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PINHEIRO, Elayne Bessa Ferreira. Estudo químico, biológico e In Silico de Plectranthus grandis (Cramer) Willense. 2016. 173 f. Tese (Doutorado em Química)-Universidade Federal do Ceará, Fortaleza, 2016. / Submitted by Aline Mendes (alinemendes.ufc@gmail.com) on 2017-01-19T17:28:14Z No. of bitstreams: 1 2016_tese_ebfpinheiro.pdf: 3644833 bytes, checksum: 01854d30ec14ae187221746b0690db8c (MD5) / Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2017-01-23T20:16:01Z (GMT) No. of bitstreams: 1 2016_tese_ebfpinheiro.pdf: 3644833 bytes, checksum: 01854d30ec14ae187221746b0690db8c (MD5) / Made available in DSpace on 2017-01-23T20:16:01Z (GMT). No. of bitstreams: 1 2016_tese_ebfpinheiro.pdf: 3644833 bytes, checksum: 01854d30ec14ae187221746b0690db8c (MD5) Previous issue date: 2016 / The use of plants for medicinal purposes is one of the oldest forms of human practices to treat various diseases. The selected species whose study is reported in this work was Plectranthus grandis (Cramer) Willense which is popularly known bush in Brazil as the "boldo-grande". This work includes the description of the procedures used in the isolation and structural determination of isolated Plectranthus grandis compounds and the study of seasonal and circadian variation of barbatusin composed pharmacologically active present in P. grandis, through the implementation and validation of an analytical method able to detect and quantify this metabolite. The method developed by HPLC was performed using a Phenomenex C18 column (250 mm x 4.60 mm - 5 µm), a binary gradient of water and acetonitrile (8: 2, v / v) at a flow rate of 0.8 mL / min it proved to be simple, accurate, precise and selective and can be routinely applied for the quantification of barbatusin in P. grandis samples at any time of year and is found in higher concentration in the 0 hr time and the month March. Additionally, a study was performed in silico to determine the antimalarial potential, antitumor and anti-inflammatory by molecular docking assays, molecular and physico-chemical descriptors in a database implemented with all compounds isolated to date Plectranthus the genus where the diterpene plecostonol stands out as the most promising drug candidate among the 270 identified compounds. Chemical and biological assays (antioxidant activity determination of polyphenols and flavonoids, inhibition of angiotensin-converting enzyme I and assay for inhibition of the enzyme acetylcholinesterase) were also performed with the ethanol extract of the species under study and the barbatusin where both showed low activity or any activity which does not rule out the possibility of other studies. / A utilização de plantas com fins medicinais é uma das mais antigas formas de práticas da humanidade para tratar as diversas enfermidades. A espécie selecionada cujo estudo é relatado nesse trabalho foi Plectranthus grandis (Cramer) Willense que é um arbusto popularmente conhecido no Brasil pelo nome de "boldo grande". Esse trabalho compreende a descrição dos procedimentos utilizados no isolamento e determinação estrutural dos compostos isolados de Plectranthus grandis, bem como o estudo da variação sazonal e circadiana da barbatusina, composto farmacologicamente ativo presente em P. grandis, através da implementação e validação de um método analítico capaz de detectar e quantificar este metabólito. O método desenvolvido por CLAE foi realizada com uma coluna Phenomenex C18 (250 mm x 4,60 mm - 5 µm), um gradiente binário de água e acetonitrila (8: 2, v / v) a um fluxo de 0,8 mL/ min o mesmo mostrou-se simples, exato, preciso e seletivo, podendo ser rotineiramente aplicado para a quantificação de barbatusina em amostras de P. grandis em qualquer época do ano, sendo detectada em maior teor no horário de 0 hr e no mês março. Adicionalmente, foi realizado um estudo in silico para a determinação do potencial anti-malárico, antitumoral e anti-inflamatório através de ensaios de docagem molecular, descritores moleculares e físico-químicos de uma base de dados implementada com todos os compostos isolados até o presente momento do gênero Plectranthus, onde o diterpeno plecostonol destaca-se como sendo o mais promissor candidato a fármaco dentre os 270 compostos identificados. Ensaios químicos e biológicos (atividade antioxidante, determinação de polifenóis e de flavonoides, inibição da enzima conversora de angiotensina I e ensaio para inibição da enzima acetilcolinesterase) também foram realizados com o extrato etanólico da espécie em estudo e com a barbatusina onde ambos apresentaram uma baixa atividade ou nenhuma atividade o que não descarta a possibilidade de outros estudos.

