Descritores da atividade antimalarial de derivados de febrifugina obtidos via mecânica qüântica

Plasmodium falciparum resistant strain development has encouraged the search for new antimalarial drugs. Febrifugine is a natural substance with high activity against P. falciparum presenting strong emetic property and liver toxicity, which prevent it from being used as a clinical drug. The search for analogues that could have a better clinical performance is a current topic. We aim to investigate the theoretical electronic structure by means of febrifugine derivative family semi-empirical molecular orbital calculations, seeking the electronic indexes that could help the design of new efficient derivatives. The theoretical results show there is a clustering in well-defined ranges of several electronic indexes of the most selective molecules. The model proposed for achieving high selectivity was tested with success.O desenvolvimento de linhagens resistentes de Plasmodium falciparum tem encorajado a busca por novas drogas antimalariais. A febrifugina é uma substância natural com alta atividade contra o P. falciparum que apresenta propriedade emética e toxicidade para o fígado tal que não permitem o seu uso clínico. A busca por análogos que possam ter uma performance clínica melhor é um tema de pesquisa atual. Nosso objetivo é investigar a estrutura eletrônica teórica de uma família de derivados da febrifugina empregando cálculos semi-empíricos de orbitais moleculares, procurando por índices eletrônicos que possam ajudar a modelar novos derivados mais eficientes. Os resultados teóricos mostram que para as moléculas mais seletivas existe um agrupamento dos valores de determinados índices em intervalos bem definidos. O modelo proposto para se obter alta seletividade foi testado com sucesso

Machine Learning-based Analysis of Electronic Properties as Predictors of Anticholinesterase Activity in Chalcone Derivatives

In this study, we investigated the correlation between the electronic properties of anticholinesterase compounds and their biological activity. While the methodology of such correlation is well-established and has been effectively utilized in previous studies, we employed a more sophisticated approach: machine learning. Initially, we focused on a set of $22$ molecules sharing a common chalcone skeleton and categorized them into two groups based on their IC50 indices: active and inactive. Utilizing the open-source software Orca, we conducted calculations to determine the geometries and electronic structures of these molecules. Over a hundred parameters were collected from these calculations, serving as the foundation for the features used in machine learning. These parameters included the Mulliken and Lowdin electronic populations of each atom within the skeleton, molecular orbital energies, and Mayer's free valences. Through our analysis, we developed numerous models and identified several successful candidates for effectively distinguishing between the two groups. Notably, the most informative descriptor for this separation relied solely on electronic populations and orbital energies. By understanding which computationally calculated properties are most relevant to specific biological activities, we can significantly enhance the efficiency of drug development processes, saving both time and resources.Comment: to be submitted to Journal of Chemical Information and Modelin

Febrifugine Derivative Antimalarial Activity: Quantum Mechanical Predictors.

Plasmodium falciparum resistant strain development has encouraged the search for new antimalarial drugs. Febrifugine is a natural substance with high activity against P. falciparum presenting strong emetic property and liver toxicity, which prevent it from being used as a clinical drug. The search for analogues that could have a better clinical performance is a current topic. We aim to investigate the theoretical electronic structure by means of febrifugine derivative family semi-empirical molecular orbital calculations, seeking the electronic indexes that could help the design of new efficient derivatives. The theoretical results show there is a clustering in well-defined ranges of several electronic indexes of the most selective molecules. The model proposed for achieving high selectivity was tested with success.5021-

Investigação da atividade biológica de taxóides e Benzo[c]quinolizin-3-onas através de descritores teóricos

