FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria

Submitted by Sandra Infurna ([email protected]) on 2019-07-09T11:33:32Z No. of bitstreams: 1 AnaPaulaC_Assef_etal_IOC_2019.pdf: 1229680 bytes, checksum: 3f189d37debf3938623bdbf2886b967d (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2019-07-09T11:45:06Z (GMT) No. of bitstreams: 1 AnaPaulaC_Assef_etal_IOC_2019.pdf: 1229680 bytes, checksum: 3f189d37debf3938623bdbf2886b967d (MD5)Made available in DSpace on 2019-07-09T11:45:07Z (GMT). No. of bitstreams: 1 AnaPaulaC_Assef_etal_IOC_2019.pdf: 1229680 bytes, checksum: 3f189d37debf3938623bdbf2886b967d (MD5) Previous issue date: 2019CAPES, FAPERJ, CNPq e FIOCRUZ (INOVA-FIOCRUZ VPPCB-007-FIO-18-2-29) for financial support.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Muniz. Programa de Pós-Graduação em Biotecnologia para Saúde e Medicina Investigativa. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Bioquímica Experimental e Computacional de Fármacos. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ. Brasil.Healthcare-associated infections (HAIs) are a serious public health problem. They can be associated with morbidity and mortality and are responsible for the increase in patient hospitalization. Antimicrobial resistance among pathogens causing HAI has increased at alarming levels. In this paper, a robust method for analyzing genome-scale metabolic networks of bacteria is proposed in order to identify potential therapeutic targets, along with its corresponding web implementation, dubbed FindTargetsWEB. The proposed method assumes that every metabolic network presents fragile genes whose blockade will impair one or more metabolic functions, such as biomass accumulation. FindTargetsWEB automates the process of identification of such fragile genes using flux balance analysis (FBA), flux variability analysis (FVA), extended Systems Biology Markup Language (SBML) file parsing, and queries to three public repositories, i.e., KEGG, UniProt, and DrugBank. The web application was developed in Python using COBRApy and Django

New insights in Trypanosoma cruzi proteomic map: further posttranslational modifications and potential drug targets in Y strain epimastigotes

Submitted by Sandra Infurna ([email protected]) on 2016-08-25T14:58:10Z No. of bitstreams: 1 daniela_beghini_etal_IOC_2012.pdf: 3445600 bytes, checksum: 1baceccd0d3e03f791c02e5153a75bae (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2016-08-25T15:09:37Z (GMT) No. of bitstreams: 1 daniela_beghini_etal_IOC_2012.pdf: 3445600 bytes, checksum: 1baceccd0d3e03f791c02e5153a75bae (MD5)Made available in DSpace on 2016-08-25T15:09:37Z (GMT). No. of bitstreams: 1 daniela_beghini_etal_IOC_2012.pdf: 3445600 bytes, checksum: 1baceccd0d3e03f791c02e5153a75bae (MD5) Previous issue date: 2012Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Bioquímica de Proteínas e Peptídeos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Celular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Bioquímica de Proteínas e Peptídeos. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Celular. Rio de Janeiro, RJ, Brasil.Chagas´ disease is a neglected sickness endemic in Latin America, caused by the protozoa Trypanosoma cruzi. 1e current treatment for the disease is unsatisfactory, and the development of potent compounds for novel molecular targets is critical. In this framework, proteomics could be a powerful tool in the evaluation of possible candidates for drug intervention. In this work, a two-dimensional electrophoresis (2- DE) and mass spectrometry (MS) approaches were employed in T. cruzi epimastigotes (Y strain). Di8erent gel staining protocols (Coomassie Blue, Pro-Q-Diamond and Pro-Q-Emerald) were performed to assess the protein content and possible post-translational modi)cations of this parasite. Here, 78 most intense spots were identi)ed by Coomassie staining, 22 by Pro-Q-Diamond (phosphoproteins) and 15 by Pro-QEmerald (glycoproteins). Compared with the results of other large-scale T. cruzi proteomic studies, 15 novel proteins were identi)ed here using MALDI-TOF/TOF, and 12 of these have not yet been described at the protein level. Functional analysis of the identi)ed proteins pointed to protein metabolism, and the localisation prediction indicated cytosol as the most prevalent localisation of these proteins. Eight proteins presented no similarity to human sequences and thus represent a group of promising biomolecules for chemotherapy intervention. Our data provides novel insights in the metabolic pathways of T. cruzi, which could aid in the discovery of alternative drugs for Chagas´ disease

