Exploring interactions of polar fluoroaliphatic motifs with biomolecules.

The project will explore the properties and applications of two novel organo-fluorine motifs which have emerged from an understanding that partially fluorinated aliphatics have particularly polar properties.These partially fluorinated motifs can be contrasted with super hydrophobic fluorinated perfluorcarbons, and also hydrocarbons which are nonpolar and also hydrophobic. These classes of compounds are also chemically persistent eg PFASs, and there are concerns associated with their accumulation in the environment. It emerges that an intermediate situation with fluoromethyl (-CH2F) or fluoromethylene (-CHF-) generate compounds have a much greater affinity for water and are much more susceptible to biodegradation and improved environmental performance. This programme selects two such motifs for investigation is a variety of circumstances associated with bio-actives discovery or as tools in chemical biology. These are Janus face cyclohexanes which have fluoromethylene groups (-CHF) around the ring, and particularly in a stereochemical arrangement that has the fluorines on one face of the ring and hydrogens on the other, as this offers maximum polarity. The second is the unexplored tert-buty-trifluoro motif (TBTF) which transforms the highly hydrophobic properties of a tert-butyl group and renders it much more hydrophilic. The programme is arranged into three work-packages (WPs). WP-1 will investigate the binding of analogues of the W-peptide, a high affinity agonist of an important receptor (FPR2) associated with a range of disorders extending from heart disease to Alzheimers. The interaction of W-peptide with the receptor is very well characterised. These novel motifs will be placed into specific side chains of the W-peptide to assess relative efficacy and explore binding interactions with the receptor as a means to understanding their interactions in a protein active site. WP-2 will take a surface science approach using Atomic Force Microscopy (AFM) to assess the interactions of surfaces and cantilever tips coated in monolayers of molecules terminated with the organofluorine motifs. A wide range of experiments is designed to explore the strength of interactions with polar substituents (eg RCO2-, RN4+) and the strength of interactions between the motifs themselves, and how those interactions are influenced in different ionic solutions. The study will extend to exploring the strength of interactions with double- and single- stranded DNA and DNA. This WP aims to understand interactions between the motifs and molecules found widely in biochemistry. WP-3 will extend very specifically to nucleic acids and builds on an observation that the Janus face cyclohexanes appear to interact very strongly with double stranded DNA and much less so with single stranded DNA. These studies will be explored using techniques which can detect single molecule-molecule interactions using fluorescence microscopy. We will explore if the interactions can be strengthened by increasing the number of motifs (avidity) or if two or more molecules of dsDNA will attach to one probe with several Janus face motifs (crosslinking), essentially manipulating dsDNA on the nanoscale, with applicatiosn extending to docking cargo to dsDNA for specific functions such as splicing and cross linking etc. This WP will also explore interactions with the organofluorine motifs on G-quadruplex DNA, another DNA morphology which is of great significance in the cell cycle and programmed cell death (apoptosis), the control of which has implications in treating cancerous (immortal) cells. We will modify established G-quadruplex molecules (drug candidates) with our organofluorine motifs and examine their interactions by X-ray crystallography and a range of biophysical techniques. At the end of the programme we aim to deliver new tools and knowledge which should contribute to the development of next generation therapeutics and diagnostics in healthcare.