Orientador: Douglas Soares GalvãoTese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb WataghinResumo: Este trabalho envolveu a investigação da atividade biológica de fármacos por meio de descritores quânticos teóricos e a investigação de um sistema molecular de chaveamento ótico. Em uma primeira parte, apresentamos o estudo realizado para um conjunto de 20 taxóides, compostos caracterizados por uma estrutura molecular complexa, e por uma atuação diferenciada no combate ao câncer. Investigamos a estrutura destes compostos através de métodos semiempíricos partindo de seu precursor sintético 10-deacetilbaccatin III. Investigamos a relação entre a atividade experimental dos taxóides e descritores teóricos através de três metodologias de reconhecimento de padrões: a metodologia de índices eletrônicos, a análise de componentes principais e análise hierárquica de clusters. Para estas três investigações distintas pudemos correlacionar a atividade dos taxóides estudados com parâmetros teóricos, em sua maioria eletrônicos. Seguindo o mesmo tipo de análise aplicada para os taxóides, estudamos um conjunto de 41 derivados da benzo[c]quinolizin-3-onas, compostos inibidores das enzimas 5alfa-reductase humana. Aplicando os três métodos acima citados selecionamos descritores relacionados à resposta biológica destes compostos e construímos regras e padrões que os diferenciasse quanto à atividade biológica. Numa investigação especulativa, aplicando as regras e padrões construídos, sugerimos a atividade biológica para alguns compostos ainda não avaliados experimentalmente. Na segunda parte deste trabalho investigamos um sistema orgânico de chaveamento, baseado no comportamento fotocrômico de moléculas quirais. Este é um sistema de grande interesse no desenvolvimento de memórias moleculares que utilizem uma lógica binária. Utilizamos métodos semiempíricos na investigação estrutural e energética do sistema e propusemos uma rota para o funcionamento do sistema, capaz de explicar qualitativa e quantitativamente o seu comportamentoAbstract: This work deals with the structure-activity relationship investigation of pharmacological compounds using theoretical quantum descriptors, and the investigation of an optical molecular switching system. In the first part, we present a study of 20 taxoids, remarkable molecules by their complex molecular structure and dissimilar mode of action as antitumor agent. We investigated the compounds structure with semiempirical methods initiating with their synthetic precursor 10-deacetilbaccatin III. Taxoids experimental activity relationship was investigated with theoretical descriptors applying three pattern recognition methodologies: the electronic indices methodology, principal component analysis and hierarchical cluster analysis. With these three distinct methods we were able to correlate the biological activity of the studied taxoids with theoretical parameters. In a similar approach we studied a set of 41 benzo[c]quinolizin-3-ones derivatives, applied as human 5alpha-reductase inhibitors. Making use of the three methods mentioned above we selected the descriptors related to the compounds biological indices and constructed the rules and patterns able to separate them according to their activity. Considering a speculative approach, we proposed the biological activity to untested compounds, via the obtained rules. In a second part of the work we investigated an organic switching system, based on the photocromic behavior of chiral molecules. This is a system of great interest for molecular memories development based on binary logics. We applied semiempirical methods in the system structural and energetic investigations, and proposed a route able to explain qualitative and quantitatively how the system worksDoutoradoFísicaDoutora em Ciência

Theoretical analysis and simulations applied to rational design strategies of nanostructured materials

Orientador: Douglas Soares GalvãoTese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb WataghinResumo: Esse documento apresenta uma coleção de trabalhos realizados dentro do amplo campo de materiais nanoestruturados, focando-se em descrições teóricas analíticas e simulações computacionais de diversos novos materias desse tipo. Uma nova fibra supereslástica e condutora é reportada. Essa fibra altamente esticável (até 1320%) é criada envolvendo-se um núcleo cilíndrico de borracha com uma camada de folha de nanotubos de carbono. O material resultante exibe uma interessante estrutura de enrugamentos hierárquicos na sua superfície, o que lhe garante propriedades elétricas úteis como conservar a sua resistencia constante enquanto esticada. Adicionando-se mais camadas de borracha ou nanotubos podemos obter aplicações como sensores de movimento ou deformação, atuadores/músculos artificiais ativados por corrente ou temperatura e operados reversivelmente por um mecanismo de acoplamento entre tensão e torção. Nós explicamos suas propriedades de condução elétrica e os fenômenos físicos envolvidos em cada uma dessas aplicações. Também desenvolvemos um novo método para o desenho racional de polímeros molecularmente impressos usando dinâmica molecular para simular o processo de impressão molecular e a análise subsequente utilizando experimentos de cromatografia simulada. Obtivemos com sucesso a primeira evidência teórica do mecanismo de impressão exibindo afinidade e seletividade para a substância alvo 17-beta-estradiol. Desenhamos e simulamos uma nova estrutura com formato de piramide em kirigami de grafeno, composta de uma folha de grafeno cortada em um padrão específico a fim de formar uma pirâmide quando sofre tensão na direção normal ao plano. Nós calculamos a resposta dessa estrutura a uma carga estática, quando ela age como uma mola de proporções nanométriacs. Também, utilizando simulações de dinâmica molecular de colisões balísticas, constatamos que a resistência desse material a impactos é ainda maior que de uma folha de grafeno puro, sendo ainda mais leve. Um novo método de reforçar fios de nanotubos de carbono, chamado ITAP, também é reportado. Esse método foi capaz de melhorar a resistencia mecanica do fio em até 1,5 vezes e torná-lo muito mais resistente ao ataque de ácido quando comparado com um fio não tratado. Utilizamos simulações de dinâmica molecular para testar a hipótese de que esse tratamento é suficiente para gerar ligações covalentes entre as paredes externas de nanotubos diferentes, o que seria responsável pelas propriedades do material. Aplicamos um algoritmo genético modificado ao problema do folding de proteínas em um modelo de rede 3D HP. Testamos o algoritmo utilizando um conjunto de sequencias de teste que têm estado em uso pelos últimos 20 anos na literatura. Fomos capazes de melhorar um dos resultados e demonstramos a aplicação e utilidade de operadores não canônicos que evitam a convergência prematura do algoritmo, sendo eles o operador de compartilhamento e efeito maternalAbstract: This document presents a colection of works done within the broad subject of nano-structured materials, focusing on analytical theoretical descriptions and computational simulations of new kinds of this class of materials. A new superelastic conducting fiber is reported, with improved properties and functionalities. They are highly stretchable (up to 1320%) conducting fibers created by wrapping carbon nanotube sheets on stretched rubber fiber cores. The resulting structure exhibited an interesting hierarchical buckled structure on its surface. By including more rubber and carbon nanotube layers, we created strain sensors, and electrically or thermally powered tensile and torsional muscles/actuators operating reversibly by a coupled tension-to-torsion actuation mechanism. We explain its electronic properties and quantitatively explain the compounded physical effects involved in each of these applications. We also developed a new method for the rational design of molecularly imprinted polymers using molecular dynamics to simulate the imprinting process and subsequent chromatography studies. We successfully obtained the first theoretical evidence of actual imprinting happening under unconstrained simulations showing affinity and selectivity to the target substance 17-beta estradiol. We designed and simulated a new graphene kirigami pyramid structure, composed of a cut graphene sheet in a specific pattern in order to form a pyramid when under stress perpendicular to the plane. We calculated the response to static loading of this structure that acts like a nano-sized spring. Also, with simulated ballistic collisions we obtained increased resistance to impact in comparison with a pure graphene sheet. A new method of strengthening carbon nanotube yarns, called ITAP, consisting of annealing at high temperature in vacuum is reported. This method is shown to increase the mechanical resistance of the wire up to 1.5 times and make it much more resistant to acid corrosion when compared to pristine non-treated wires. We applied a modified genetic algorithm to the protein folding problem using an 3D HP lattice model using known test sequences that have been in use for the last 20 years and obtained an improvement for the best solution found for one of these proteins. Also, the importance of new non-canonical operators that prevent rapid convergence of the algorithm was demonstrated, namely the Sharing and Maternal Effect operatorsDoutoradoFísicaDoutor em Ciências141198/2012-5CNP