abstract: Circular RNAs (circRNAs) are a class of endogenous, non-coding RNAs that are formed when exons back-splice to each other and represent a new area of transcriptomics research. Numerous RNA sequencing (RNAseq) studies since 2012 have revealed that circRNAs are pervasively expressed in eukaryotes, especially in the mammalian brain. While their functional role and impact remains to be clarified, circRNAs have been found to regulate micro-RNAs (miRNAs) as well as parental gene transcription and may thus have key roles in transcriptional regulation. Although circRNAs have continued to gain attention, our understanding of their expression in a cell-, tissue- , and brain region-specific context remains limited. Further, computational algorithms produce varied results in terms of what circRNAs are detected. This thesis aims to advance current knowledge of circRNA expression in a region specific context focusing on the human brain, as well as address computational challenges. The overarching goal of my research unfolds over three aims: (i) evaluating circRNAs and their predicted impact on transcriptional regulatory networks in cell-specific RNAseq data; (ii) developing a novel solution for de novo detection of full length circRNAs as well as in silico validation of selected circRNA junctions using assembly; and (iii) application of these assembly based detection and validation workflows, and integrating existing tools, to systematically identify and characterize circRNAs in functionally distinct human brain regions. To this end, I have developed novel bioinformatics workflows that are applicable to non-polyA selected RNAseq datasets and can be used to characterize circRNA expression across various sample types and diseases. Further, I establish a reference dataset of circRNA expression profiles and regulatory networks in a brain region-specific manner. This resource along with existing databases such as circBase will be invaluable in advancing circRNA research as well as improving our understanding of their role in transcriptional regulation and various neurological conditions. / Dissertation/Thesis / Appendix file containing list of enriched pathways and functions identified in Chapter 4 / Doctoral Dissertation Biomedical Informatics 2018

A molecular receptor for mephedrone, an amphetamine-like NPS, was developed using host-guest chemistry and pharmacophoric design. The in-field detection of new psychoactive substances (NPS) is an area that has garnered considerable attention in the last few years. With the continuously expanding number of NPS on the market, traditional detection mechanisms lack the selectivity needed. In this project a new methodology has been developed for the design of host molecules for use in in-field detection, based on biomimetic design. To understand what a sensory molecular needs to be selective against, GC-MS and HPLC analysis were employed to identify and quantify thirteen aminoindane internet samples. It was found that the composition of internet samples varies greatly in terms of concentration of active ingredient, with a range of 17-95 % w/w of active ingredient identified. It was also found that caffeine was the most common cutting agent with a range of 27.7-30.2 % w/w identified. This highlights the need for both selectivity and sensitivity in detection mechanisms. Using the principles of biomimetic design, a methodology for the treatment of protein-ligand interactions was developed. Protein-ligand binding data collected from the Protein Databank was analysed for mephedrone related structures and common cutting agents, identified through aminoindane internet sample analysis and literature sources. From this work a three-point pharmacophoric model was developed, upon which two host molecules were considered, macrocyclic calixarenes and acyclic anthraquinones. Both contained the three binding interactions deduced from the pharmacophore design; two p-stacking interactions and one hydrogen bond acceptor. The final host molecule taken forward for testing was 1,8-dibenzylthiourea anthracene (Probe 1). The binding affinity of Probe 1 to mephedrone was tested using 1H-NMR. An estimated association constant of 104 M-1 was calculated, with a 1:1 binding stoichiometry. Along with ESI-MS and DFT calculations, it was found that mephedrone binds to Probe 1 in a concerted fashion with a three-point binding geometry, with two hydrogen bonds and one p-stacking interaction. A modest optical response using fluorescence spectroscopy was also observed between mephedrone and Probe 1 at high molar concentrations. A more pronounced response was observed upon addition of high molar concentrations of flephedrone. 1H-NMR showed that Probe 1 selectively bound mephedrone over methamphetamine as well as the four most common cutting agents identified from literature: lidocaine, caffeine, paracetamol and benzocaine, which have been shown to cause false positives in previous studies. Probe 1 showed significant selectivity for the β-ketoamine arrangement. This is supported by the systematic analysis of mephedrone, methamphetamine, mephedrone precursor and flephedrone. This is the first time this has been achieved using host-guest chemistry. A protocol was developed to successfully detect mephedrone via Probe 1 using NMR spectroscopy in a simulated street sample containing two of the most common cutting agents, benzocaine and caffeine. To further aid future design of small host molecules a methodology for the in silico analysis of small molecule host-guest binding using metadynamics was explored. Solvent interactions with the host and guest molecules were observed, highlighting the importance of solvent choice in binding studies. Metadynamics shows potential to be used in further work for improving the approach in which host molecules are designed in future.