New insights in Trypanosoma cruzi proteomic map: further post-translational modifications and potential drug targets in Y strain epimastigotes

 Chagas´ disease is a neglected sickness endemic in Latin America, caused by the protozoa Trypanosoma cruzi. The current treatment for the disease is unsatisfactory, and the development of potent compounds for novel molecular targets is critical. In this framework, proteomics could be a powerful tool in the evaluation of possible candidates for drug intervention. In this work, a two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) approach was employed in T. cruzi epimastigotes (Y strain). Different gel staining protocols (Coomassie Blue, Pro-Q-Diamond and Pro-Q-Emerald) were performed to assess the protein content and possible post-translational modifications of this parasite. Here, 78 most intense spots were identified by Coomassie staining, 22 by Pro-Q-Diamond (phosphoproteins) and 15 by Pro-Q-Emerald (glycoproteins). Compared with the results of other large-scale T. cruzi proteomic studies, 15 novel proteins were identified here using MALDI-TOF/TOF, and 12 of these have not yet been described at the protein level. The predominant localisation and function of the identified proteins was cytosol and protein metabolism, respectively. Regarding the potentially interesting drug targets, 8 proteins presented no similarity to human sequences and promising characteristics for chemotherapy intervention. Our data provides novel insights in the metabolic pathways of T. cruzi, which could aid in the discovery of alternative drugs for Chagas´ disease.

Influence of temperature for the azide displacement in benzodiazepine derivatives: Experimental and DFT study of competing SN1, SN2 and double SN2 reaction pathways

Molecules carrying the azido functionality are widely used as intermediates in medicinal chemistry. Pyrrolobenzodiazepines are molecules with a broad range of interesting pharmacological properties. Due to the wide importance of azido-PBD as a key intermediate in many synthetic pathways, in this work we have investigated the effect of a variety of experimental parameters on the mechanism of nucleophilic substitution reaction for introducing an azide group into the PBD scaffold. This study was carried out by combined experimental and DFT approaches, showing that SN2 and double SN2 pathways are possible and highly dependent on the reaction temperature

Insights into cytochrome bc1 complex binding mode of antimalarial 2-hydroxy-1,4-naphthoquinones through molecular modelling

BACKGROUND Malaria persists as a major public health problem. Atovaquone is a drug that inhibits the respiratory chain of Plasmodium falciparum, but with serious limitations like known resistance, low bioavailability and high plasma protein binding. OBJECTIVES The aim of this work was to perform molecular modelling studies of 2-hydroxy-1,4-naphthoquinones analogues of atovaquone on the Qo site of P. falciparum cytochrome bc1 complex (Pfbc1) to suggest structural modifications that could improve their antimalarial activity. METHODS We have built the homology model of the cytochrome b (CYB) and Rieske iron-sulfur protein (ISP) subunits from Pfbc1 and performed the molecular docking of 41 2-hydroxy-1,4-naphthoquinones with known in vitro antimalarial activity and predicted to act on this target. FINDINGS Results suggest that large hydrophobic R2 substituents may be important for filling the deep hydrophobic Qo site pocket. Moreover, our analysis indicates that the H-donor 2-hydroxyl group may not be crucial for efficient binding and inhibition of Pfbc1 by these atovaquone analogues. The C1 carbonyl group (H-acceptor) is more frequently involved in the important hydrogen bonding interaction with His152 of the Rieske ISP subunit. MAIN CONCLUSIONS Additional interactions involving residues such as Ile258 and residues required for efficient catalysis (e.g., Glu261) could be explored in drug design to avoid development of drug resistance by the parasite