Aplicação de ferramentas de quimioinformática na comparação da estrutura tridimensional da dihidrofolato redutase expressa em diferentes organismos / Application of cheminformatics tools for comparing dihydrofolate reductase's tridimensional structure expressed by different organisms

A quimioinformática, definida como o emprego de técnicas informáticas na solução de problemas da química, evolui em conjunto com o desenvolvimento de ferramentas computacionais e é de grande relevância para o planejamento racional de fármacos ao otimizar etapas do desenvolvimento de novas moléculas e economizar recursos e tempo. Dentre as técnicas disponíveis destacam-se o planejamento de fármacos baseado na estrutura e no ligante, que quando combinadas auxiliam na identificação e otimização de moléculas ativas frente a alvos farmacológicos. A Dihidrofolato Redutase (DHFR) é uma importante enzima da via dos folatos que catalisa a redução do dihidrofolato em tetrahidrofolato, utilizando NADPH como cofator, reação essencial para a replicação celular, visto que este ciclo resulta na síntese de precursores das bases nitrogenadas que compõem o DNA, consequentemente, inibidores de DHFR são utilizados no tratamento de infecções bacterianas e alguns tipos de câncer. Trypanosoma cruzi, protozoário causador da doença de chagas, é um dos organismos que expressam a DHFR, além do próprio Homo sapiens. Analisaram-se ligantes conhecidos e as estruturas da proteína expressa pelos dois organismos, visando identificar pontos de divergência que possam ser explorados no planejamento de moléculas seletivas para o tratamento da doença de Chagas. Os 6 modelos cristalográficos de T. cruzi e 2 de H. sapiens foram obtidos do banco de dados de proteínas (PDB) após aplicação de filtros de qualidade. Foram analisadas as sequências de aminoácidos dos modelos, com o uso do Cluster Ômega, sua estrutura tridimensional com os programas Pymol e Chimera X, além da análise das cavidades proteicas com o CavityPlus, que também gerou os farmacóforos de ambos alvos. A análise de estrutura primária identificou mutações em três aminoácidos nos cristais do parasita, que podem ser explicados por diferentes caminhos evolutivos de grupos segregados, embora nenhuma mutação observada esteja em regiões de sítio ativo. A análise dos modelos permitiu que fossem identificados os 25 aminoácidos que estão a menos de 5 Å de distância dos ligantes de T. cruzi, sendo 5 aminoácidos responsáveis por interações de hidrogênio com pelo menos um dos ligantes analisados. Destes, 18 se repetem na proteína humana ou são substituídos por outro aminoácido que mantém a mesma interação. Quanto às diferenças observadas, destacam-se a asparagina 44 substituída por uma prolina na proteína humana e a prolina 92, substituída por uma lisina. A análise de cavidades identificou três cavidades em cada proteína, embora somente as cavidades correspondentes ao sítio ativo sejam druggables. A cavidade da proteína humana é maior e mais alongada, além de apresentar o aspecto de um túnel, enquanto a cavidade da proteína parasita é mais aberta, tal abertura permite que ligantes com o anel benzeno meta substituídos explorem uma região existente na cavidade de T. cruzi que é fechada na humana. O farmacóforo de ambas proteínas foi identificado, apresentando diferenças no tamanho e angulação que também podem ser explorados no planejamento de fármacos seletivos

Chemoinformatic, defined as the use of informatic techniques to solve chemical problems, has evolved together with new computational tools and it is quite important for rational drug designing, by optimizing different steps on the development pipeline of new molecules, saving resources and time. From all the available tools, structure and ligand based drug design shall be highlighted, when combined, they support the identification and optimization of active molecules from pharmaceutical targets. Dihydrofolate reductase (DHFR) is an important enzyme of the folate pathway that catalyzes the reduction of dihydrofolate to tetrahydrofolate, by using NADPH as cofactor. This reaction is essential for cell replication, as this pathway results in the synthesis of nucleobases that build the DNA. That's the reason why DHFR inhibitors are used for treating bacterial infections and some types of cancer. Trypanosoma cruzi, a protozoa that causes Chagas disease, is one of the organisms that express DHFR, besides Homo sapiens itself. This work analyzed known ligands and the structure of the protein expressed by both organisms, aiming to identify divergence points that could be explored for designing selective drugs for Chagas disease treatment. The 6 proteins crystallographic models from T. cruzi and 2 from H. sapiens were obtained from protein data bank (PDB) after the application of quality filters. The amino acid sequence of each model was analyzed by Clustal Omega, its tridimensional structure by Pymol and Chimera X and the cavity analysis by CavityPlus, that also generated the pharmacophore from both targets. The primary structure analysis identified mutations on three amino acids on the parasite christal, which may be explained by different evolutive paths from segregated groups, although none of the observed mutations are on the active site region. The model's analysis allowed the identification of 24 amino acids that are closer than 5 Å from the T. cruzi ligands, 5 of them responsible for hydrogen interactions on at least one of the ligands analyzed. 18 of them are repeated on the human protein or are replaced by another amino acid that preserves the same interaction. As by the differences observed that shall be highlighted, asparagine 44 is replaced by a proline on the human protein, and proline 92 by a lysin. The cavity analysis identified three cavities on each protein, although only the cavities of the active site are druggables. The human protein cavity is bigger and longer, besides it looks like its a tunnel, when the parasite protein is open, that opening allows ligands with benzene ring meta substituted to explore the existing regions of the T. cruzi protein that is closed on the human protein. Lastly, the pharmacophore from both proteins was identified, it shows differences on size and angulation that also could be explored in the designing of selective drugs

