terapêuticas atualmente consolidadas para os casos mais severos de AR. As limitações ao uso dessa classe de medicamentos têm sido o alto custo e a dificuldade em fabricar genéricos ou similares com composição, qualidade e desempenho equivalentes na mesma dose e via de administração. O presente estudo avaliou a hipótese de que drogas sintéticas que inibam a produção de TNF-α e / ou fatores relacionados teriam potencial para tornarem-se terapias complementares ou alternativas eficientes para esta doença. Para isso, foram utilizados ratos submetidos ao modelo CIA e tratados cronicamente com pentoxifilina (PTX), rolipram (ROL), talidomida (TAL) e rupatadina (RUP). Um tratamento com prednisolona (PRED) foi também efetuado para avaliar sua influência na eventual ação antiartrítica de PTX, ROL, TAL e RUP, de modo a mimetizar seu efeito imunossupressor, quando administrada agudamente (AG) antes de medicamentos biológicos, bem como pelo seu conhecido efeito anti-inflamatório, quando administrada cronicamente (CR) no tratamento da AR. O desenvolvimento da AR e a efetividade dessas drogas sobre a AR foram avaliadas, de forma seletiva e sequencial, por meio da detecção de eritema e cianose, bem como medidas de edema, massa corporal, hemograma, TNF-α no plasma, fator reumatoide (FR) e anticorpo antinuclear (ANA) no soro, interleucina (IL)-1β e IL-6 no soro e líquido sinovial, atividade de aminopeptidase básica (APB) na fração solúvel (FS) do tecido sinovial (TS) e de células mononucleares do sangue periférico (PBMCs), densitometria óssea e análise histológica. A hepatotoxicidade dessas drogas foi avaliada pelas medidas de alanina-transaminase (ALT) e aspartato-transaminase (AST) no plasma. A AR caracterizou-se pelo aumento de TNF-α plasmático e de IL-1β e IL-6 no líquido sinovial, alterações histológicas na articulação tíbio-tarsal, bem como edema, cianose, eritema, diminuição de linfócitos e atividade APB de FS aumentada no TS e diminuída em PBMCs. A AR aumentou ALT e AST. O tratamento com PRED crônico promoveu um efeito antiedematogênico. O coquetel (MIX de PTX+ROL+RUP+TAL) também apresentou efeito antiedematogênico. A administração concomitante de PRED AG ou PRED CR com MIX não produziu sinergismo ou potenciação do efeito antiedematogênico da administração isolada do MIX ou da PRED crônica. Além do MIX, ROL e TAL diminuíram o edema. MIX, ROL e TAL melhoraram TNF-α no plasma e APB na FS do TS e não causaram hepatotoxicidade, tal como refletido nos níveis de ALT e AST. TAL recuperou ALT e AST, sem alteração do hemograma. Uma vez que PTX e RUP não apresentaram efeito antiedematogênico, ROL e TAL foram hipotetizados como os prováveis responsáveis pela atividade antiartrítica do MIX. Então, os tratamentos com ROL, TAL e ROL+TAL foram selecionados para avaliação da histologia óssea e medidas de parâmetros diferenciais entre animais controles sadios e artríticos. Esta avaliação mostrou que o tratamento isolado da AR com ROL ou TAL não alterou IL-6, mas recuperou IL-1β no líquido sinovial, efeitos esses que não se diferenciaram do tratamento combinado de ROL+TAL, exceto pelo fato de que essa combinação também diminuiu a massa corporal. TAL se destacou por seu efeito hepatoprotetor nos animais AR. Considerando os efeitos conhecidos de RUP, PTX, TAL e ROL é possível hipotetizar que a ação antiartrítica de TAL e ROL deve-se à inibição da síntese de TNF-α decorrente da inibição de PDE4 em suas principais fontes celulares. Os dados deste estudo prospectivo fornecem subsídios adicionais que estimulam a realização de novos ensaios clínicos, mais amplos e sistematizados, sobre os efeitos antiartríticos de ROL e TAL. Conclui-se que o uso isolado de TAL emerge como uma alternativa terapêutica econômica, simples e eficaz para a AR, enquanto a combinação de ROL+TAL pode ser uma opção viável para portadores de AR com sobrepeso ou obesidade / Rheumatoid arthritis (RA) is an autoimmune, inflammatory, chronic and systemic disease with unknown etiology that can be experimentally induced in animals by administration of collagen and adjuvant (CIA). Biological drugs against tumor necrosis factor (TNF)- α are therapeutic indications currently consolidated for the most severe cases of RA. The limitations for the use of this class of drugs have been the high cost and the difficulty to manufacture a generic or similar ones with equivalent composition, quality and performance under the same dosage and route of administration. The present study