Comparison of Proteomic Responses as Global Approach to Antibiotic Mechanism of Action Elucidation

Abstract

New antibiotics are urgently needed to address the mounting resistance challenge. In early drug discovery one of the bottlenecks is the elucidation of targets and mechanisms. To accelerate antibiotic research, we provide a proteomic approach for the rapid classification of compounds into those with precedented and unprecedented modes of action. We established a proteomic response library of Bacillus subtilis covering 91 antibiotics and comparator compounds, and a mathematical approach was developed to aid data analysis. The Comparison of Proteomic Responses (CoPR) allows the rapid identification of antibiotics with dual mechanisms of action as shown for atypical tetracyclines. It also aids in generating hypotheses on mechanisms of action as presented for salvarsan (arsphenamine) and the antirheumatic agent auranofin, which is under consideration for repurposing. Proteomic profiling also provides insights into the impact of antibiotics on bacterial physiology through analysis of marker proteins indicative of the impairment of cellular processes and structures. As demonstrated for trans-translation, a promising target not yet exploited clinically, proteomic profiling supports chemical biology approaches to investigating bacterial physiology.

A flat embedding method for transmission electron microscopy reveals an unknown mechanism of tetracycline

“…It has been shown that chelocardin, another member of the tetracycline group of antibiotics, inhibits translation but at higher concentrations also causes membrane stress 53 . Very recently, a similar observation was made for anhydrotetracycline 54 . Both compounds are often referred to as "atypical tetracyclines", which are characterized by being bactericidal.…”

Influence of the ABC Transporter YtrBCDEF of Bacillus subtilis on Competence, Biofilm Formation and Cell Wall Thickness

“…Based on its expression pattern, the ytr operon was described as a reporter for glycopeptide antibiotics, such as vancomycin or ristocetin (Hutter et al, 2004) and antibiotics that interfere with the lipid II cycle, such as nisin (Wenzel et al, 2012). Whether this induction of ytrGABCDEF expression leads to an increased resistance toward those antibiotics is not clear, but recent results indicate that it has indeed an impact on nisin resistance (Senges et al, 2021). Interestingly, the substrate binding lipoprotein YtrF contains a MacB-like periplasmic core domain in its N-terminus.…”

The current state of SubtiWiki, the database for the model organism Bacillus subtilis

“…Furthermore, we have added a large set of protein expression information. This information is based on a large-scale study that sought to compare proteomic responses to 91 different antibiotics and comparator compounds in an attempt to elucidate antibacterial modes of action ( 19 ). To supplement this representation, we also provide the possibility to download the entire dataset under the new Downloads section ( http://www.subtiwiki.uni-goettingen.de/v4/download ).…”