A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major

We present an approach for detecting enzymes that are specific of Leishmania major compared with Homo sapiens and provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific for L major compared with H sapiens, only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific of L major and 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with H sapiens. Among the 40 strictly specific enzymes, we identified sterol 24-C-methyltransferase, pyruvate phosphate dikinase, trypanothione synthetase, and RNA-editing ligase as 4 essential enzymes for L major that may serve as targets for drug development.

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Preliminary Characterization of a Ni2+-Activated and Mycothiol-Dependent Glyoxalase I Enzyme from Streptomyces coelicolor

Inorganics ◽

10.3390/inorganics7080099 ◽

2019 ◽

Vol 7 (8) ◽

pp. 99 ◽

Cited By ~ 1

Author(s):

Uthaiwan Suttisansanee ◽

John F. Honek

Keyword(s):

Leishmania Major ◽

Homo Sapiens ◽

Streptomyces Coelicolor ◽

Glyoxalase I ◽

Glyoxalase System ◽

Genetic Studies ◽

Preliminary Characterization ◽

Glyoxalase Ii ◽

Activation Profile

The glyoxalase system consists of two enzymes, glyoxalase I (Glo1) and glyoxalase II (Glo2), and converts a hemithioacetal substrate formed between a cytotoxic alpha-ketoaldehyde, such as methylglyoxal (MG), and an intracellular thiol, such as glutathione, to a non-toxic alpha-hydroxy acid, such as d-lactate, and the regenerated thiol. Two classes of Glo1 have been identified. The first is a Zn2+-activated class and is exemplified by the Homo sapiens Glo1. The second class is a Ni2+-activated enzyme and is exemplified by the Escherichia coli Glo1. Glutathione is the intracellular thiol employed by Glo1 from both these sources. However, many organisms employ other intracellular thiols. These include trypanothione, bacillithiol, and mycothiol. The trypanothione-dependent Glo1 from Leishmania major has been shown to be Ni2+-activated. Genetic studies on Bacillus subtilis and Corynebacterium glutamicum focused on MG resistance have indicated the likely existence of Glo1 enzymes employing bacillithiol or mycothiol respectively, although no protein characterizations have been reported. The current investigation provides a preliminary characterization of an isolated mycothiol-dependent Glo1 from Streptomyces coelicolor. The enzyme has been determined to display a Ni2+-activation profile and indicates that Ni2+-activated Glo1 are indeed widespread in nature regardless of the intracellular thiol employed by an organism.

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AGFusion: annotate and visualize gene fusions

10.1101/080903 ◽

2016 ◽

Cited By ~ 7

Author(s):

Charlie Murphy ◽

Olivier Elemento

Keyword(s):

Fusion Proteins ◽

Homo Sapiens ◽

Domain Architecture ◽

Protein Domain ◽

Gene Fusions ◽

Functional Interpretation ◽

Protein Coding ◽

Link Type ◽

Functional Consequences ◽

Python Package

AbstractSummaryThe discovery of novel gene fusions in tumor samples has rapidly accelerated with the rise of next-generation sequencing. A growing number of tools enable discovery of gene fusions from RNA-seq data. However it is likely that not all gene fusions are driving tumors. Assessing the potential functional consequences of a fusion is critical to understand their driver role. It is also challenging as gene fusions are described by chromosomal breakpoint coordinates that need to be translated into an actual amino acid fusion sequence and predicted domain architecture of the fusion proteins. Currently there are no easy-to-use tools that can automatically reconstruct and visualize fusion proteins from genomic breakpoints. To facilitate the functional interpretation of gene fusions, we developed AGFusion, available as an online web tool that can be readily used by non-computational researchers as well as a python package that can be built into computational pipelines. With minimal input from the user, AGFusion predicts the cDNA, CDS, and protein sequences of all gene fusion products based on all combinations of gene isoforms. For protein coding fusions, AGFusion can annotate and visualize the protein domain architecture. AGFusion currently supports Homo sapiens (genome builds GRCh37 and GRCh38) and Mus musculus (genome build GRCm38) and new genomes can easily be added.AvailabilityAGFusion python package is freely available at https://github.com/murphycj/AGFusion under the MIT license. The AGFusion web app is available at http://agfusion.info

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DHODH hot spots: an underexplored source to guide drug development efforts

Current Topics in Medicinal Chemistry ◽

10.2174/1568026621666210804122320 ◽

2021 ◽

Vol 21 ◽

Author(s):

Thamires Quadros Froes ◽

Maria Cristina Nonato ◽

Marcelo Santos Castilho ◽

Luana Carlos Campisano Zapata ◽

Juliana Sayuri Akamine

Keyword(s):

