Applications and Improvements in the Molecular Modeling of Protein and Ligand Interactions

Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include: 1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can treat alpha-1-antitrypsin deficiency, 2.) an application of multi-protein docking and metabolism prediction, specifically, modeling the cytochrome P450 metabolism and estrogen receptor activity of an environmental pollutant (PCB-30), and 3.) providing evidence to support the inclusion of anion-pi interactions in molecular modeling by demonstrating the biological roles of anion-pi interactions in stabilizing protein and protein-ligand structures. This work has direct applications for mitigating disease and toxicity, but it also demonstrates useful ways of integrating computational and experimental data to improve upon modeling protein and ligand interactions

Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus

BACKGROUND: Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes. RESULTS: The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database. CONCLUSION: In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation

Doctor of Philosophy

dissertationOver 40 years ago, the first computer simulation of a protein was reported: the atomic motions of a 58 amino acid protein were simulated for few picoseconds. With today's supercomputers, simulations of large biomolecular systems with hundreds of thousands of atoms can reach biologically significant timescales. Through dynamics information biomolecular simulations can provide new insights into molecular structure and function to support the development of new drugs or therapies. While the recent advances in high-performance computing hardware and computational methods have enabled scientists to run longer simulations, they also created new challenges for data management. Investigators need to use local and national resources to run these simulations and store their output, which can reach terabytes of data on disk. Because of the wide variety of computational methods and software packages available to the community, no standard data representation has been established to describe the computational protocol and the output of these simulations, preventing data sharing and collaboration. Data exchange is also limited due to the lack of repositories and tools to summarize, index, and search biomolecular simulation datasets. In this dissertation a common data model for biomolecular simulations is proposed to guide the design of future databases and APIs. The data model was then extended to a controlled vocabulary that can be used in the context of the semantic web. Two different approaches to data management are also proposed. The iBIOMES repository offers a distributed environment where input and output files are indexed via common data elements. The repository includes a dynamic web interface to summarize, visualize, search, and download published data. A simpler tool, iBIOMES Lite, was developed to generate summaries of datasets hosted at remote sites where user privileges and/or IT resources might be limited. These two informatics-based approaches to data management offer new means for the community to keep track of distributed and heterogeneous biomolecular simulation data and create collaborative networks

Molecular Similarity and Xenobiotic Metabolism

MetaPrint2D, a new software tool implementing a data-mining approach for predicting sites of xenobiotic metabolism has been developed. The algorithm is based on a statistical analysis of the occurrences of atom centred circular fingerprints in both substrates and metabolites. This approach has undergone extensive evaluation and been shown to be of comparable accuracy to current best-in-class tools, but is able to make much faster predictions, for the first time enabling chemists to explore the effects of structural modifications on a compound’s metabolism in a highly responsive and interactive manner.MetaPrint2D is able to assign a confidence score to the predictions it generates, based on the availability of relevant data and the degree to which a compound is modelled by the algorithm.In the course of the evaluation of MetaPrint2D a novel metric for assessing the performance of site of metabolism predictions has been introduced. This overcomes the bias introduced by molecule size and the number of sites of metabolism inherent to the most commonly reported metrics used to evaluate site of metabolism predictions.This data mining approach to site of metabolism prediction has been augmented by a set of reaction type definitions to produce MetaPrint2D-React, enabling prediction of the types of transformations a compound is likely to undergo and the metabolites that are formed. This approach has been evaluated against both historical data and metabolic schemes reported in a number of recently published studies. Results suggest that the ability of this method to predict metabolic transformations is highly dependent on the relevance of the training set data to the query compounds.MetaPrint2D has been released as an open source software library, and both MetaPrint2D and MetaPrint2D-React are available for chemists to use through the Unilever Centre for Molecular Science Informatics website.----Boehringer-Ingelhie

Annotation of Cytochrome P450 Genes In Harmonia axyridis\u27 And a Comparative Study of CYP Genes in Harmonia axyridis\u27 and Tribolium castaneum\u27

