Molecular and in-silico interrogation (rotation two)


Lab rotation project description

This project will involve the design and synthesis of novel ligands designed to further validate our recently published modelling simulations which predict an unusual binding mode for certain molecules, when binding to the 1- and 2-adrenoceptors. Until recently, ligands for these receptors were believed to bind in a canonical fashion, making discrete interaction with key residues in each receptor. Building on an existing series of compounds, this approach will attempt to target a flexible region of the 1-adrenoceptor that is predicted to transform in order to accommodate certain ligands.

The project will provide you with experience in:

• small molecule organic synthetic chemistry

• a range of chemical purification techniques (flash column and preparative layer silica chromatography, preparative and analytical reverse-phase HPLC)

• structural elucidation through a number of techniques (1H/13-NMR, LCMS, Infra-red spectroscopy)

This arm of the triangle will be supervised by Dr Shailesh Mistry (BSMC, School of Pharmacy). In addition, there will be the opportunity to learn how synthesised ligands undergo pharmacological evaluation in cell based affinity and functional assays. The second part of the triangle (Laughton/Emtage) will focus on computational modelling of this phenomenon and understanding how synthesised ligand interact with the receptor. The third part of the triangle will be pharmacologically based, with a number of potential projects being offered by collaborators in the School of Life Sciences. 

Fact file

Research theme







2nd supervisor

Charles Laughton 

BBSRC Doctoral Training Partnerships

Linked PhD Project Outline

GPCRs are important signal transduction proteins residing in the cell membrane and are essential regulators of many homeostatic processes and targeted by >30% of drugs. The adrenoceptors (family A GPCRs), are key regulators of the cardiovascular and respiratory systems and well-established drug targets. 1, 2, and 3 subtypes have distinct tissue distributions and pharmacological activity. A recent study within the group has reported highly 1-selective, high affinity ligands with future clinical developmental potential.

Thus far, traditional computational approaches (based on models of published x-ray crystal structures) to rationalise how these novel ligands interact with the receptor do not offer a valid explanation for experimentally observed activity, or are unable to sensibly accommodate the ligands in the receptor.

We have recently identified, through advanced molecular modelling methods, a possible novel mode of binding for these ligands. This mode of binding may explain structure-activity relationship data that otherwise appears contradictory. An understanding of how these prototypical GPCRs interact with ligands is likely to be highly relevant to other members of the wider GPCR family.

The aim of this multidisciplinary project will be to design, synthesise and pharmacologically characterise a library of ligands to test this hypothesis more rigorously. In parallel, molecular modelling studies will be performed that will be correlated with pharmacological data.

The objectives of this project are to:

• design and synthesise a novel library of beta adrenoceptor ligands (related to rotation one).

• characterise these ligands pharmacologically, using cell-based or kinetic assays (related to rotation three).

• use advanced molecular modelling methods, including flexible docking and molecular dynamics simulations, to predict the mode of binding of new beta adrenoceptor ligands to the proteins. Note – the inter-campus nature of the supervisory team (UK/Malaysia) means there may be the opportunity to carry out some of the computational work at the Malaysia campus (related to rotation two).

• make calculations of the binding affinities, and identify structure-activity relationships.

The major methods you will use are:

• synthetic organic chemistry and structural elucidation.

• cell culture and basic pharmacological techniques including both binding and functional assays, pharmacological analysis and interpretation.

• molecular modelling of ligand-protein complexes and analysis of structure-activity data.

This chemical biology-focused project will span the disciplines of synthetic chemistry, pharmacology and computational chemistry to increase our understanding of the way ligands interact with the adrenoceptors. The prototypical nature of these proteins, means our findings are likely to be strongly impactful on the wider field of GPCR research.


Biotechnology and Biological Sciences Doctoral Training Programme

The University of Nottingham
University Park
Nottingham, NG7 2RD

Tel: +44 (0) 115 8466946