Antistaphylococcal activity of DNA-interactive pyrrolobenzodiazepine (PBD) dimers and PBD-biaryl conjugates

Abstract

ObjectivesPyrrolobenzodiazepine (PBD) dimers, tethered through inert propyldioxy or pentyldioxy linkers, possess potent bactericidal activity against a range of Gram-positive bacteria by virtue of their capacity to cross-link duplex DNA in sequence-selective fashion. Here we attempt to improve the antibacterial activity and cytotoxicity profile of PBD-containing conjugates by extension of dimer linkers and replacement of one PBD unit with phenyl-substituted or benzo-fused heterocycles that facilitate non-covalent interactions with duplex DNA.MethodsDNase I footprinting was used to identify high-affinity DNA binding sites. A staphylococcal gene microarray was used to assess epidemic methicillin-resistant Staphylococcus aureus 16 phenotypes induced by PBD conjugates. Molecular dynamics simulations were employed to investigate the accommodation of compounds within the DNA helix.ResultsIncreasing the length of the linker in PBD dimers led to a progressive reduction in antibacterial activity, but not in their cytotoxic capacity. Complex patterns of DNA binding were noted for extended PBD dimers. Modelling of DNA strand cross-linking by PBD dimers indicated distortion of the helix. A majority (26 of 43) of PBD-biaryl conjugates possessed potent antibacterial activity with little or no helical distortion and a more favourable cytotoxicity profile. Bactericidal activity of PBD-biaryl conjugates was determined by inability to excise covalently bound drug molecules from bacterial duplex DNA.ConclusionsPBD-biaryl conjugates have a superior antibacterial profile compared with PBD dimers such as ELB-21. We have identified six PBD-biaryl conjugates as potential drug development candidates.

From Anthramycin to Pyrrolobenzodiazepine (PBD)‐Containing Antibody–Drug Conjugates (ADCs)

“…Other groups are now developing PBD monomers as stand-alone anticancer agents (particularly as transcription factor inhibitors [7,129] ), and as antibacterial agents. [130] A further interesting development, pioneered by Sanofi S.S. and ImmunoGen Inc, is attachment of the antibody to a PBD dimer-type payload through a substituted aromatic ring in the center of the C8/C8'-linker that joins the two DNA-interactive units together. This has the advantage Figure 22.…”

“…However, ImmunoGen Inc. has spearheaded a resurgence of interest in molecules analogous to PBD monomers by developing a PBD dimer‐type ADC payload (DGN462) with one active N10–C11 imine functionality disabled (i.e., by conversion to a non‐electrophilic secondary amine) resulting in an ADC (i.e., IMGN779) which has just entered the clinic,115 and this promising technology was sub‐licenced by Takeda in late 2015. Other groups are now developing PBD monomers as stand‐alone anticancer agents (particularly as transcription factor inhibitors7, 129), and as antibacterial agents 130. A further interesting development, pioneered by Sanofi S.S. and ImmunoGen Inc, is attachment of the antibody to a PBD dimer‐type payload through a substituted aromatic ring in the center of the C8/C8′‐linker that joins the two DNA‐interactive units together.…”

“…[12] The unique structure of the PBD dimers which contain two alkylating imine functionalities allows them to form interstrand or intrastrand DNA cross-links in addition to mono-alkylated adducts, [14] thus resulting in greater DNA stabilization [10,15] compared to monomeric PBDs. Due to the additional types of DNA adducts possible and the greater adduct stability, the C8-linked PBD dimers generally have significantly greater cytotoxicity, [9] antitumor activity [16] and antibacterial activity [17] compared to PBD monomers, and one such agent, SJG-136, has reached Phase II clinical trials in ovarian cancer and leukaemia. [18] Furthermore, related PBD Julia Mantaj graduated as a pharmacist from the Technical University of Braunschweig (Germany), and then completed her Ph.D. at King's College London with studies on the interaction of DNA minor-groove binding agents with DNA and their effects on gene expression.…”

DNA sequence-selective C8-linked pyrrolobenzodiazepine–heterocyclic polyamide conjugates show anti-tubercular-specific activities

“…[21][22][23] The di-or tri-heterocyclic polyamide 80 chains of 1-12 are comprised of combinations of pyrrole (Py), imidazole (Im) and thiazole (Th) rings 81 known for their ability to modulate the ligands' DNA-binding affinity. 24 C8-linked PBD-polyamide 82 conjugates, unlike PBD dilactams, retain the ability to form covalent DNA-adducts, characteristic 83 responsible for their improved cancer cell cytotoxicity and antibacterial activities, 15 and have a more 84 favourable cytotoxicity profile compared to the PBD dimers. 15,17 85 PBD-conjugates 1-12 were screened against slow-growing Mycobacterium bovis BCG and M. 86 tuberculosis H37Rv and fast-growing Escherichia coli, Pseudomonas putida and Rhodococcus sp.…”

“…24 C8-linked PBD-polyamide 82 conjugates, unlike PBD dilactams, retain the ability to form covalent DNA-adducts, characteristic 83 responsible for their improved cancer cell cytotoxicity and antibacterial activities, 15 and have a more 84 favourable cytotoxicity profile compared to the PBD dimers. 15,17 85 PBD-conjugates 1-12 were screened against slow-growing Mycobacterium bovis BCG and M. 86 tuberculosis H37Rv and fast-growing Escherichia coli, Pseudomonas putida and Rhodococcus sp. and 87 minimum inhibitory concentration values (MIC) were determined.…”