In silico investigation of possible caffeine interactions with common inflammation-related targets

Caffeine (CA) is a methylxanthine alkaloid widely used in anti-inflammatory drug associations due to itsvasoconstricting properties. Although CA is acknowledged to interact with a plethora of macromolecules inhuman organism, there was to the best of our knowledge, no survey regarding its possible interactions withcommon inflammation-related targets. Henceforth, this work was concerned in the investigation of CA possibleinteractions with cyclooxygenases-1 and -2 (COX-1 and COX-2), as well as prostaglandin H2 synthase-1and leukotriene A4 hydrolase through in silico approaches. CA molecule was studied as a ligand whereas theligand-macromolecules docking models were created through AutoDock Vina tools. Results showcased that,although the thermodynamic features of the best scoring models did not render enough information to affirmstable interaction between CA and the analyzed macromolecules, more studies are needed to shed light on thepossible role of methylxanthines towards inflammation targets.

Automated QSAR and Docking Study of Phyto-Ligands of Chromolaena odorata as Inhibitor of Bacteria Beta-lactamase Enzyme

Bacteria resistance to antibacterial antibiotics is made possible by theproduction of beta-lactamase. Beta-lactamase enzyme confers resistance by breakingopen the Beta-lactam structure of antibiotics, thereby deactivating their antibacterialproperties. As a result of this, attention shifted into identifying potential lead inhibitorof beta-lactamase, with ability to reduce resistance encountered in bacteria antibiotics.The computational approach was employed in the generation of QSAR model usingAutomated QSAR, and in the docking of ligands from Chromolaena odorata with Betalactamase. The best model obtained was KPLS_Dendritic_43 (R2 = 0.8564 andQ2=0.7819), and was used in predicting the bioactivity of the lead compounds. Dockingstudy revealed that the ligands bind with a higher binding score than co-crystallizedligand and other standard drug employed in this study. Tianshic acid and chromomoraterecorded binding energy of -9.305 and -7.989 respectively. The drug-like properties ofthe ligands were evaluated using the Lipinski rule of Five, which revealed that C. odorataligands do not only inhibit the activity of beta-lactamase, but the ligands are also druglike. Therefore, further studies are needed to adequately justify the mechanism of actionof these ligands as a beta-lactamase inhibitor.

Antibacterial and Pharmacological Evaluation of Fluoroquinolones: A Chemoinformatics Approach

Fluoroquinolone (FQ) antibiotics are an important class of synthetic antibacterial agents. These are the most extensively used drugs for treating bacterial infections in the field of both human and veterinary medicine. Herein, the antibacterial and pharmacological properties of four fluoroquinolones: lomefloxacin, norfloxacin, ciprofloxacin, and ofloxacin have been studied. The objective of this study was to analyze the antibacterial characteristics of the different fluoroquinolones. Also, the pharmacological properties of the compounds including the Lipinski rule of five, absorption, distribution, metabolism, and excretion, LD50, drug likeliness, and toxicity were evaluated. We found that among all four FQ molecules, ofloxacin showed the highest antibacterial activity through in silico assays with a strong interaction (−38.52 kJ/mol) with the antibacterial target protein (topoisomerase-II DNA gyrase enzyme). The pharmacological and pharmacokinetic analysis also showed that the compounds ciprofloxacin, ofloxacin, lomefloxacin and norfloxacin have good pharmacological properties. Notably, ofloxacin was found to possess an IGC50 (concentration needed to inhibit 50% growth) value of 0.286 μg/L against the Tetrahymena pyriformis protozoa. It also tested negative for the Ames toxicity test, showing its non-carcinogenic character.