Exploring the mechanism and scope of the enzymatic formation of five membered ring

Lead Research Organisation: University of St Andrews
Department Name: Chemistry


Many of todays drugs that we rely on for treatment of cancer, bacterial infection, immune disorders and viral infections are either natural products or are derived from natural products. Natural products remain, even today, a source of drugs and diagnostic molecules. In contrast to man made chemicals natural products are complex in terms of shape and composition. This structural novelty is in part the reason that they work in specific ways, (less side effects). In general, these natural products are made in bacteria rather than in humans or animals. Humans have evolved to ditch much of their complex chemistry. We need vitamins in food, because we cannot make them; rather rely on bacteria or plants to make them and we eat them. Bacteria have an amazing repetoire of complex chemistry that organic chemists can only dream of. In making new man made materials, a key challenge is often to identify plausible new scaffolds or skeletons. Molecules which are easy to draw are hard to make. Yet new scaffolds and motifs (known as chemical diversity) is at the heart of drug discovery. We are going to study the bacterial enzyme that makes heterocyclic amino acids. These five membered rings are a common motif in biologically active compounds but there does not exist any good way of making them in natural products by synthetic chemistry. The use of bacterial enzymes to accomplish chemical tasks is very well known, washing powder being the best known example but they are widespread in the food industry and increasingly the organic chemistry lab. By working out how the enzyme which makes five membered rings works, we will gain control of the enzyme. By doing this we will be able to make novel materials and we believe completely new biologically active compounds. What is more these enzymes work in water at room temperature without producing noxious waste materials.

Technical Summary

We propose to investigate the mechanism of the formation of heterocycles by enzyme. These five membered rings are critical components of many important biologically active molecules. We have made significant progress in determining the chemical mechanism, which is the first step to harnessing the enzyme. We intend to pursue the mechanism by novel labeling strategies including stable isotope labeling of substrates. We will also probe the basis of recognition using NMR approaches to identify the crucial residues involved in binding substrate to the enzyme. This is important because in the long term we would wish to replace amino acids by non peptide like groups. We have shown that NMR appears to detect intermediates that form during the reaction. The oxidation state of the rings is important, since even this subtle modification controls activity and stability of the compounds. We have shown that air can be sued to replace in part the enzyme mechanism. We intend to develop further the chemical route but also to study the enzymatic route. There are important and puzzling differences between enzymes that catalyse this reaction. The ability to control the stereocentres of amino acids is also central the activity of these compounds. The mechanism by which residues adjacent to thiazolines are epimerised is unknown. We will determine whether it is spontaneous or enzyme catalysed. We have developed an approach using a combination of peptide synthesis and protein ligation that will allow us incorporate non natural amino acids. This will not only give us exquisite control of the biochemical experiments but lead to more interesting chemical scaffolds in the future.

Planned Impact

Academic impact
New tools for scientist interested in natural products. Importantly our work will establish new routes to incorporation of non natural amino acids into biologically active molecules, this will enable scientists in other fields to pursue their use in other challanging problems. The mechanistic and structural insights will transform other scientists ability to manipulate natural product biosynthetic pathways.

Naismith is very active in outreach with school children. If funded we will offer summer placements to local children to experience chemical biology. We also intend to create experiments suitable for University undergraduates in the first instance at St Andrews, that could become part of chemistry courses in the UK.

Research and professional skills
The UK has identified synthetic biology and Industrial biotechnology as key deficits in scientists' training for the future workforce. This project is at the cutting edge of such tools and will therefore provide excellent training for Koehnke. Koehnke intends to set up a lab of his own (in Industry or academia) and this project will give him the skills required for this. We will ensure maximum diffusion of these skills by recruting a PhD student to work alongside him but on a defined and distinct project. Researchers will have access to the award winning "Gradskills" courses run by the University of St Andrews, which aim to provide a wide variety of life skills. Naismith runs a summer school for UK and EU graduate students held every two years.

Economic and Societal Impact
The work will generate new biologically active molecules and moreover allow their generation in useful quantities. This means they can be used in drug development programs and in screening cmapaigns. We are setting up collaborations with Industry to maximise their benefit. If funded we can pursue such parnterships. We expect to transfer technology through service agreement (we make compounds) or by technology licence (we have filed a patent). We will consider founding our own spin out company as the project develops.


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Bent AF (2013) Structure of PatF from Prochloron didemni. in Acta crystallographica. Section F, Structural biology and crystallization communications

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Brás NF (2016) The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac. in Chemistry (Weinheim an der Bergstrasse, Germany)

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Czekster CM (2016) Mechanisms of cyanobactin biosynthesis. in Current opinion in chemical biology

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Houssen WE (2014) An efficient method for the in vitro production of azol(in)e-based cyclic peptides. in Angewandte Chemie (International ed. in English)

Description We have engineered enzymes that can make entirely new molecules. The molecules are hydrids of peptides and organic molecules. These molecules have value as drugs and diagnostics. We have formuated an entirely new process for making complex macrocycles.
Along the way there are many key enabling findings. These include the characterisation of the kinetics of the enzymes that control modification of peptides including macrocyclisation. We have also presented findings on how the enzymes in the pathway control the timing of the formation of modifications. These findings were crucial in moving to reach the key finding, the making of a new molecule.
Exploitation Route We are going to try form a company. The company is called GyreOx.
Sectors Chemicals,Healthcare,Pharmaceuticals and Medical Biotechnology

Description We have been able to solve the structure of a novel protein that may be involved in the epimerisation of amino acids. This is important as controlled epimerisation is chemically very useful in the pharmaceutical industry. Our work has inspired new efforts in peptide drug discovery. We have shown that it is possible to combine organic chemistry to make highly diverse and modifiable macrocycles. This has changed how people think about peptides in medicine.
First Year Of Impact 2014
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

Title PDB coordinates 
Description Protein structures and X-ray data 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Widely used to study the mechanism of methylation 
Description Ingenza 
Organisation Ingenza Ltd
Country United Kingdom 
Sector Private 
PI Contribution Our task was to improve the macrocyclisation of peptides. Having identified the enzymes we modified their behaviour in order for them to work on more chemically relevant problems.
Collaborator Contribution Ingenza were able to construct polycistronic sequences with individual genes under the control of different promoters. This enabled the organisms
Impact We created new technology for macrocyclising peptides
Start Year 2017
Description Primary school visit toHamilton 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact I spent a whole day with primary school children conducting science experiments. The initial focus was for children with special educational needs. The visit was carried at St John Primary School in Hamilton.
Year(s) Of Engagement Activity 2016
Description Schools visits 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Each year I host visits to my lab from local secondary school (10's of pupils) and I also give a talk to visiting school pupils on science (approx 50 pupils).

Some of the children seemed to appreciate that chemistry was important in biology.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014
Description Training and workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Between 20 to 50 pupils per year visit St Andrews and as part of this, they are exposed to structural biology.

Teachers report increased enthusiasm for biomedical science
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010,2011,2012,2013
Description workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Helped in the training of post-graduate students in structural biology at the following meetings.
CCP4/ZCAM workshop, Zaragoza, Spain March 2012
CCP4/ APS workshop, Argonne, USA, June 2012
CCP4/APS workshop, Argonne, USA, June 2013
CCP4/CeBEM workshop, Montevideo, Uruguay, April 2013

Widespread use of UK authored software.
Year(s) Of Engagement Activity 2013,2014
URL http://www.ccp4.ac.uk