evaluated the hypothesis that synthetic drugs that inhibit the production of TNF-α and/or related factors would have potential to become efficient complementary or alternative therapies for this disease. For this purpose, male rats submitted to the CIA model were chronically treated with pentoxifylline (PTX), rolipram (ROL), thalidomide (TAL) and rupatadine (RUP). The treatment with prednisolone (PRED) was also performed to evaluate its influence on the possible antiarthritic action of PTX, ROL, TAL and RUP, in order to mimic its immunosuppressive effect when acutely (AG) administered prior to biological drugs, as well as due to its known anti-inflammatory effect when administered chronically (CR) to treat RA. The development of RA and the efficacy of these drugs on RA were evaluated, by selective and sequential ways, through the detection of erythema and cyanosis, as well as measurements of edema, body mass, hemogram, plasma TNF-α, rheumatoid factor (FR) and anti-nuclear antibody (ANA) in serum, interleukin (IL)-1β and IL-6 in serum and synovial fluid, basic aminopeptidase activity (APB) in soluble fraction (FS) from synovial tissue (TS) and from peripheral blood mononuclear cells (PBMCs), bone densitometry and histological analysis. The hepatotoxicity of these drugs was evaluated by measurements of alanine-transaminase (ALT) and aspartate-transaminase (AST). RA was characterized by increased TNF-α in plasma and IL-1β and IL-6 in synovial fluid, histological alterations in the tibio-tarsal joint, as well as edema, cyanosis, erythema, decreased lymphocyte number and increased APB activity in TS and decreased APB activity in PBMCs. RA produced increased ALT and AST. As expected, the chronic treatment with PRED promoted an antiedematogenic effect. The cocktail (MIX of PTX+ROL+RUP+TAL) also presented antiedematogenic effect. Concomitant administration of acute or chronic PRED with MIX did not produce synergism or potentiation of the antiedematogenic effect due to the single administration of MIX or chronic PRED. In addition to MIX, ROL and TAL were also antiedematogenic. MIX, ROL and TAL ameliorated plasma TNF-α and APB in FS from TS without hepatotoxicity, as reflected by ALT and AST levels. TAL recovered ALT and AST, but it did not affect the hemogram. Since PTX and RUP did not present antiedematogenic effects, ROL and TAL were hypothesized as probable responsible for the antiarthritic activity of MIX. Thus, the treatments with ROL, TAL and ROL+TAL were selected for evaluation of bone histology and measurements of differential parameters between healthy control and arthritic animals. This evaluation showed that the treatment of RA with ROL or TAL alone did not alter IL-6 levels, but recovered IL-1β in the synovial fluid. Both these effects were not different from those of the concomitant treatment with ROL+TAL, except that this combination also decreases the body mass. TAL stands out for its hepatoprotective effect in RA animals. Considering the known effects of RUP, PTX, TAL and ROL it can be hypothesized that antiarthritic action of TAL and ROL is due to the inhibition of TNF-α synthesis as consequence of its inhibition in its main cellular sources by PDE4. Data from this prospective study provide additional subsidies that stimulate further and more comprehensive clinical trials on the antiarthritic effects of ROL and TAL. In conclusion, the treatment with TAL alone emerges as an economical, simple and effective therapeutical alternative for RA, while the combination of ROL+TAL can be a viable option for RA sufferers with overweight or obesity

L’identification d’antiviraux à large spectre est un des défis majeurs de la rechercheactuelle en virologie. Une des stratégies les plus prometteuses consiste à cibler une interactionvirus/hôte conservée. Ainsi, avec la technique d’AlphaScreen® et le modèle d’interactionprotéine VI de l’Adénovirus (AdV)/Nedd4-2, nous avons réalisé un criblage biochimique àhaut débit contre l’interaction virus/hôte [LP]PxY/Nedd4, commune à différentes familles devirus. Nous avons trouvé des candidats inhibiteurs issus d’une banque de composés approuvéspar les agences de santé. Nous les avons testés, caractérisés et validé leur effet antiviral surdeux familles de virus totalement différentes. Ainsi, les composés C9 (Sulconazole) et C4(Flunarizine) que nous avons identifiés diminuent la réplication de l’AdV, un virus à ADNenveloppé et du virus de Marburg, un virus à ARN, non