Synthesis and biological activity of novel bis-indole inhibitors of bacterial transcription initiation complex formation

Abstract

The increasing resistance of bacteria against clinically approved antibiotics is resulting in an alarming decrease in therapeutic options for today's clinicians. We have targeted the essential interaction between bacterial RNA polymerase and σ(70)/σ(A) for the development of lead molecules exhibiting a novel mechanism of antibacterial activity. Several classes of structurally related bis-indole inhibitors of bacterial transcription initiation complex formation were synthesized and their antimicrobial activities were evaluated. Condensation of indole-7- and indole-2-carbohydrazides with 7- and 2-trichloroacetylindoles or indole-7- and indole-2-glyoxyloyl chlorides resulted in the successful synthesis of 7,7'-, 2,2'-, 2,7'- and 3,2'-linked bis-indole derivatives with -CO-NH-NH-CO- and -CO-CO-NH-NH-CO- linkers. Indole-7-glyoxyloyl chlorides were reacted with hydrazine hydrate in different ratios to afford respective -CO-CO-NH-NH-CO-CO- bis-indole or hydrazide derivatives. The resulting compounds were found to be active against the β'-CH-σ(70)/σ interaction in ELISA assays and inhibited the growth of both Gram-positive and Gram-negative bacteria. Structure-activity relationship (SAR) studies were performed in order to identify the structural features of the synthesized inhibitors required for biological activity.

Identification of inhibitors of bacterial RNA polymerase

“…Screening an in-house indole-based peptidomimetic library (N. Kumar, UNSW, Australia) we selected just 9 compounds for further screening of which 5 showed the ability to inhibit HE formation. Although the majority of the peptidomimetic compounds in the in-house library presented here had molecular weights >500 one of the compounds identified in this screen, GKL003, showed excellent in vitro activity [19], and has been derivatised extensively to explore its potential as a future lead molecule [21][22][23].…”

“…When testing compounds for their ability to inhibit the r-b 0 CH interaction, ELISAs were performed as above except the GST tagged wild-type CH-domain fragment (200 nM) was pre-mixed with 15 lM of the test compound at 37°C for 15 min before being added into the r A coated wells [21][22][23]. Compounds showing good levels of inhibition were further tested at a range of concentrations to determine preliminary K i values (Fig.…”

Discovery of 4,6‐bis(2‐((E)‐benzylidene)hydrazinyl)pyrimidin‐2‐Amine with Antibiotic Activity

“…Our critical reliance on antibiotics has engendered government initiatives and global strategies to rejuvenate the antibiotic pipeline, such as the Combating Antibiotic Resistant Bacteria Biopharmaceutical Accelerator (CARB‐X) initiative and “The 10×20 Initiative” seek to combat this crisis and has the ambitious target of ten new antibacterial drugs by 2020 . Whilst these ambitious targets have stimulated a resurgence in antibacterial research at the academic level, this research has failed to translate into new antibiotics with novel mechanisms of action . Of particular concern is the lack of efficacious compounds which treat Gram‐negative bacteria, owing to the poor drug penetration of the outer membrane and the efficient efflux systems widespread within this group of microbes, making these pathogens extremely challenging to treat .…”

Bacterial Transcription as a Target for Antibacterial Drug Development

“…Despite having excellent activity in vitro, GKL003 had poor activity against live cultures of bacteria, probably due to its low solubility in aqueous media and inability to cross bacterial membranes. Nevertheless, it did exhibit broad-spectrum antibacterial activity at high concentrations and has been extensively derivatized to establish structure-activity relationships (181)(182)(183). Determination of the structures of GKL compounds in complex with RNAP will be important for their continued development.…”