Primed for Discovery

Abstract

Antibiotics are essential components of current medical practice, but their effectiveness is being eroded by the increasing emergence of antimicrobial-resistant infections. At the same time, the rate of antibiotic discovery has slowed, and our future ability to treat infections is threatened. Among Christopher T. Walsh's many contributions to science was his early recognition of this threat and the potential of biosynthesis─genes and mechanisms─to contribute solutions. Here, we revisit a 2006 review by Walsh and co-workers that highlighted a major challenge in antibiotic natural product discovery: the daunting odds for identifying new naturally occurring antibiotics. The review described strategies to mitigate the odds challenge. These strategies have been used extensively by the natural product discovery community in the years since and have resulted in some promising discoveries. Despite these advances, the rarity of novel antibiotic natural products remains a barrier to discovery. We compare the challenge of discovering natural product antibiotics to the process of identifying new prime numbers, which are also challenging to find and an essential, if underappreciated, element of modern life. We propose that inclusion of filters for functional compounds early in the discovery pipeline is key to natural product antibiotic discovery, review some recent advances that enable this, and discuss some remaining challenges that need to be addressed to make antibiotic discovery sustainable in the future.

Keywords: Antibiotic discovery; Antimicrobial resistance; Discovery pipeline; Functional compounds; Natural products; Phenotypic screens.

Figure 1

Antibiotic frequency and timeline of discovery. The estimated frequency of antibiotics among Streptomyces is plotted on the top of the image on a base ten logarithmic scale; for actinomycin and chloramphenicol, only a range was reported, so the positions of those antibiotics within the range are arbitrary. The lower part of the image shows the corresponding year of discovery plotted on a linear scale.