enveloppé de la famille desFiloviridae. Ces résultats ont permis de valider l’interaction [LP]PxY/Nedd4 comme unecible idéale d’un antiviral à large spectre et de proposer un repositionnement de ces moléculesC9 et C4 comme antiviraux potentiels. Nous avons également synthétisé de nouvellesmolécules analogues du composé C9 et démontré qu’elles étaient tout aussi efficaces que lecomposé lui-même sur la réplication de l’AdV. Ces résultats nous ont permis de présenter laclasse des dérivés imidazolés comme structure de base pour l’élaboration de nouveauxantiviraux, potentiellement à large spectre. / Broad-spectrum antiviral identification is considered as one of the major aims of theactual virology research and one strategy consists in targeting virus/host interaction. Using theAlphaScreen® technology and the adenoviral model protein VI/Nedd4-2, we performed highthroughputbiochemical screening targeting the [LP]PxY/Nedd4 interaction, a commoninteraction of different virus families. We identified candidate inhibitors from a librarycompound approved by health agencies. We tested, characterized and validated the antiviraleffect of those compounds on two very different virus families. Indeed, compounds C9(Sulconazole) and C4 (Flunarizine) decrease replication of the adenovirus, a DNA nonenvelopedvirus and the replication of the Marburg virus, an RNA enveloped virus from theFilovirus family. Taken together, those results permit us to validate the [LP]PxY/Nedd4interaction as good target for a broad spectrum antiviral and to propose the “repositioning” ofcompounds C4 and C9 as antivirals. Moreover, we have synthesized new analogues from C9showing similar effect on AdV replication compared to the original molecule (C9). Inconclusion, our work on developing new broad-spectrum antivirals highlights the possibilityto use imidazole derivatives as a new class of antiviral compounds.

The rapid pace of scientific advances is enabling a greater understanding of diseases at the molecular level. In turn, the process for researching and developing new medicines is growing in difficulty, costs, and length as a result of the scientific, technical, and regulatory challenges related to the development process. In light of these challenges, drug repositioning, the utilization of known drugs for a new medical indication, has emerged as an increasingly important strategy for the new drug discovery. Availability of prior knowledge regarding safety, efficacy and the appropriate administration route significantly reduces the development costs and cuts down the development time resulting in less effort to successfully bring a repositioned drug to market. In another aspect, a protein’s shape is closely linked with its function; thereby, the ability to predict this structure unlocks a greater understanding of what it does and how it works. Nowadays, more than 10,000 biologically relevant protein structures are yearly released and available to the scientific community. A number suspected to triple over the following years due to the recent breakthroughs in structure prediction techniques. This work introduces a novel structure-based drug repositioning approach, exploiting the similarities of drugs’ binding mode via identification and virtual screening of interaction patterns. Such patterns are uncovered with the use of PLIP, an automated tool for the in silico detection of non-covalent interactions defining the binding mode between drugs and their protein targets. Besides, the approach has been applied to a series of case studies with tangible results: the uncovering of an antimalarial drug as potential chemoresistance treatment, the explained binding mode of ibrutinib to the target VEGR2 as potential B-cells deactivator in autoimmune diseases, and three over the counter drugs with a proved anti-trypanocidal activity as treatments for Chagas disease. Overall the structure-based approach with interaction patterns proved to be a suitable framework for identifying novel repositioning candidates. The uncovered candidates were structurally unrelated to the currently available treatments, and experimental assays successfully demonstrated their inhibitory activity on the protein targets of interest. Furthermore, the approach represents a promising option for the 'in high demand' diseases and all rare and neglected diseases for which no reliable treatment has yet been found and for which the pharmaceutical industry makes only a little investment.