Our knowledge of beetle cytochrome P450 (CYP) genes was primarily obtained from studies of the model beetle and grain pest Tribolium castaneum.To gain additional insight into beetle CYPs and ultimately to inform our understanding of beetle CYP evolution, we identified and annotated all of the CYP genes present in a new draft genome of Harmonia axyridis by using traditional and automated methods for gene annotation. Overall, we identified somewhat fewer CYPs in H. axyridis (at least 94 genes and 3 pseudo genes representing 17 families and 42 subfamilies) compared to the number of of known CYPs in T. castaneum (137 plus 2 slight variants and 10 pseudogenes). The H. axyridis CYPs could be divided into 4 distinct clans: Mito, CYP2, CYP3 and CYP4 clans are major (monophyletic ) groups with strong support for most relationships and illustrates the presence of CYP blooms in T. castaneum that are lacking in H. axyridis. Several additional CYPs that are present in H. axyridis are missing in T. castaneum. The Mito clan of H. axyridis contains 6 genes in 5 families and 6 subfamilies . We found 7 genes in CYP2 clan with 5 families and 6 sub-families. We found 2 distinct families (4 and 349) and a minimum of 22 genes in the CYP4 clan in H. axyridis. Interestingly, both H. axyridis and T. castaneum carry CYP4G genes, which are candidate resistance genes for insecticides, including permethrins. The function of CYP4G was associated with pesticide resistance. The CYP3 clan has 59 genes in t families in 5 families H.axyridis: CYP6, CYP9, CYP345, CYP435 and CYP436. These 5 families in CYP3 are classified into at least 21 subfamilies. Our work focused on the automated annotation of CYP genes involved several software programs, the most efficient and sensitive of which are Augustus, GenScan and Fgenesh. Although it is likely that a few CYP genes remain to be identified in H.axyridis genome, our ongoing work suggests that the vast majority of CYPs have been identified

Fingolimod (Gilenya; FTY720): a recently approved multiple sclerosis drug based on a fungal secondary metabolite and the creation of a natural products pure compound database and organized storage system

Fingolimod (Gilenya; FTY720), a synthetic compound based on the fungal secondary metabolite, myriocin (ISP-I), is a potent immunosuppressant that was approved in September 2010 by the U.S. FDA as a new treatment for multiple sclerosis (MS). Fingolimod was synthesized by the research group of Tetsuro Fujita at Kyoto University in 1992 while investigating structure-activity relationships of derivatives of the fungal metabolite, ISP-I, isolated from Isaria sinclairii. Fingolimod becomes active in vivo following phosphorylation by sphingosine kinase 2 to form fingolimod-phosphate, which binds to specific G protein-coupled receptors (GPCRs) and prevents the release of lymphocytes from lymphoid tissue. Fingolimod is orally active, which is unique among current first-line MS therapies, and it has the potential to be used in the treatment of organ transplants and cancer. The first chapter reviews the discovery and development of fingolimod, from an isolated lead natural product, through synthetic analogues, to an approved drug. Natural products play an important role in the pharmaceutical industry, accounting for approximately half of all drugs approved in the U.S. between 1981 and 2006. Given the importance of natural product research and the vast amount of data that is generated in the process, it is imperative that the pure compounds and data are stored in a manner that will allow researchers to derive as much value as possible. The field chemoinformatics, interchangeable termed cheminformatics, has set the standards for electronic storage of chemical data, as chemistry was one of the first scientific disciplines to pursue electronic means of data storage. In this project an electronic database was created to capture all of the relevant data for each pure compound isolated via natural product research in Dr. Oberlies lab. A system was also implemented to catalogue and store the compounds in an organized manner

Population pharmacokinetic modelling to address the gaps in knowledge of commonly used HIV and TB drugs in children

