title: DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70.
abstract: DnaK, the bacterial homolog of human Hsp70, plays an important role in pathogens survival under stress conditions, like antibiotic therapies. This chaperone sequesters protein aggregates accumulated in bacteria during antibiotic treatment reducing the effect of the cure. Although different classes of DnaK inhibitors have been already designed, they present low specificity. DnaK is highly conserved in prokaryotes (identity 50-70%), which encourages the development of a unique inhibitor for many different bacterial strains. We used the DnaK of Acinetobacter baumannii as representative for our analysis, since it is one of the most important opportunistic human pathogens, exhibits a significant drug resistance and it has the ability to survive in hospital environments. The E.coli DnaK was also included in the analysis as reference structure due to its wide diffusion. Unfortunately, bacterial DnaK and human Hsp70 have an elevated sequence similarity. Therefore, we performed a differential analysis of DnaK and Hsp70 residues to identify hot spots in bacterial proteins that are not present in the human homolog, with the aim of characterizing the key pharmacological features necessary to design selective inhibitors for DnaK. Different conformations of DnaK and Hsp70 bound to known inhibitor-peptides for DnaK, and ineffective for Hsp70, have been analysed by molecular dynamics simulations to identify residues displaying stable and selective interactions with these peptides. Results achieved in this work show that there are some residues that can be used to build selective inhibitors for DnaK, which should be ineffective for the human Hsp70.
authors.affiliation: Institute of Biomedical Technologies, National Research Council (CNR), Segrate (Mi), Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Chiappori
authors.affiliation: Institute of Biomedical Technologies, National Research Council (CNR), Segrate (Mi), Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fumian
authors.affiliation: Institute of Biomedical Technologies, National Research Council (CNR), Segrate (Mi), Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
authors.affiliation: Institute of Biomedical Technologies, National Research Council (CNR), Segrate (Mi), Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Merelli
mesh_terms: D040981:Acinetobacter baumannii / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry; D018840:HSP70 Heat-Shock Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; D018840:HSP70 Heat-Shock Proteins; C063842:dnaK protein, E coli