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Natural products and their cellular targets: A multidisciplinary strategy for antibacterial drug discovery

Final Report Summary - ANTIBACTERIALS (Natural products and their cellular targets: A multidisciplinary strategy for antibacterial drug discovery)

Pathogenic bacteria such as Staphylococcus aureus cause devastating infectious diseases which were effectively treated by antibiotics for a long time. However, the occurrence of multiresistant clinical isolates (MRSA) now represents a major challenge for modern medicine. In the past, natural products have been a rich source of privileged antibiotic lead structures that address a limited set of cellular targets including cell-wall biosynthesis, protein biosynthesis and DNA replication. With constant exposure to natural product antibiotics bacteria have evolved efficient strategies to overcome selective pressure e.g. by modifying the corresponding targets and deactivating the most effective anti-infective drugs. After the golden age of antibiotics in the 1960s and 1970s not many new compounds have been identified and frequent re-discoveries of alredy known natural products occurred.
In this research project we developed a multidisciplinary strategy aiming to overcome some of the limitations that impede current antibiotic drug discovery. We implemented a chemical-proteomic strategy that utilizes natural products as source and inspiration for novel antibacterial compounds. In order to obtain new natural product scaffolds we devised small molecule tool compounds that selectively capture a subclass of natural products with pre-validated antibacterial bioactivity. We synthesized a set of capture molecules and tested them in extracts of microorganisms. Our tools indeed streamlined the discovery process by enhancing the detection of low abundant natural products. We hope that this methodology will be inspiration for other researchers in the field of natural product isolation to further adjust the methodology for the identification of new antibiotic entities. In addition, we introduced alpha-pyrones, a common structural motif of many natural products, as photoreactive entities that covalently interact with their target proteins upon irradiation with UV-light. This intrinsic reactivity represents an attractive alternative to the use of bulky photocrosslinkers for a selected natural product subclass.
As the target scope of currently applied antibiotics is narrow an additional aim of this research was the identification of unprecedented and resistance-free bacterial targets involved in major pathogenesis pathways. We therefore identified a panel of already known natural products with privileged electrophilc scaffolds and utilized our proteome profiling platform to unravel their cellular mode of action. Among those were several virulence-associated proteins such as the transcriptional activators SarA and SarR and the manganese transporter MntC. The molecules exhibited potent bioactivities and were able to reduce the production of S. aureus and MRSA toxins. In case of the manganese transport inhibitor we demonstrated even suitable pharmacological properties enabling further pre-clinical testing. In the course of these studies we analyzed the mode of action of several natural products and in some case made surprising observations that contradicted previous knowledge. In case of duocarmycins and fimbrolides unprecedented targets could be identified that revise their mode of action and consolidate previous contradictory reports, respectively. This inventory of natural product targets enables their exploitations for inhibitor development in future studies and thus represents a major outcome of this research project.