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In silico Structural Modelling of Ribokinase from Salmonella Typhi

Hassana Abubakar, Yakubu Ndatsu, Achimugu Dickson Musa, Cyril Ogbiko, Hamza Boko Usman, Fatima Gogo Mayaki, Audu Mohammed
Published: 24 December 2020
Earthline Journal of Chemical Sciences , Volume 5, pp 191-206; doi:10.34198/ejcs.5121.191206

Abstract: The knowledge of identifiable differences in the metabolism and macromolecular structure between infective agents and their host can be exploited in rational drug design. Ribokinase, an enzyme that plays an important role in the phosphorylation of several metabolites is one of such that can be exploited. This study was therefore aimed at structurally modelling ribokinase from Salmonella Typhi, the causative agent of typhoid fever, with several known multi-drug resistant strains. NCBI BLASTp was carried out against Protein Data Bank (PDB) to run a similarity search. Multiple sequence alignment between the query sequence and the templates was carried out using clustal omega and MEGA6.0 software. The amino acid sequence was submitted to modelling servers. The predicted models from the servers were evaluated with RAMPAGE and superimposed in the template using PyMOL. Model with highest Ramachandran plot score was further validated. BLASTp result showed low identity of (41%) with pyridoxal kinase from Trypanosoma brucei in PDB database. Conserved sequence motifs were confirmed. Template 4X8F was chosen based on its high identity, query cover and appearance in the modeling tools. Swiss model showed best Ramachandran plot score (94.9%). ERRAT analysis showed quality factor: 92.9078 and VERIFY3D server showed that 84.43% of the residues have an average score of 3D/ ID score >=0.2. Superimposition confirmed the alignment of the active site residues having aspartic acid as the catalytic residue. This study can serve as a means for rational drug design for the treatment of typhoid fever.
Keywords: Protein / Treatment / phosphorylation / modelling / design / score / rational / servers / ribokinase / structurally

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