A Structure-activity Study Of Taxol, Taxotere, And Derivatives Using The Electronic Indices Methodology (eim)

Among the new families of effective anticancer drugs, the natural product paclitaxel (Taxol/Bristol-Myers-Squibb) and its semisynthetic derivative docetaxel (Taxotere/Rhone-Poulenc Rorer) are probably the most promising agents under investigation. Surprisingly considering their importance no detailed quantum mechanical studies have been carried out for these drugs. In this work we report the first structure-activity relationship (SAR) studies for 20 taxoid structures using molecular descriptors from all-electron quantum methods. The used methods were the pattern-recognition Principal Component Analysis (PCA), Hierarchical Clustering Analysis (HCA), and the recently developed Electronic Indices Methodology (EIM). The combined use of EIM with PCA/HCA methodologies was able to correctly classify active and inactive taxoids with 100% of accuracy using only a few "universal" quantum molecular descriptors. It was possible to identify the electronic features defining active molecules. 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Diagnostic Significance of Exosomal miRNAs in the Plasma of Breast Cancer Patients

Poster Session AbstractsBackground and Aims: Emerging evidence that microRNAs (miRNAs) play an important role in cancer development has opened up new opportunities for cancer diagnosis. Recent studies demonstrated that released exosomes which contain a subset of both cellular mRNA and miRNA could be a useful source of biomarkers for cancer detection. Here, we aim to develop a novel biomarker for breast cancer diagnosis using exosomal miRNAs in plasma. Methods: We have developed a rapid and novel isolation protocol to enrich tumor-associated exosomes from plasma samples by capturing tumor specific surface markers containing exosomes. After enrichment, we performed miRNA profiling on four sample sets; (1) Ep-CAM marker enriched plasma exosomes of breast cancer patients; (2) breast tumors of the same patients; (3) adjacent non-cancerous tissues of the same patients; (4) Ep-CAM marker enriched plasma exosomes of normal control subjects. Profiling is performed using PCR-based array with human microRNA panels that contain more than 700 miRNAs. Results: Our profiling data showed that 15 miRNAs are concordantly up-regulated and 13 miRNAs are concordantly down-regulated in both plasma exosomes and corresponding tumors. These account for 25% (up-regulation) and 15% (down-regulation) of all miRNAs detectable in plasma exosomes. Our findings demonstrate that miRNA profile in EpCAM-enriched plasma exosomes from breast cancer patients exhibit certain similar pattern to that in the corresponding tumors. Based on our profiling results, plasma signatures that differentiated breast cancer from control are generated and some of the well-known breast cancer related miRNAs such as miR-10b, miR-21, miR-155 and miR-145 are included in our panel list. The putative miRNA biomarkers are validated on plasma samples from an independent cohort from more than 100 cancer patients. Further validation of the selected markers is likely to offer an accurate, noninvasive and specific diagnostic assay for breast cancer. Conclusions: These results suggest that exosomal miRNAs in plasma may be a novel biomarker for breast cancer diagnosis.link_to_OA_fulltex