CORDIS - EU research results

Synthetic biology approach for the design of new-to-nature peptide-based antibiotic molecules

Final Report Summary - PTM-FLEX (Synthetic biology approach for the design of new-to-nature peptide-based antibiotic molecules)

Antibiotic resistance poses a grave threat to public health, and threatens to undo most of the remarkable progress we have made in modern medicine. The drugs that made its very successful implementation possible by suppressing and eliminating bacterial infection are becoming increasingly ineffective. Neither surgery, nor chemotherapy or skin transplantation for example, could be achieved without the use of anti-infective agents.
Contrary to surprisingly widespread popular belief, resistance to antibiotics is not acquired by the human body, but by the bacteria themselves. Resistance factors are frequently carried on mobile genetic elements that can be passed with ease between bacteria, even of different species, and can thus spread rapidly. Moreover, microorganisms can acquire resistance to multiple classes of antibiotics concurrently, resulting in “multidrug-resistant” pathogens. Weakened patients are at risk in hospital settings, but community-acquired antibiotic resistance is emerging as an epidemic in many urban areas, affecting healthy individuals equally. Unchecked, it might lead us back to a pre-antibiotic age, where a single scratch could result in fatal infection. To date, more than 700’000 people per year die world-wide because tried and trusted antibiotic medication no longer works. According to the World Health Organization (WHO), this number could increase to 10 million by 2050 if no action is taken. Increased healthcare costs and an increased economic burden for patients’ families and society are additional consequences.
New resistance mechanisms emerge constantly and spread globally. In the first quarter of 2016 the news was all about the discovery that resistance to colistin, a last-resort antibiotic that is deployed when nothing else works against multidrug-resistant bacteria, is not only being passed on as a transferable gene in the human pathogen E. coli as well as other human pathogens, but is moreover already found all over Europe, Asia and for the first time now also in the USA. The need for novel antibiotics is obvious and urgent.

With the Marie Curie IEF-project PTM-FLEX I sought to develop new-to-nature peptide-based antibiotics with strong antimicrobial activity, using a highly innovative synthetic biology approach. Natural products, antibiotics are only one example thereof, have played key roles over the past century in advancing our understanding of biology and in the progress of medicine. One of the major classes are ribosomally synthesized and post-translationally modified peptides (RiPPs). RiPPs are DNA encoded, translated from mRNA at the ribosome into precursor peptides, and subsequently processed by one or more enzymes of the post-translational modification (PTM) machinery to endow them with features such as increased stability, molecular target specificity and expanded functionality. Different RiPPs have different modes of antibiotic action, such as inhibition of cell division or membrane permeabilization. Different PTM enzymes each catalyze a particular variety of modification, such as introduction of lanthionine rings or epimerization. Most PTM enzymes requires a unique “access code” in form of a leader peptide on the ribosomally translated peptide precursor in order to exert their precise and specific function.
PTM-FLEX proposes to combine RiPP precursor peptides with different access codes and different PTM enzymes, to create novel peptides with antibiotic function that nature has not seen before. Therewith, PTM-FLEX addresses several of the issues present with traditional approaches such as molecule mining and scaffold modification. For one, new-to-nature molecules will likely not encounter corresponding resistance genes in nature, as they attempt to circumvent co-evolution. Secondly, the implementation of a modular ‘plug-and-play’ system based on post-translational modification of peptide scaffolds affords the exploration of a vast combinatorial space. Thirdly, the nature of a RiPP and its enzyme catalyzed chemical modifications are encoded by precise and known genetic information, which is essential for lead optimization. Established in an E. coli expression platform, promising RiPP producer strains can directly be isolated and characterized. Furthermore, the heart of the project encompasses a high-throughput screening method, which allows for analysis a large number of putative antibiotic producers per day.