Drug Development ◽

Hot Spots ◽

Hot Spot ◽

Functional Characterization ◽

Protein Structures ◽

Docking Studies ◽

Dihydroorotate Dehydrogenase ◽

Review Reports ◽

First Time

Background: Dihydroorotate dehydrogenase (DHODH) has long been recognized as an important drug target for proliferative and parasitic diseases, including compounds that exhibit trypanocidal action and broad-spectrum antiviral activity. Despite numerous and successful efforts in structural and functional characterization of DHODHs, as well as in the development of inhibitors, DHODH hot spots remain largely unmapped and underexplored. Objective: This review describes the tools that are currently available for the identification and characterization of hot spots in protein structures and how freely available webservers can be exploited to predict DHODH hot spots. Moreover, it provides for the first time a review of the antiviral properties of DHODH inhibitors. Method: X-ray structures from human (HsDHODH) and Trypanosoma cruzi DHODH (TcDHODH) had their hot spots predicted by both FTMap and Fragment Hotspot Maps web servers. Result: FTMap showed that hot spot occupancy in HsDHODH is correlated with the ligand efficiency (LE) of its known inhibitors, and Fragment Hotspot Maps pointed out the contribution of selected moieties to the overall LE. The conformational flexibility of the active site loop in TcDHODH was found to have a major impact on the druggability of the orotate binding site. In addition, both FTMap and Fragment Hotspot Maps servers predict a novel pocket in TcDHODH dimer interface (S6 site). Conclusion: This review reports how hot spots can be exploited during hit-to-lead steps, docking studies or even to improve inhibitor binding profile and by doing so using DHODH as a model, points to new drug development opportunities.

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DAVI: a tool for clustering and visualising protein domain architectures

10.1101/2021.09.24.461671 ◽

2021 ◽

Author(s):

Nathan Jawadi Chadi ◽

Paul Saighi ◽

Fabio Rocha Jimenez Vieira ◽

Juliana Silva Bernardes

Keyword(s):

Domain Architecture ◽

Protein Sequences ◽

Protein Domain ◽

Computational Approaches ◽

Prediction Tools ◽

Protein Functions ◽

Visualization Tools ◽

Protein Domain Architecture ◽

User Friendly

The characterization of protein functions is one of the main challenges in bioinformatics. Proteins are often composed of individual units termed domains, motifs that can evolve independently. The domain architecture of a given protein is the particular order and the content of its numerous domains. Some computational approaches predict the most likely domain architecture for a set of proteins. However, a few numbers of visualization tools exist, and most of them are unavailable. Here we present DAVI, an efficient and user-friendly web server for protein domain architecture clustering and visualization. DAVI accepts the output of most used domain architecture prediction tools and also produces domain architectures for a set of protein sequences. It provides a rich visualization for comparing, analyzing, and visualizing domain architectures.

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Purification and characterization of a novel and conserved TPR-domain protein that binds both Hsp90 and Hsp70 and is expressed in all developmental stages of Leishmania major

Biochimie ◽

10.1016/j.biochi.2020.12.017 ◽

2021 ◽

Author(s):

Sara A. Araujo ◽

Gustavo H. Martins ◽

Natália G. Quel ◽

Annelize Z.B. Aragão ◽

Edna G.O. Morea ◽

...

Keyword(s):

Leishmania Major ◽

Developmental Stages ◽

Purification And Characterization ◽

Domain Protein ◽

Tpr Domain

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Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

BMC Plant Biology ◽

10.1186/s12870-021-02989-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haifeng Yan ◽

Huiwen Zhou ◽

Hanmin Luo ◽

Yegeng Fan ◽

Zhongfeng Zhou ◽

...

Keyword(s):

Carbon Fixation ◽

Developmental Stages ◽

Genomic Data ◽

Saccharum Officinarum ◽

Full Length ◽

Rna Seq ◽

Pyruvate Phosphate Dikinase ◽

Sugarcane Yield ◽

Tiller Bud

Abstract Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

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Characterization and selective inhibition of myristoyl-CoA:protein N-myristoyltransferase from Trypanosoma brucei and Leishmania major

Biochemical Journal ◽

10.1042/bj20051886 ◽

2006 ◽

Vol 396 (2) ◽

pp. 277-285 ◽

Cited By ~ 46

Author(s):

Chrysoula Panethymitaki ◽

Paul W. Bowyer ◽

Helen P. Price ◽

Robin J. Leatherbarrow ◽

Katherine A. Brown ◽

...

Keyword(s):

Trypanosoma Brucei ◽

Leishmania Major ◽

Homo Sapiens ◽

Selective Inhibition ◽

Fungal Species ◽

Chemotherapeutic Agents ◽

Human Pathogens ◽

Ic50 Values

The eukaryotic enzyme NMT (myristoyl-CoA:protein N-myristoyltransferase) has been characterized in a range of species from Saccharomyces cerevisiae to Homo sapiens. NMT is essential for viability in a number of human pathogens, including the fungi Candida albicans and Cryptococcus neoformans, and the parasitic protozoa Leishmania major and Trypanosoma brucei. We have purified the Leishmania and T. brucei NMTs as active recombinant proteins and carried out kinetic analyses with their essential fatty acid donor, myristoyl-CoA and specific peptide substrates. A number of inhibitory compounds that target NMT in fungal species have been tested against the parasite enzymes in vitro and against live parasites in vivo. Two of these compounds inhibit TbNMT with IC50 values of <1 μM and are also active against mammalian parasite stages, with ED50 (the effective dose that allows 50% cell growth) values of 16–66 μM and low toxicity to murine macrophages. These results suggest that targeting NMT could be a valid approach for the development of chemotherapeutic agents against infectious diseases including African sleeping sickness and Nagana.

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