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.

Role and mechanism of the Hsp70 molecular chaperone machines in bacterial pathogens

“…The DnaK machinery is involved in the antibiotic-resistant mechanism of A. baumannii under stress conditions [45]. S. aureus DnaK mutants showed reduced viability and increased susceptibility under stressed conditions in a host during systemic infection [46].…”

Screening of Neem extracts for microbial anti-chaperone activity by employing in vitro enzyme refolding assay

“…Rajan et al (2014) modeled and characterized Hsp60 from Chlamydophila pneumoniae as drug target. In silico identification of hot spots for inhibition of DnaK (Hsp70) which is involved in the pathogenicity and antibiotic resistance of Acitnectobacter baumannii has been recently reported (Chiappori et al 2015). However, not many studies have been reported on the analysis of therapeutic potential of Hsp/chaperone inhibitors in microbial infections.…”

Dual-targeting GroEL/ES chaperonin and protein tyrosine phosphatase B (PtpB) inhibitors: A polypharmacology strategy for treating Mycobacterium tuberculosis infections

“…While some compounds were nearly equipotent between the two chaperonin systems, many exhibited selectivity towards E. coli GroEL/ES. We previously noted this SAR for the pseudosymmetric (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) and R-series asymmetric full molecules (16R-34R), demonstrating that it is possible to tune this scaffold to selectively target GroEL/ES. 43,44 However, as noted above, this may be inconsequential for cytotoxicity purposes as the mitochondrial membrane is highly impermeable to penetration by small molecules, and thus inhibitors may never reach HSP60/10 in the mitochondrial matrix.…”

“…A new paradigm in antibiotic research is to exploit protein homeostasis pathways, such as targeting molecular chaperones. [12][13][14][15][16][17][18][19][20][21][22][23][24] A network of molecular chaperones and proteases collectively functions to maintain protein homeostasis by assisting proteins to fold to their native, functional states, or ensuring their proper degradation. [25][26][27][28][29][30][31] In particular, all organisms contain at least one homolog of the 60 kDa class of molecular chaperone (HSP60) that is essential under all conditions.…”