Estudo estrutural e comparativo entre Sirtuínas 2 de diferentes espécies de Leishmania / Structural and comparative study between Sirtuins 2 of different species of Leishmania by means of Comparative Modeling and Molecular Dynamic

As leishmanioses são doenças negligenciadas que afetam mais de um bilhão e meio de pessoas ao redor do mundo, principalmente nos países em desenvolvimento, provocando grandes impactos socioeconômicos. Os fármacos disponíveis para o tratamento dessas doenças são ineficazes e apresentam graves efeitos adversos. O processo de pesquisa de novos fármacos envolve, entre outras coisas, a seleção de alvos bioquímicos essenciais para a sobrevivência e desenvolvimento do agente causador. Neste sentido, a Sirtuína 2, uma enzima epigenética com atividade hidrolase essencial para a sobrevivência dos parasitas do gênero Leishmania se apresenta como um alvo validado na busca de novos fármacos contra essas parasitoses. O planejamento de fármacos baseado na estrutura do receptor requer o conhecimento da estrutura tridimensional da proteína alvo. Desta forma, a elucidação estrutural e um estudo minucioso das Sirtuínas das várias espécies do gênero Leishmania apresenta-se como uma importante abordagem na aplicação desta estratégia na busca por agentes quimioterápicos. Até o momento, na família Trypanosomatidae, a única estrutura tridimensional resolvida experimentalmente de uma enzima Sirtuína 2 é a da espécie L. infantum. Assim, este trabalho aplicou a abordagem de Modelagem Comparativa utilizando o software Modeller na construção de modelos da Sir2rp1 das espécies L. infantum, L. major e L. braziliensis, cujas sequências de aminoácidos foram extraídas do banco de dados UNIProt. Os modelos construídos foram validados por meio da função de escore DOPE do Modeller e dos servidores PROCHECK, MolProbity e QMEAN, avaliando sua qualidade estereoquímica e seu enovelamento. Os ligantes naturais da enzima foram sobrepostos nos modelos construídos por alinhamento estrutural utilizando o software PyMol e os complexos validados foram submetidos a simulações de Dinâmica Molecular através do pacote GROMACS. Os complexos refinados foram então analisados por meio dos softwares PyMol e LigPlotPlus e dos pacotes GROMACS e gmx_MMPBSA, e foram estudados os sítios de ligação dos substratos e os resíduos de aminoácidos relevantes envolvidos em sua ligação e reconhecimento. A Modelagem Comparativa da Sirtuína 2 humana e seus homólogos das espécies L. infantum, L. major e L. braziliensis, as simulações de Dinâmica Molecular realizadas com os modelos enzimáticos construídos e validados complexados com seus ligantes naturais, os cálculos de energia de interação entre os modelos e seus substratos e o estudo estrutural comparativo realizado entre eles nos fornecem uma base teórica para a busca de novos inibidores da Sirtuína 2 que sejam mais seletivos e potentes contra as enzimas parasitárias, abrindo caminho para o desenvolvimento de candidatos a fármacos leishmanicidas mais seguros e eficazes

