Department of Biology

Plant products

Artemisinin synthesis

The Centre for Novel Agricultural Products uses chemistry to advance our understanding of biology in a range of projects.  For example, in the CNAP Artemisia Research project, led by Ian Graham, with funding of $26M from The Bill and Melinda Gates Foundation, the medicinal plant Artemisia annua, is being studied. This plant is currently the sole source of the leading anti malaria drug artemisinin, a sesquiterpene. High-throughput LC-MS based screening of metabolites in mutant populations has identified high yielding individuals. Combining metabolite profiles, metabolic pathway maps and knowledge of terpenoid chemistry has led to the identification of a suite of genes associated with the synthesis of artemisinin and related metabolites. A major breakthrough has been the construction of the first genetic map of A. annua, which contains markers representing key genes associated with metabolic and developmental processes (Graham et al (2010) Science 327, 328). 

Glycosylation

Small molecule chemical modification and the role this plays in plant biology is another major focus in CNAP. Robert Edwards’ group in CNAP, have expertise in the glycosylation of synthetic compounds and the role of such reactions in determining plant interactions with herbicides and other xenobiotics.  Recent work in this area has included studies on unusual conjugations involving the N- andC-glycosylation of a range of acceptors, extending into natural product metabolism.  In turn, the biotransformation of high value phytochemicals has been extended into the emerging field of biorefining, with specific projects directed at creating high impact flavour and fragrance compounds and flavour-enhancing molecules by biocatalysis and biofermentation. 

Biocatalysis and bioremediation

Work in the group of Neil Bruce revolves around applied enzymology, with a particular focus on the metabolism of synthetic compounds by microbes and plants. The ability of bacteria to utilise a wide and exotic range of carbon sources and their capacity to adapt and rapidly evolve new metabolic routes has enabled bacteria to take advantage of the many synthetic organic chemicals that enter the environment. Elucidating pathways for microbial degradation of synthetic compounds has led to the discovery of numerous new catabolic enzymes that catalyse an amazing range of chemistries. The Bruce group have been exploring the use of such enzymes as biocatalysts to convert inexpensive raw materials into high value end products. A current focus is oxidative biocatalysis using cytochrome P450s and using high throughput technologies to mine plant and microbial genomes for biocatalysts

Crop protection and improvement

A major focus for the Edwards lab, in CNAP is the use of chemicals in crop protection, notably in using chemical biology approaches to manipulate herbicide selectivity and yield in cereal crops.  Two approaches have been adopted, which utilize a combination of directed synthetic chemistry informed by biochemical and molecular genetic screens.  

1. The development of a novel series of chemical derivatives which activate xenobiotic detoxification responses in wheat and rice.  Such safeners elicit a co-ordinated up-regulation of detoxifying enzymes in plants which leads to an increase in herbicide tolerance in cereals.  The mechanism of action of safeners and their molecular recognition in plants is a major priority for the group.
2. The development of selective inhibitors of  glutathione transferases involved in multiple herbicide resistance in grass weeds.  In a joint programme with agrochemicals company Syngenta, the use of directed synthesis has identified a series of promising herbicide synergists capable of restoring chemical control in otherwise resistant problem grass weeds. 

The group is now interested in extending these approaches to enhancing crop yield and controlling plant development through chemical genetics.

Anti-bacterials

Work in Gavin Thomas' lab uses chemical biology approaches in two main areas: sialic acid biology and  development of novel antibiotics. We have a long-standing interest in how bacteria acquire sialic acid from their environment, which is essential for the ability of some human pathogens like Haemophilus influenzae to colonise their host. We have used a biochemical and structural approach to characterize the sialic acid binding protein component, SiaP, of the H. influenzae sialic acid transporter SiaPQM (Mulligan et al (2009) Proc Natl Acad Sci USA 106, 1778). In collaboration with Rod Hubbard(YSBL, Chemistry) we have initiated a search for small molecule inhibitors of sialic acid binding to this transporter, with the long term aim of understanding transporter function more clearly and also to develop novel antimicrobials.

In a related, but quite different project with Anne-Kathrin Duhme-Klair and Anne Routledge in the department of Chemistry, we have been directly exploiting bacterial transporter proteins to develop novel antimicrobials (Saleh et al (2009) Bioorg Med Chem Lett 19, 1496).  Here, the transporters for iron-siderophore complexes are used as routes to smuggle in novel antibiotics - molecular Trojan horses. Using total chemical synthesis of selected antibiotics and siderophore complexes, that we dub siderobiotics, we have one promising lead compound with potent antibacterial activity. Further characterization of this compound is now underway through a grant from the University of York Strategic Initiative Fund (SIF) to develop this through to commercialization.

Virulence inhibitors

One of the main research areas in Colin Kleanthous' lab is the Tol-Pal complex of the bacterial cell envelope.  Tol-Pal proteins are required for stability of the bacterial outer membrane and for virulence in several Gram-negative pathogens but the biological role of the assembly remains elusive.  They are using a chemical biology to help unravel the mechanism of the assembly in a two-pronged approach:

1. Determining how naturally occurring protein antibiotics known as bacteriocins subvert the system in order to translocate across the outer membrane,
2. Using this information to develop small molecules that target the interactions of the Tol-Pal assembly as a route for the creation of novel antimicrobials.

Recent advances include crystal structures of TolB bound to the translocation domain of the endonuclease bacteriocin colicin E9 which, when compared to the complex with its endogenous periplasmic binding partner Pal, reveal how the colicin manipulates the allosteric transition of TolB to promote contact with the inner membrane protein TolA (Bonsor et al (2009) EMBO J 28, 2846).  In collaboration with David Spring, a synthetic chemist in Cambridge, they are taking a small molecule-based approach to find modulators of the Tol-Pal assembly.

Immune response

Work in the Coles lab in the Centre for Immunology and Infection is focused on stromal cells and their role in development and function of the immune system.  The ectopic development of activated stroma is associated with autoimmune diseases and tumour metastasis.  Despite the importance of stroma in modulating immune responses and tumour metastasis, drug development has focused entirely on targeting lymphocytes and tumour cells rather than the underlying stromal cells that support their growth and function.   By modulating stromal cell function they hope to develop a new generation of pharmaceuticals that can modulate immune responses and tumour growth by entirely different mechanisms.  Working with Beining Chen, a synthetic chemist at Sheffield University, and 3D stromal cultures they are screening novel small molecule agonists and antagonists that can modulate stromal cell function.  Through the application of synthetic chemical methods to the emerging field of stromal cell biology they aim to identify new inhibitors of signalling pathways that can be used to modulate immune responses.