Submitted by MELISSA REMLINGER null (melissa.remlinger@yahoo.com.br) on 2017-05-15T18:49:13Z No. of bitstreams: 1 DissertacaoMestradoMelissaRemlinger.pdf: 6915267 bytes, checksum: 6abcf69dca1b6149f3cab02b71fbd6e3 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-05-16T14:48:11Z (GMT) No. of bitstreams: 1 remlinger_m_me_araiq.pdf: 6915267 bytes, checksum: 6abcf69dca1b6149f3cab02b71fbd6e3 (MD5) / Made available in DSpace on 2017-05-16T14:48:11Z (GMT). No. of bitstreams: 1 remlinger_m_me_araiq.pdf: 6915267 bytes, checksum: 6abcf69dca1b6149f3cab02b71fbd6e3 (MD5) Previous issue date: 2017-04-24 / Triterpenos são produtos naturais de plantas estruturalmente complexos com numerosas aplicações medicinais. Como exemplo, friedelina é um triterpeno pentacíclico com atividade gastroprotetora, enquanto que seus derivados quinonametídicos maitenina e pristimerina apresentam promissoras atividades antiinflamatória, antitumoral, antimicrobiana, antimalárica, espermicida e antioxidante. O único triterpeno pentacíclico cetônico formado diretamente na ciclização do oxidoesqualeno é a friedelina. Sua produção se dá a partir da enzima friedelina sintase, uma oxidoesqueleno ciclase que se difere das demais oxidoesqualeno ciclases por estabilizar a ciclização promovida pelo carbocátion formado no sítio catalítico produzindo uma cetona. As oxidoesqualeno ciclases têm o mesmo substrato, porém se diferenciam pela especificidade de seus produtos formados e, por isto, a análise da estrutura primária da friedelina sintase permite estudar sua especificidade pela produção de friedelina. Desta forma, o presente trabalho teve como objetivo realizar o estudo da especificidade da friedelina sintase clonada de Maytenus ilicifolia por meio de mutantes desta enzima. Por meio de análises de docking da molécula de friedelina no sítio ativo da enzima foram observados resíduos de aminoácidos cuja interação poderia se relacionar à produção singular de friedelina. Os mutantes destes resíduos foram então gerados por mutagênese sítiodirigida para avaliar tais interações de acordo com o produto formado heterologamente pelos mutantes expressos em Saccharomyces cerevisiae. Os resíduos estudados e gerados por mutação sítio-dirigida foram: F183L, C369A, W417H, D484E e W612F. Os produtos assim diferencialmente produzidos foram avaliados por cromatografia gasosa acoplada a espectrometria de massas (CG-EM). Assim, foi possível observar que os resíduos D484 e W417 são essenciais para a atividade da enzima, enquanto que os resíduos C369, W612 e F183 são importantes para a especificidade de produto, uma vez que a troca levou a produção de outros compostos terpênicos e/ou também a friedelina. Tais resultados permitiram avaliar resíduos importantes para a biossíntese de friedelina, contribuindo para o entendimento desta singular oxidoesqualeno ciclase. / Triterpenes are natural plant products structurally complex with numerous medicinal applications. As an example, friedelin is a pentacyclic triterpene with gastroprotective activity whereas its quinone methide derivates maytenin and pristimerin present promising anti-inflammatory, antitumor, antimicrobial, antimalarial, spermicidal and antioxidant activities. Friedelin is the only pentacyclic ketone triterpene obtained directly from ciclization of oxidosqualene. Its production occurs from the enzyme friedelin synthase, an oxidosquelene cyclase, which differs from the other oxidosqualene cyclases by stabilizing the cyclization promoted by the carbocation formed at the catalytic site forming a ketone. The oxidosqualene cyclases have the same substrate, but are differentiated by the specificity of their products formed and, therefore, the analysis of the primary structure of friedelin synthase allows to study its specificity by the production of friedelin. Thus, the present work aimed to study the specificity of the friedelin synthase cloned from Maytenus ilicifolia using mutants of the enzyme. Through the analysis of docking of the molecule friedelin in the active site of the enzyme, it was observed amino acids residues whose interation could be related to the unique production of friedelin. Mutants of these residues were generated by site-directed mutagenesis to evaluate such interactions according to the product formed heterologously by the mutants expressed in Saccharomyces cerevisiae. Residues studied and generated by site-directed mutation were: F183L, C369A, W417H, D484E and W612F. The products thus differentially produced were evaluated by gas chromatography coupled to mass spectrometry (GC-MS) from the expression and production of the mutants using the heterologous S. cerevisiae system. Thus, the residues D484 and W417 are essential for enzyme activity, whereas residues C369, W612 and F183 are important for product specificity, since the exchange led to the production of other terpene compounds and / or also friedelin. These results allowed the evaluation of important residues for the biosynthesis of friedelin, contributing to the understanding of this unique oxidoesqualene cyclase.