Paper SP+AS+BI+EM+MI+NS+SE+SS-ThA3
Development of a Novel Single-Molecule Force Based Approach for Fragment Screening

Thursday, October 31, 2013, 2:40 pm, Room 202 C

The discovery and development of new chemical entities is complex and time consuming, and of great expense to the pharmaceutical industry¹. High throughput screening (HTS) is the main method used for lead identification, allowing significant numbers of compounds to be tested. However, productivity levels are still below those desired². Due to this, interest in a relatively new process termed fragment based drug discovery (FBDD) has developed³. The FBDD process starts from small, efficiently binding fragments elaborated to more drug-like molecules⁴. However, with fragments being smaller components of the traditionally screened small molecules they have lower affinities and as a result require sensitive detection systems⁵.

It has been proposed that the atomic force microscope (AFM) could be used as a novel system in fragment screening. The AFM benefits from the ability to probe single molecular interactions⁶ using only small volumes of solution that need not be of high purity. Single molecule force recognition spectroscopy (SMFRS) is the commonly termed process where an AFM tip is functionalised with probe molecules that are known to recognise specific target molecules on the opposing surface. Fragments can theoretically be screened against their potential target on the surface and if they bind will block the natural ligand on the tip from occupying the active site.

Here, the well-characterised interaction between streptavidin and biotin was used as a model in which fragments of biotin were screened using an AFM probe functionalized with a biotin-mimetic peptide. It was seen that the AFM was capable of measuring the specific interaction between the biotin mimetic peptide and streptavidin. Each competition assay worked well, with the peptide-streptavidin interaction being blocked by fragments in a concentration dependent manner. Analysis of the percentage adhesion-versus-concentration data resulted in a ranking of the fragments, which matched their known or measured affinities to streptavidin. Despite the fact that this is still in the early stages of development, the results are promising and it is hoped that with further development the approach will be introduced into drug discovery fragment screening methods.

References:

1. Murray, C. W. & Rees, D. C. T , 187-192, (2009).

2. Campbell, S. F. , 255-260, (2000).

3. Chessari, G. & Woodhead, A. J. , 668-675, (2009).

4. Schulz, M. N. & Hubbard, R. E. , 615-621, (2009).

5. Murray, C. W., Verdonk, M. L. & Rees, D. C. , 224-232, (2012).

6. Barattin, R. & Voyer, N. , 1513-1532, (2008).