The epidemiology of HIV and TB are overlapping, particularly in sub-Saharan Africa, and TB infection remains common in HIV-positive children. The combined administration of anti-tubercular and antiretroviral therapies(ART) may lead to drug-drug interactions potentially needing to be addressed with the adjustment of doses. This thesis assessed the pharmacokinetics of abacavir and ethambutol and evaluated the influence of covariates such as age and concomitant medication on the PK parameters across different studies using nonlinear mixed-effects modelling. The models developed were used to estimate area under the concentration-time curve (AUC) and maximum concentrations (Cmax) achieved with the currently-recommended weight-adjusted doses. A web-based paediatric dosing tool, which is meant to be used as a first step in the design of clinical trials for paediatric dosing was also developed. The model describing the pharmacokinetics of abacavir found: a) abacavir exposure to be 18.4% larger (CI:7.50-32.2) after the first dose of ART compared to abacavir co-treated with standard lopinavir/ritonavir for over 7 days, possibly indicating that clearance is induced with time on ART, b) malnourished HIV infected children had much higher exposures but this effect waned with a half-life of 12.2 (CI: 9.87-16.8) days as children stayed on nutritional rehabilitation and recovered, c). during co-administration of rifampicin-containing antituberculosis treatment and super-boosted lopinavir/ritonavir, abacavir exposure was decreased by 29.4% (CI: 24.3-35.8), d) children receiving efavirenz had 12.1% (CI: 2.57-20.1) increased abacavir clearance compared to standard lopinavir/ritonavir. The effects did not result in abacavir exposures lower or higher than those reported in adults and are not likely to be clinically important. The ethambutol model found lower concentrations than those reported in adults. The predicted ethambutol median (IQR) Cmax was 1.66 (1.21-2.15) mg/L for children on ethambutol with or without ART (excluding super-boosted lopinavir/ritonavir) and 0.882 (0.669-1.28) mg/L for children on ethambutol with super-boosted lopinavir/ritonavir, these are below the lower limit of the recommended Cmax range of 2 mg/L. During co-administration with super-boosted lopinavir, ethambutol exposure was decreased by 32% (CI: 23.8-38.9), likely due to drug-drug interaction involving absorption, metabolism or elimination. Bioavailability was decreased in children who were administered ethambutol in a crushed form, with an estimate decrease of 30.8% at birth, and an increase of 9.6% for each year of age up to 3.2 years where bioavailability was now similar to children taking EMB full tablet. The developed paediatric dosing tool contains two major sections. a) the ‘generic module’ which uses allometric scaling -based predictions to explore the expected AUC for a generic drug, b) the ‘drug-specific module’ which can simulate entire pharmacokinetic profiles (concentration over time after dose) by using a drug-specific population pharmacokinetic model. In summary, under the current weight-adjusted doses, abacavir exposure remained within the adult recommended levels. Ethambutol dose adjustment would be required in order to achieve adult exposures. A web-based paediatric dosing tool that uses allometric scaling -based predictions as well as drug specific predictions based on published pharmacokinetic models was successfully developed

How microplastics and adsorbed pollutants affect zebrafish development?