生技產業為我國未來六大明星產業之一，除政府成立生技創投基金，民間企業也陸續加入這波生技投資行列，如永豐餘集團旗下的上智生技創投，與潤泰集團旗下的鑽石生技投資。以籌資來源而言，又分為借款融資關係(負債端)的外部資金，以及股東投資關係(權益端)的自有資金兩種，對於公司經營各有優缺點，亦應取得平衡。唯目前多數為權益端的資金投入，尤其以該產業中風險最高的新藥研發公司為例，仍普遍高達95%以上的股東權益比率。顯示其籌資來源有限，且難以吸引負債端的投資者參與。而這樣的資金來源比例，除不符合企業融資順位理論於公司成長階段的籌資策略與負債權益比率，權益端資金多以短期獲得高利潤為目的，以資金性質亦不適合占資產達95%以上之比例。 以目前負債端籌資管道，新藥研發公司多數利用台灣中小企業信用保證基金直保部或經濟部促進產業創新或研究發展貸款計畫專案申請，唯融資額度上限遠不足以支付藥物開發費用，且非一般負債端直接經由銀行評估取得融資之方式。綜觀國際業態，單一全新藥物開發至上市平均需約USD8億元(約NTD240億元)不等，而台灣公司的研發策略多數為分段發展或老藥新用(藥物重新定位)策略，但仍有高度資金需求。唯銀行、負債端投資者普遍缺乏投入該產業的意願，主要顧慮為具冗長的產品研發週期業態、高度不確定性的產品上市審查、長期臨床試驗伴隨的高額成本。此外，對於資金專注研發之新藥研發公司，亦面臨擔保品不足之問題。而實務上，負債端資金提供者如銀行，對於複雜的生技領域與新藥研發公司業態不甚了解，為降低融資意願的另一主因。 故本研究旨在建立一套適用於新藥研發公司之一般性價值評估方式，解決此雙方認知差異問題，以增加更多元的籌資管道。其中，本文參考其他國家評估方法，選擇其中針對技術型公司、發展久遠的韓國技術信用保證基金KOTEC評估模式，導入台灣微脂體、基亞生物科技、賽德醫藥科技3間新藥研發公司個案作一評估。並於最後研究結論，經由分析比較個案公司間歷年經營狀況，得出公司整體與個別質、量性指標項目量化的相對分數，以台灣微脂體分數157分最高，基亞生技次之。本研究亦參考個案評估狀況，得出該類公司較佳的一般性經營策略結論，發現公司創立早期可先以開發週期短、風險較低的老藥新用開發以代替副業產生短期營收的效用，同時累積本業開發經驗，待時機成熟再轉入全新藥物開發為一攻守兼具的經營模式，以供新藥研發公司參考。此外，本研究屬於探索性研究，僅於評估新藥研發公司分數階段，尚未轉換為公司融資評等。該部分尚待具一定案源量後，以統計模型將評估分數與還款違約率關聯性做一分析，方能計算融資評等。而建立內部評等模型、資訊系統對台灣銀行規模而言，為一額外高昂成本，亦建議可效法韓國由政府主導為可行方式之一。 / The biotechnology industry is one of the six future stars of the industries in Taiwan. The government established Biotechnology Venture Capital (BVC), and the more and more private companies joined the procession of biotech investments, such as the two famous biotech funds, Taiwan Global BioFund (TGB) and Diamond BioFund Inc.. According to sources of funding, we can divided them into two groups: one is the loan of external funds (liability side), and the other is the shareholder investment of internal funds (equity side), both of them have different advantages and disadvantages for the company, and the company should strike a balance between these advantages and disadvantages. However, the majority of the funds are invested from the equity side, especially the new drug development companies, which are the highest risk types in the industry, and most of their equity ratio is higher than 95 %. This information indicates the limited sources of funding, and the difficulty to attract liability side’s investors to participate. That proportion of funding sources doesn’t comply with the company’s financing strategy and debt to equity ratio in the growth stage of the enterprise life cycle in the pecking order theory, and equity side’s funds are not suitable for accounting for more than 95% of assets in balance sheet because most of them want to get high profits in the short-term. Currently, major new drug development companies usually apply for loans from the Direct Guarantee Dept. of the Small & Medium Enterprise Credit Guarantee Fund of Taiwan (Taiwan SMEG) or the Promote Industrial Innovation or R&D Loan Program of Industrial Development Bureau in Taiwan, but the amount of loan is insufficient to cover the costs for the new drug development, and this method is not a general way to obtain liability side’s financing from the bank’s direct evaluation. In the international situation, the progress from development to sale of a single new drug spends about US $800 million (about NT $24 billion) on average. Despite Taiwan's R&D strategies only cover the sectional development progress or the policy of the new usage of old drugs (drug repositioning), there is still a high degree of capital requirement. However, in the present, banks and other liability side’s investors still lack the will to invest in the new drug development companies. These investors concern about several major problems, including the lengthy product development cycle, high uncertainty of the product examination and approval, the high cost of long-term clinical trials in this industry. In addition, these companies are also faced with the problem of lacking collateral, because they invest much money in new drug R&D. On the other hand, liability side’s investors, such as banks, don’t understand the complex field of new drug development companies' business models, and this situation becomes another reason for reducing the financing will. Therefore, we should establish a general evaluation method applicable to new drug development companies, to solve the problem of cognitive differences between liability side’s investors and the borrowers, and expand the funding sources of these companies. This article refers to the actual evaluation method in other countries, chooses the most suitable and well developed evaluation model --- Korea Technology Finance Corporation (KOTEC)’s evaluation method for the technology-based company, and utilizes the method to evaluate three cases of the new drug development companies in Taiwan, including Taiwan Liposome Co., Medigen Biotechnology Crop., and CytoPharm, Inc.. In conclusion of the study, by analyzing and comparing the three companies’ operating situations in recent years, we can get relative quantified scores from the companies’ overall and individual qualitative, quantitative indicators, and the result is that Taiwan Liposome Co. gets the highest score, 157 points, then Medigen Biotechnology Crop. gets the middle one. This study also refers the case situations, to find a better general business strategy for such companies. We find that new drug development company in the early stage can focus on new usage development of old drugs ,which has advantages of short development cycle and lower risk, to replace the sideline that generates short-term revenue, and accumulate the experience of drug development. When the time is ripe, it can transfer to new drug development. This way is the general suggestion of both offensive and defensive business model for new drug development companies. In addition, this study is an exploratory research, which only focuses on the evaluation stage, and has not converted the result into a corporate financing credit rating. To calculate financing credit ratings, we require a lot of historical cases data to establish a statistical analysis model, and link evaluation scores with repayment default rates. The establishment of an internal rating model or information system incurs high additional costs for the size of the banks in Taiwan, so the recommended one of the possible ways is that we can follow the example led by the South Korea Government.

