Bioinformatics of thymidine metabolism in Trypanosoma evansi: exploring nucleoside deoxyribosyltransferase (NDRT) as a drug target

Abstract

Decoding camel (Camelus genus) genome sequences (Jirimutu et al., 2012) will accelerate drug discovery studies against camel pathogens. One specific line of inquiry is investigating pyrimidine metabolic pathways, and finding unique differences in structure, function, sequence, or phylogeny associated with these pathways could contribute to identifying new drug targets. KEGG maps have been used (Ogata et al., 1998;Kanehisa et al., 2007;Kanehisa et al., 2016) to compare the enzymes involved in thymidine metabolism pathways in camels and T. evansi.In this work, comprehensive bioinformatic tools were used to investigate enzyme sequences in camels and T. evansi and compare their domains and motif content, searching for similar proteins and identifying their phylogenetic relationships. We plotted the pathway of thymidine metabolism in the two organisms, providing bioinformatics evidence of unique differences between camels and T. evansi that could be exploited for future drug discovery processes. MATERIALS AND METHODS Construction of the metabolic mapThe Kyoto Encyclopedia of Genes and Genomes (KEGG) website was used to retrieve the thymidine pathway maps.The map was accessed at the following link (https:// www.genome.jp/kegg-bin/show_pathway?map00240). The structure of nucleotides and the pathways were written by ChemDraw software (Figure 1). Retrieval of protein sequencesThe NCBI protein database was used to obtain the sequences of camel enzymes (http://www.ncbi.nlm.nih.gov/protein), and the T. evansi protein sequences were retrieved from the Kinetoplastom genome project (http://tritrypdb.org/tritrypdb). The sequence files in FASTA format were stored and processed by multiple software programs, including the CLC main workbench, Geneious, and Genedoc. The accession numbers of the retrieved sequences are provided in Figures 2-5. Basic local alignment search tool (BLAST)A BLAST search was performed using the NCBI search engine (Madden, 2013). The BLAST tool was used to find orthologues with high similarity to the retrieved sequences by searching a database of non-redundant (nr) protein sequences using the default settings. The retrieved camel and T. evansi sequences were input into the protein BLAST server at ( h t t p s : / / b l a s t . n c b i . n l m . n i h . g o v / B l a s t . c g i ? P R O G R A M =blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) using the FASTA sequences and searching the nr protein