Biopolym. Cell. 2022; 38(3):186-194.
http://dx.doi.org/10.7124/bc.000A7A
Bioinformatics
Identification of potential novel membrane drug targets of Acinetobacter baumannii ATCC 19606 using subtractive proteomics approach
1Shmatkov M. V., 2, 3Volynets G. P., 2Bdzhola V. G., 2, 3Matiushok V. I., 2Chubukov O. M., 2Yarmoluk S. M.
  1. Institute of High Technologies,
    Taras Shevchenko National University of Kyiv
    2, korp.5, Pr. Akademika Hlushkova, Kyiv, Ukraine, 03022
  2. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143
  3. LLC "Scientific and service firm "Otava"
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143

Abstract

Aim. To identify the potential novel membrane drug targets of Acinetobacter baumannii ATCC 19606. Methods. Clustering of paralogues was performed by USEARCH software, the identification of essential non-homologous proteins to the human proteome was done with BLASTp and Database of essential genes, determination of proteins from unique metabolic pathways was carried out using KAAS server at KEGG. The drug target novelty was estimated with DrugBank. The sub-cellular localization of the proteins was predicted with PSORTb v. 3.0.3, CELLO v. 2.5 and BUSCA. Tertiary structures of proteins were built with trRosetta and 3D models quality was analyzed using MolProbity server. The potential binding sites were predicted with PrankWeb, BIOVIA Discovery studio 2021 visualizer and Caver analyst 2.0. Results. Six potential novel membrane drug targets were identified within the Acinetobacter baumannii ATCC 19606 proteome such as rod shape-determining protein RodA, DedA family protein, undecaprenyl-diphosphate phosphatase, putative lipid II flippase FtsW, prolipoprotein diacylglyceryl transferase, apolipoprotein N-acyltransferase. Tertiary structures of the proteins were built and ligand-binding sites were predicted. Conclusions. The identified potential novel mem-brane-associated drug targets of Acinetobacter baumannii ATCC 19606 can be useful for further drug development in order to find novel treatments of the infectious diseases caused by Acinetobacter baumannii.
Keywords: Acinetobacter baumannii, subtractive proteomics, drug targets, membrane proteins
Full text: (PDF, in English)

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