The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus

Abstract

ObjectivesThe antistaphylococcal pyrrolobenzodiazepine dimer ELB-21 forms multiple adducts with duplex DNA through covalent interactions with appropriately spaced guanine residues; it is now known to form interstrand and intrastrand adducts with oligonucleotide sequences of variable length. We determined the DNA sequence preferences of ELB-21 in relation to its capacity to exert a bactericidal effect by damaging DNA.MethodsFormation of adducts by ELB-21 and 12- to 14-mer DNA duplexes was investigated using ion-pair reversed phase liquid chromatography and mass spectrometry. Drug-induced changes in gene expression were measured in prophage-free Staphylococcus aureus RN4220 by microarray analysis.ResultsELB-21 preferentially formed intrastrand adducts with guanines separated by three nucleotide base pairs. Interstrand and intrastrand adducts were formed with duplexes both longer and shorter than the preferred target sequences. ELB-21 elicited rapid bactericidal effects against prophage-carrying and prophage-free S. aureus strains; cell lysis occurred following activation and release of resident prophages. Killing appeared to be due to irreparable damage to bacterial DNA and susceptibility to ELB-21 was governed by the capacity of staphylococci to repair DNA lesions through induction of the SOS DNA damage response mediated by the RecA-LexA pathway.ConclusionsThe data support the contention that ELB-21 arrests DNA replication, eliciting formation of ssDNA-RecA filaments that inactivate LexA, the SOS repressor, and phage repressors such as Cl, resulting in activation of the DNA damage response and de-repression of resident prophages. Above the MIC threshold, DNA repair is ineffective.

DNA Targeting as a Likely Mechanism Underlying the Antibacterial Activity of Synthetic Bis-Indole Antibiotics

“…the SOS response, a stress response that is induced by the presence of single-stranded DNA resulting from DNA damage (40), or certain conditions that inhibit DNA replication (41)(42)(43). To examine this possibility, we measured the induction of the SOS response in E. coli and S. aureus cells that were exposed to bis-indoles.…”

Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site

“…For example, the DNA minor groove continues to be an important target for the development of anti-cancer (1–5,15), anti-microbial and anti-viral compounds (6–9,12,14). Minor groove binders also have a number of other properties, such as inhibition, as well as activation of transcription that have provided fundamental new information on gene expression with the potential for development of entirely new and highly specific methods of disease treatment (4–6,16–18).…”

DNA as a target for antimicrobials

“…for testing as an antitumour compound [58]. Some clinical data on toxicity of this compound are thus available, suggesting that PDB dimers are effective at concentrations below the toxicity threshold [57]. A further development of the PBD dimers are PBD-biaryl conjugates; some of these also have excellent antimicrobial activity and, importantly, initial results indicate that these compounds are well tolerated in mice and that therefore their therapeutic index is much better than that of the PBD dimers [58].…”