Novel hybrid anti-MRSA antibiotics from manipulation of the mupirocin and thiomarinol biosynthetic pathways

Lead Research Organisation: University of Bristol
Department Name: Chemistry

Abstract

For centuries mankind has used natural products in crude extracts from plants and fungi as well as in purified form as remedies to cure disease. Many such compounds have become house-hold names e.g. the penicillin antibiotics which kill bacteria. Natural products and their derivatives are still vitally important, representing a large proportion of drugs currently on the market. Understanding of how they are made in nature (biosynthesis) opens new opportunities in drug development. Polyketides, an important class of natural products, exhibit huge diversity of structures and biological activities e.g. antibacterial, antifungal and anticancer. Mupirocin, a mixture of four pseudomonic acids (PAs) isolated from the bacterium Pseudomonas fluorescens, is an example of a polyketide with an intriguing biosynthetic pathway. It is clinically important, being active against MRSA (methicillin resistant Staphylococcus aureus), but is only used topically due to its instability. In an adventurous interdisciplinary programme involving microbial molecular genetics, biochemistry and chemistry we have learnt much about PA biosynthesis which has many intriguing features but requires further study for a full understanding. In our new programme we aim to create new hybrids between molecules with proven biological activity to increase the chance of developing new antibiotics that can overcome problems associated with resistance. The thiomarinol family of antibacterial compounds produced naturally by marine bacteria consists of two elements: one, a PA is similar (but not identical) to mupirocin; the other is like the core of a less well understood compound, holomycin (more generically called pyrrothine). Our recent studies confirm that the genes responsible for making thiomarinol resemble both those for mupirocin in the bacterium Pseudomonas fluorescens and an as yet un-characterised gene cluster from the filamentous bacterium Streptomyces clavuligerus which we can now assign to holomycin biosynthesis. From this new gene cluster we can deduce that holomycin is produced by an unusual form of a protein factory called a non-ribosomal peptide synthetase and starts by joining two molecules of the amino acid cysteine. We have shown that both elements of thiomarinol are made separately and then linked together. Using mutants we can join holomycin to mupirocin itself allowing it to overcome mupirocin resistance in its target enzyme, isoleucyl tRNA synthetase. This therefore identifies a way that an existing antibiotic can be modified to overcome the resistance that is spreading clinically. One of our aims is to use genetic manipulation to replace the pyrrothine by other chemical species to create favourable new properties. We will use diverse gene clusters to determine what can be joined to PA and with what biological activity against a range of current superbugs and other important medically important targets. We will also feed chemically synthesised substrates to mutants that do not make the pyrrothine in order to generate families of new compounds. Also, because the genes that make the pyrrothine are unusual we will study them in detail in case their properties teach us new ways to build small molecules that could become part of novel antibiotics. It is also vital to understand how key steps in mupirocin and thiomarinol biosynthesis are controlled - particularly the timing and mechanism of specific biotransformations. The mupirocin biosynthetic pathway is an archetype of its class and is well placed to answer a number of general questions that apply to related systems. Finally we will study the interaction of the antibiotics with their target enzymes, modelling their structures and docking the small antibiotics with the proteins to predict which parts of the molecules are important and why. This should help direct desirable modifications that will create novel biological properties effective against key bacterial pathogens

Technical Summary

The mupirocin biosynthetic gene cluster is one of the archetypes of the 'atypical' type I polyketide synthases that have trans-acting Acyl Transferases which deliver the starter and extender (malonate) units. We have studied it for a approximately 10 years in order to understand what controls a number of key features - most notably beta branch insertion via the HMGCoASynthase cassette, pyran ring formation and synthesis of the hydroxyl fatty acid that is joined to the monic acid core via a labile ester bond. We have recently sequenced the genomes of two marine bacteria to reveal the biosynthetic genes for the related thiomarinol compounds. These are essentially a hybrid between pseudomonic acid C (a minor component of mupirocin which is mainly pseudomonic acid A) and a pyrrothine. The new genes have provided the basis of comparative genomics and gene swap experiments. By comparing all known acyl carrier proteins that are associated with beta-branch insertion via an HCS cassette we have identified a uniquely conserved tryptophan that must be a signature for this activity. We will test knockouts and knockins to generate a general strategy for polyketide backbone modification. We will add selected modules from other pathways to extend the backbone to create analogues lacking the ester bond that is one reason for rapid inactivation of mupirocin. Gene knockouts have identified the pseudomonic acid and the pyrrothine biosynthetic genes as well as a gene, tmlU, encoding an amide ligase that joins the two components together. We have shown that the addition of pyrrothine is critical to potentiate the activity of the pseudomonic acid against both Gram-postive and negative bacteria and in the new grant part of the work will seek to understand how this occurs and whether we can substitute other molecules for the pyrrothine in order to generate families of new molecules that may have desirable properties.

