The molecular basis of the action of the antibiotic simocyclinone D8 on DNA gyrase

Lead Research Organisation: John Innes Centre
Department Name: Biological Chemistry


Antibiotics are drugs used to treat infections caused by bacteria. Most antibiotics are natural products and many of these are derived originally from soil bacteria (called Actinomycetes). Although antibiotics have generally been very successful over the last 40 years or so, recent years have seen the emergence of antibiotic-resistant bacteria (the so-called 'Superbugs'). These include MRSA (methicillin-resistant Staphylococcus aureus) and C. difficule, which have led to significant concern, particularly in UK hospitals. Unfortunately fewer new antibiotics are coming on the market, raising the prospect of untreatable bacteria diseases in the future. Simocyclinone D8 is a relatively recently discovered antibiotic that is not currently in clinical use. We have been able to show that it targets an enzyme in bacteria (DNA gyrase) by a novel mechanism. We aim to understand this mechanism of action in detail in order to reveal principles of drug-target interaction that will be applicable to other systems. We anticipate that this knowledge will provide information that will be used, particularly in the pharmaceutical industry, in the design of more-potent, more-specific antibiotics that will avoid the resistance problems that we are currently encountering.

Technical Summary

DNA topoisomerases are very effective targets for antibiotics and anti-cancer agents; DNA gyrase in particular has proved to be very successful as a target for antibacterials, such as the fluoroquinolone ciprofloxacin. However, the emergence of quinolone resistance has rendered these compounds less effective and therefore we need to search for new ways of targeting DNA gyrase. Natural products are a rich source of antibiotics, e.g. aminocoumarins, which are excellent inhibitors of gyrase. The discovery of simocyclinone D8 (SD8), an aminocoumarin antibiotic with an entirely different mode of action on gyrase, means we can explore new ways of targeting this enzyme. We have recently determined the crystal structure SD8 bound to the A subunit of gyrase; this structure has revealed several novel features: 1. All the other aminocoumarin drugs (such as novobiocin and clorobiocin) bind to the ATPase domain of the gyrase B protein, but SD8 binds to the DNA-binding domain of GyrA. 2. SD8 has two ends: an aminocoumarin end (AC) and a polyketide end (PK). Both ends bind to the target (GyrA) with the two binding pockets lying close together on the protein. The crystal structure shows that 4 SD8 molecules cross-link two GyrA dimers with the AC moiety of one drug molecule bound to one dimer and the PK moiety bound to the other. 3. Although the crystal structure shows SD8 cross-linking two GyrA dimers, biophysical data support a model in which a single SD8 molecule can bind to both pockets (AC and PK) within the same monomer in a 'bent-over' conformation. 4. Mass spec and CD data indicate that cooperativity may be a feature of the interaction of SD8 with gyrase. Using X-ray crystallography and a range of biophysical/biochemical techniques we are now in a position to explore these features and obtain a fundamental understanding of the interaction of SD8 with its target.

Planned Impact

Who will benefit? 1. Academic researchers in the areas of ligand-protein interaction, inhibitor design and topoisomerase research (see Academic Beneficiaries). 2. Pharmaceutical companies involved in antibacterial drug discovery (e.g. Pfizer, AstraZeneca, GSK). 3. UK government in terms of showing that investment is being channelled into areas that will underpin future drug discovery. 4. Charities concerned with the threat of third-world diseases (e.g. tuberculosis). 5. For the general public, the work offers hope for potential new treatments for infectious diseases. How will they benefit? a. Improved understanding of ligand-target interactions. b. New ideas for drug discovery. c. Evaluation of the potential of simocyclinones as future candidates for drug development. What will be done to ensure that they have the opportunity to benefit from this research? i. Publication in high-profile journals. ii. Media involvement via JIC TOC Comms. iii. Collaborations with UK and overseas partners (industrial and academic). iv. Investigation of exploitation potential via PBL. v. Establishment of BBSRC-CASE studentships based on work stimulated by this project. vi. Continued engagement with local schools.
Description We have established the molecular basis of the action of a new group of antibiotics, the simocyclinones, and made a large number of new derivatives and evaluated them. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), reveal fascinating insight into how molecular recognition is achieved. This knowledge gives both generic understanding of ligand-protein interactions and specific information that we and others can use to make new antibiotics.
Exploitation Route Others will be able to design new antibiotics based on our findings, either in commercial or academic sectors.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

Description Our findings have informed others about the possibility of exploiting this new mechanism of antibiotic action.
First Year Of Impact 2014
Sector Pharmaceuticals and Medical Biotechnology
Impact Types Policy & public services

Description London International Youth Forum 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact • Aug 2017 - lecture to students visiting as part of London International Youth Science Form: 'Where will the new antibiotics come from?'
Year(s) Of Engagement Activity 2017