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Protein model built through molecular modeling by homology of a potential target of anti-leishmania drugs
Published: 06 December 2017 by MDPI AG in MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition in MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition
MDPI AG, 10.3390/mol2net-03-05062

Molecular modeling by homology is a methodology widely used for the construction of protein structures that have not yet been crystallized. The constructed models can be used for the identification of inhibitors, representing a great method for the rational planning of drugs. Thus, the objective of the study was to construct the three-dimensional model of the protein structure of the enzyme Pteridine reductase 1 from Leishmania donovani (LdPTR1). PTR1 is an enzyme used in the metabolism of pterin from GTP, being considered an excellent specific target of drugs of Leishmania. The target protein and template sequences were obtained from the National Center for Biotechnology Information database and the 3D template structures through the Protein Data Bank (PDB). Sequence alignment was performed on the FASTA, yielding 91.0% identity and 97.2% similarity to the Leishmania major template protein (LmPtr1). The LdPtr1 model was constructed using MODELLER software 9.18. The stereochemical quality was evaluated in PROCHECK and the structural quality in VERIFY 3D and WHAT IF software. The Discovery Studio Visualizer software was used for graphical visualization of the modeled protein. Due to the high level of identity and similarity of the target enzymes and template, the results revealed that a good model was constructed. The Ramachandran graph showed that the conformations of the main chain of amino acids are in allowed and favored regions. Besides that; 85.07% of the residues have the protein sequence compatible with their 3D structure and do not have unusual atomic contacts.

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