Planned Impact

Natural products are key to the health and well-being of mankind providing us with, amongst others, antibiotics, antifungal and antiparasitic compounds for use in medicine and agriculture. By fully understanding how Nature assembles such a diversity of valuable structures, there is enormous potential to exploit this knowledge in the design and synthesis of novel bioactive compounds. Our primary aim is to understand and utilise the mupirocin and thiomarinol biosynthetic pathways to provide novel compounds of potential value as antibiotics. Mupirocin is currently used widely to combat MRSA but cannot be used systemically due to problems of stability. The new compounds are expected to have altered biophysical properties which may make them more bioavailable, more potent, and able to overcome developing modes of resistance to the existing mupirocin drugs. Thus if successful this programme will have a major health and economic impact for society. Research into polyketides is of world-wide interest both in academia and industry and several spin-out companies have been established e.g. Biotica in Cambridge. The knowledge generated in this programme will be of immediate value to other groups to make advances in the understanding and exploitation of polyketide biosynthesis. This particularly applies to these atypical Type I PKS systems where each step forward with one system seems to have almost immediate impact for other systems because of the large number of genes or groups of genes that are found in more than one context. The logic that underpins these biosynthetic systems allows a great deal of predictive biology to underpin our development work. The knowledge that we generate will impact on how secondary metabolic pathways, particularly polyketides, are understood. These compounds are a topic in many industrial biotechnology courses so our work will impact on the university curriculum and we hope will provide examples of how bacteria can be manipulated for benefit to man. In order that the results can be fully exploited by others and the wider scientific community, communication is vital. The work will be published in leading peer-reviewed journal, communicated at conferences and in the longer term it is anticipated that the work will appear in reviews and books. Future advances in science depend upon the availability of well-trained researchers. This programme will give the PDRA valuable experience at the interface between chemistry and biological science and arm them with skills for success in a future career in academia and industry. This topic is attractive to undergraduates and will provide a context in which to gain a bredth of knowledge and may enthuse them to continue a research career. In order to exploit potential new antibiotics it will be important to liaise with industry. We currently have contacts at the UK manufacturer of mupirocin (GSK, although no formal collaborative links). On thiomarinol we are working closely with the Japanese Pharmaceutical company Daiichi-Sankyo who have expressed a desire to develop and exploit its potential properties and who have already funded a member of their staff to work with us for two years. On the one hand they are interested in the possibility that thiomarinol or derivatives could be used against MRSA and on the other hand they would be open to alternative lines of development - for example, the possibility that compounds related to thiomarinol could be developed as anticancer agents if derivatives turned out to be toxic to human normal or cancerous cell lines. There is a Material Transfer and IPR agreement in place that allows the University of Birmingham to have an appropriate stake in any practical application of work derived from the studies on the strains of thiomarinol-producing bacteria owned by Daiichi-Sankyo. The Research and Development Office at the University of Bristol is well placed to advise on any commercially exploitable issues.

Publications

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Description The biosynthetic pathways to the antibiotics mupirocin and thiomarinol have been determined in great detail. The mechanism for introduction of specific methyl branches into the structures of these compounds and other generic molecules has been established and the role of specific amino acids in the acyl carrier proteins have been established and the sequences of these proteins used to identify which carrier proteins are involved in branching. Novel hybrid nupirocin-thiomarinaol metabolites, many of which have good antibiotic activities have been produced.
This has now led to our current work on engineering the pathways to deliver new antibiotic compounds.
Exploitation Route Thiomarinol and mupirocin belong to a family of antibiotics produced by the "Trans-AT" polyketide syntheses. Our work has complemented studies from other laboratories and influenced the direction of their experiments.
Sectors Chemicals,Education,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Responsive mode
Amount £724,350 (GBP)
Funding ID BB/R007853/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2018 
End 05/2021