A presença de microplásticos no ecossistema aquático é, nos dias de hoje, uma realidade extremamente preocupante que acarreta sérios riscos para o meio ambiente e para a saúde pública. A capacidade dos microplásticos de adsorverem poluentes orgânicos, como é o caso do benzo[α]pireno (BaP), levanta preocupações adicionais, pois cria uma nova rota de entrada de compostos tóxicos na cadeia alimentar. No entanto, o conhecimento atual sobre o impacto dos microplásticos, inalterados e/ou contaminados, nos organismos aquáticos é ainda insuficiente e requer estudos adicionais. O trabalho desenvolvido no âmbito desta tese pretende assim fornecer novos dados sobre os efeitos biológicos dos microplásticos utilizando como modelo o peixe-zebra (Danio rerio). Pequenos teleósteos, como é o caso do peixe-zebra, oferecem vantagens significativas relativamente aos modelos animais clássicos e são atualmente utilizados como organismos de primeira linha para avaliar os riscos ambientais associados aos compostos tóxicos presentes nos meios aquáticos. Estudos toxicológicos requerem o uso de materiais inertes e condições controladas, todavia, nenhum dos sistemas atualmente comercializados é adequado para avaliar o efeito tóxico dos microplásticos. Estes sistemas contêm componentes feitos de polímeros plásticos que podem libertar partículas plásticas micrométricas, lixiviar os constituintes químicos ou adsorver os compostos químicos em estudo. O sistema de aquários autônomo ZEB316 foi desenvolvido no âmbito deste trabalho com o objetivo de suprimir esta necessidade e de facultar uma solução económica e fácil de implementar que permita a realização de estudos toxicológicos de última geração. Este sistema é construído com materiais inertes e resistentes à corrosão e proporciona boas condições de alojamento através de um sistema eficiente de recirculação e filtragem da água. A avaliação dos parâmetros da água e do desempenho do crescimento dos peixes mostrou que o sistema ZEB316 oferece condições de alojamento comparáveis à dos sistemas comercialmente disponíveis. A maioria dos resultados obtidos no âmbito desta dissertação provêm da análise de imagens de microscopia de campo claro e/ou fluorescência. Embora o uso de imagens de microscopia seja comum na maioria dos laboratórios e permita obter uma quantidade considerável de informação, a análise destas imagens é geralmente um processo moroso, em parte devido à falta de ferramentas automáticas/semiautomáticas dedicadas que permitam a sua análise. Nesse sentido, desenvolvemos diversas macros para o software ImageJ, com o objetivo de reduzir o erro associado à análise pelo usuário, aumentando assim a reprodutibilidade dos dados e a padronização das metodologias experimentais. Uma vez que o foco deste trabalho está centrado no estudo da osteotoxicidade, é de salientar o desenvolvimento de um conjunto de macros específicas para esse fim e denominadas ZFBONE. Este conjunto de ferramentas permite aos usuários avaliar, a partir de imagens 2D, parâmetros morfométricos de várias estruturas ósseas (por exemplo, opérculo, raios e escamas da barbatana caudal), mas também a extensão e a intensidade das colorações específicas do osso. Além disso, outras macros foram desenvolvidas para outros fins, por exemplo, para analisar os vários parâmetros morfométricos relativos aos embriões de peixe ou para avaliar cortes histológicos. Uma vez desenvolvidos os meios e técnicas necessários para a execução dos ensaios toxicológicos, e subsequente análise dos resultados, procedeu-se à realização das várias experiências que visam compreender efeito biológico dos microplásticos e contaminates no peixe-zebra. Assim, larvas de peixe-zebra foram produzidas e mantidas no sistema previamente descrito, ZEB316, e expostas cronicamente, durante o seu desenvolvimento, a partículas de polietileno de 20- 27 μm, inalteradas (MP) ou contaminadas com benzo[α]pireno (MP-BaP). Estas partículas foram adicionadas à dieta dos peixes através de uma suplementação a 1% m/m. Apesar de não se ter registado qualquer alteração ao nível dos parâmetros morfológicos aos 30 dias pós-fertilização (dpf), a presença de MP e MP-BaP acabou por ter um efeito negativo no crescimento dos espécimes aos 90 e 360 dpf. A fecundidade relativa, a morfologia do ovo/embrião e a área do vitelo também sofreram um impacto negativo em peixes-zebra alimentados com MP-BaP. No que respeita ao estado geral do esqueleto, os peixes expostos a dietas experimentais contendo MP e MP-BaP sofreram um aumento significativo na incidência de deformações esqueléticas aos 30 dpf quando comparados com peixes alimentados com a dieta controlo, bem como um desenvolvimento anómalo da barbatana caudal e escamas, e uma diminuição da qualidade do osso aos 90 dpf. Um comprometimento da formação óssea intergeracional foi também observado na prole de espécimes expostos a MP ou MP-BaP, que se refletiu numa redução do osso opercular dos descendentes aos 6 dpf. Além de um claro efeito no desenvolvimento ósseo, a análise histológica do intestino revelou ainda um número reduzido de células caliciformes em peixes alimentados com dieta MP-BaP, um claro sinal de inflamação intestinal. Finalmente, a exposição das larvas a MP-BaP levou a um aumento da expressão de genes associados à via de resposta do BaP, ao mesmo tempo que impactou