Leishmaniasis are neglected diseases that affect more than one and a half billion people around the world, mainly in developing countries, causing major socioeconomic impacts. The drugs available for the treatment of these diseases are ineffective and have serious adverse effects. The process of researching new drugs involves, among other things, the selection of biochemical targets essential for the survival and development of the causative agent. In this sense, Sirtuin 2, an epigenetic enzyme with hydrolase activity essential for the survival of parasites of the Leishmania genus, presents itself as a validated target in the search for new drugs against these parasites. Structure-Based Drug Design requires knowledge of the three-dimensional structure of the target protein. In this way, structural elucidation and a detailed study of Sirtuins from various species of the genus Leishmania presents itself as an important approach in the application of this strategy in the search for chemotherapeutic agents. To date, in the Trypanosomatidae family, the only experimentally resolved three-dimensional structure of a Sirtuin 2 enzyme is that of the species L. infantum. Thus, this work applied the Comparative Modeling approach using the Modeller software in the construction of Sir2rp1 models of the species L. infantum, L. major and L. braziliensis, whose amino acid sequences were retrieved from the UNIProt database. The constructed models were validated using Modeller's DOPE score function and the PROCHECK, MolProbity and QMEAN servers, evaluating their stereochemical quality and folding. The enzyme's natural ligands were superimposed on the built models by structural alignment using the PyMol software and the validated complexes were subjected to Molecular Dynamics simulations using the GROMACS package. The refined complexes were then analyzed using the PyMol and LigPlotPlus softwares and the GROMACS and gmx_MMPBSA packages, and the substrate binding sites and relevant amino acid residues involved in their binding and recognition were studied. The Comparative Modeling of human Sirtuin 2 and its homologues from the species L. infantum, L. major and L. braziliensis, the Molecular Dynamics simulations carried out with the constructed and validated enzymatic models complexed with their natural ligands, the interaction energy calculations between the models and their substrates and the comparative structural study carried out between them provide us with a theoretical basis for the search for new Sirtuin 2 inhibitors that are more selective and potent against the parasitic enzymes, paving the way for the development of safer and more effective leishmanicidal drug candidates

Similitud molecular empleando Índices Híbridos / Molecular similarity using Hybrid Indices

Se presenta un método para la detección de semejanza entre moléculas basado en macheo inexacto de grafos. Se parte del grafo molecular completo ponderado en sus vértices por propiedades químico-físicas particionadas sobre los mismos, se reduce el grafo por el procedimiento CALEDE que define Centros Descriptores o fragmentos de primer orden, los cuales son subgrafos ponderados por la suma de los valores de los vértices ponderados individualmente a su vez, y se construyen fragmentos denominados de segundo orden que incluyen la distancia entre los centros de masas de ambos centros descriptores. Se presenta el método de búsqueda aplicado a una base de datos de más de 300 moléculas con sus respectivas estructuras en tres dimensiones. Esos compuestos se encuentran evaluados como anticancerígenos en la base de datos de compuestos del NCBI-USA. En el experimento computacional se encuentra que, en dependencia de la función de similitud empleada, es posible detectar compuestos que a pesar de poseer diferente topología, poseen valores de las propiedades empleadas para el macheo lo cual sugiere la presencia de potenciales farmacóforos como hallazgo relevante, lo cual constituiría un novedoso enfoque para el diseño computacional de fármacos(AU)

A method for detecting similarity between molecules based on inexact matching graph is presented. We start from a complete molecular graph vertices weighted by several hybrid indices. The molecular graph is reduced by CALEDE procedure, which define descriptors centers or first order fragments. These fragments are subgraphs weighted with the sum of values of the vertices weighted with the hybrid indices. It also define second order fragments by including the distance between the centers of mass of both descriptors centers. The search method applied to a database of over 300 molecules with their respective threedimensional structures is presented. These compounds are reported in the NCBI-USA database of compounds whish were evaluated in anticancer tests. In the computational experiment, depending on the similarity function used, is possible to detect compounds that despite having different topology have property values suggesting the presence of potential pharmacophore. It suggest the possibility to use this approach as a novel approach for computational drug design(AU)

Analyzing resistance pattern of non-small cell lung cancer to crizotinib using molecular dynamic approaches.

Crizotinib is the potential anticancer drug used for the treatment of non-small cell lung cancer (NSCLC) approved by FDA in 2011. The main target for the crizotinib is anaplastic lymphoma kinase (ALK). Evidences available indicate that double mutant ALK (L1196M and G1269A) confers resistance to crizotinib. However, how mutation confers drug resistance is not well-understood. Hence, in the present study, molecular dynamic (MD) simulation approach was employed to study the impact of crizotinib binding efficacy with ALK structures at a molecular level. Docking results indicated that ALK double mutant (L1196M and G1269A) significantly affected the binding affinity for crizotinib. Furthermore, MD studies revealed that mutant ALK-crizotinib complex showed higher deviation, higher fluctuation and decreased number of intermolecular H-bonds, when compared to the native ALK-crizotinib complex. These results may be immense importance for the molecular level understanding of the crizotinib resistance pattern and also for designing potential drug molecule for the treatment of lung cancer.