Indiana University-Purdue University Indianapolis (IUPUI) / Traditional treatment strategy development for diseases involves the identification of target proteins related to disease states, and the interference of these proteins with drug molecules. Computational drug discovery and virtual screening from thousands of chemical compounds have accelerated this process. The thesis presents a comprehensive framework of computational drug discovery using system biology approaches. The thesis mainly consists of two parts: disease biomarker identification and disease treatment discoveries. The first part of the thesis focuses on the research in biomarker identification for human diseases in the post-genomic era with an emphasis in system biology approaches such as using the protein interaction networks. There are two major types of biomarkers: Diagnostic Biomarker is expected to detect a given type of disease in an individual with both high sensitivity and specificity; Predictive Biomarker serves to predict drug response before treatment is started. Both are essential before we even start seeking any treatment for the patients. In this part, we first studied how the coverage of the disease genes, the protein interaction quality, and gene ranking strategies can affect the identification of disease genes. Second, we addressed the challenge of constructing a central database to collect the system level data such as protein interaction, pathway, etc. Finally, we built case studies for biomarker identification for using dabetes as a case study. The second part of the thesis mainly addresses how to find treatments after disease identification. It specifically focuses on computational drug repositioning due to its low lost, few translational issues and other benefits. First, we described how to implement literature mining approaches to build the disease-protein-drug connectivity map and demonstrated its superior performances compared to other existing applications. Second, we presented a valuable drug-protein directionality database which filled the research gap of lacking alternatives for the experimental CMAP in computational drug discovery field. We also extended the correlation based ranking algorithms by including the underlying topology among proteins. Finally, we demonstrated how to study drug repositioning beyond genomic level and from one dimension to two dimensions with clinical side effect as prediction features.

High-throughput drug screening (HTS) in live cells is often a vital part of the preclinical anticancer drug discovery process. So far, two-dimensional (2D) monolayer cell cultures have been the most prevalent model in HTS endeavors. However, 2D cell cultures often fail to recapitulate the complex microenvironments of in vivo tumors. Monolayer cultures are highly proliferative and generally do not contain quiescent cells, thought to be one of the main reasons for the anticancer therapy failure in clinic. Thus, there is a need for in vitro cellular models that would increase predictive value of preclinical research results. The utilization of more complex three-dimensional (3D) cell cultures, such as multicellular tumor spheroids (MCTS), which contain both proliferating and quiescent cells, has therefore been proposed. However, difficult handling and high costs still pose significant hurdles for application of MCTS for HTS. In this work, we aimed to develop novel assays to apply MCTS for HTS and drug evaluation. We also set out to identify cellular processes that could be targeted to selectively eradicate quiescent cancer cells. In Paper I, we developed a novel MCTS-based HTS assay and found that nutrient-deprived and hypoxic cancer cells are selectively vulnerable to treatment with inhibitors of mitochondrial oxidative phosphorylation (OXPHOS). We also identified nitazoxanide, an FDA-approved anthelmintic agent, to act as an OXPHOS inhibitor and to potentiate the effects of standard chemotherapy in vivo. Subsequently, in Paper II we applied the high-throughput gene-expression profiling method for MCTS-based drug screening. This led to discovery that quiescent cells up-regulate the mevalonate pathway upon OXPHOS inhibition and that the combination of OXPHOS inhibitors and mevalonate pathway inhibitors (statins) results in synergistic toxicity in this cell population. In Paper III, we developed a novel spheroid-based drug combination-screening platform and identified a set of molecules that synergize with nitazoxanide to eradicate quiescent cancer cells. Finally, in Paper IV, we applied our MCTS-based methods to evaluate the effects of phosphodiesterase (PDE) inhibitors in PDE3A-expressing cell lines. In summary, this work illustrates how MCTS-based HTS yields potential to reveal and exploit previously unrecognized tumor-specific vulnerabilities. It also underscores the importance of cell culture conditions in preclinical drug discovery endeavors.