negativamente na expressão de genes envolvidos no estresse oxidativo. Os resultados obtidos indicaram um maior comprometimento do desenvolvimento ósseo no peixe-zebra quando sujeito a uma dieta contendo microplásticos contaminados com BaP (MP-BaP), por comparação com a dieta contendo microplásticos não contaminados (MP). Outros autores demostraram também que a presença de BaP afeta a formação das vértebras e o desenvolvimento generalizado do esqueleto, no entanto os mecanismos envolvidos nestes fenómenos permanecem pouco estudados. Desta forma, realizámos ensaios adicionais in vivo com o objetivo de avaliar os efeitos osteotóxicos do BaP durante o desenvolvimento e regeneração óssea em peixe-zebra. A exposição aguda de larvas de peixe-zebra entre os 3 e os 6 dpf ao BaP levou a uma redução do tamanho do osso opercular e uma diminuição quantitativa de células positivas para osteocalcina, indicando um efeito composto na maturação dos osteoblastos. Por sua vez, quando se trata de uma exposição crônica das larvas de peixe-zebra ao BaP, entre os 3 e os 30 dpf, verificou-se que o desenvolvimento do esqueleto axial é afetado, aumentando a incidência e gravidade das deformações esqueléticas. Em peixes jovens adultos, observou-se ainda que a exposição ao BaP afetou não só a mineralização dos raios da barbatana caudal e escamas recém-formados, como prejudicou também o seu padrão morfológico, fenómenos que têm por base uma remodelação óssea desequilibrada. Relativamente às análises de expressão genética de vários marcadores verificou-se que o BaP induziu a ativação das vias xenobióticas e metabólicas e impactou negativamente na formação e organização da matriz extracelular. Curiosamente, a exposição ao BaP regulou positivamente os marcadores de inflamação nas larvas e aumentou o recrutamento de neutrófilos. Uma interação direta entre neutrófilos e a matriz extracelular óssea, ou células responsáveis pela formação do osso, foi observada in vivo, o que sugere um papel dos neutrófilos nos mecanismos subjacentes à osteotoxicidade do BaP. Globalmente, os resultados obtidos no âmbito deste trabalho sugerem que a exposição crónica a microplásticos inalterados e/ou contaminados não prejudica apenas o crescimento dos peixes, mas também o seu desempenho a nível reprodutivo, saúde geral do seu esqueleto, e compromete a descendência por meio de efeitos intergeracionais. Além disso, este trabalho fornece novos dados sobre os principais mecanismos celulares e moleculares envolvidos na osteotoxicidade do BaP e aborda o possível papel dos neutrófilos na redução da resposta óssea inflamatória.The presence of microplastics in the aquatic ecosystem represents a major issue for the environment and human health. The capacity of organic pollutants such as benzo[α]pyrene (BaP) to adsorb onto microplastic particles raises additional concerns, as it creates a new route for toxic compounds to enter the food web. Current knowledge on the impact of pristine and/or contaminated microplastics on aquatic organisms remains insufficient, and this work aims at providing new insights by evaluating their biological effects in zebrafish (Danio rerio). The ZEB316, a standalone housing system built with inert materials, and a comprehensive set of ImageJ semi-automatic tools were first developed and optimized to perform state-of-the-art toxicological studies and obtain meaningful data from morphometric analysis of brightfield/ fluorescence images. Zebrafish larvae were exposed throughout their development to polyethylene microplastics, pristine or spiked with BaP, supplemented in the fish diet. While exposure up to 30 days post-fertilization only increased the incidence of skeletal deformities, long-term exposure to pristine/contaminated microplastics not only jeopardized fish growth, reproduction performance, and skeletal health, but it also caused an intergenerational effect. To further study the mechanisms underlying BaP osteotoxicity, several bone-related in vivo assays were used to evaluate the effects of waterborne exposure to BaP during bone development and regeneration. BaP inhibited osteoblast maturation and ECM mineralization and stimulated osteoclast activity, thus affecting bone remodeling. Transgenic and transcriptomic approaches suggested that besides the activation of xenobiotic and metabolic pathways, which may negatively impact extracellular matrix formation and organization, BaP activates inflammatory mechanisms that recruit neutrophils, which affect both osteoblast and osteoclast activity, possibly through a direct interaction of the neutrophils with the bone matrix. This work provides novel data on the effects of microplastics exposure during zebrafish development, in particular its osteotoxic effects, and gives new insights into the cellular and molecular players involved in BaP osteotoxicity.Marco Tarasco was supported by the Portuguese Foundation for Science and Technology (FCT) through the PhD grant SFRH/BD/128634/2017 and COVID/BD/151848/2021 and by NEUBIAS-COST STSM program as part of action CA15124. This work was funded by FCT through projects UID/Multi/04326/2019, UID/00350/2020, UIDB/04326/2020, UID/MAR/00350/2013 and from the operational programs MAR2020 and COMPETE 2020 through projects OSTEOMAR MAR-02.01.01-FEAMP-0057 and EMBRC.PT ALG-01-0145-FEDER-022121