A Dynamic Perspective on DNA-binding

The binding of small molecules and proteins to DNA is fundamental to biology and considerable scope exists for the development of highly-sequence-selective, DNA-binding molecules as new drug candidates and biotechnological tools to manipulate gene expression. In this proposal we focus on applying cutting-edge time-resolved spectroscopy methods developed at the STFC Central Laser Facility (CLF) to observe, in real time, the binding of small molecules to target sequences in the minor groove of B-DNA.
Minor groove binding (MGB) species have shown promise as novel antibiotics for the fight against hospital acquired infections such as Clostridium difficile, with one such MGB compound, produced by our project partner MGB Biopharma Ltd, entering preclinical trials. Obtaining, a comprehensive molecular-level understanding of the mechanisms that underpin ligand binding in this class of molecules is now critical in order to inform refinement of current candidate molecules and the design of new derivatives for applications in areas such as cancer treatment. Despite much study however, key outstanding questions remain regarding the way in which specific DNA base sequences are identified by the ligand and the role of water in promoting, mediating or inhibiting ligand binding to DNA.
The gaps in our knowledge arise because the current picture of DNA binding stems from experiments such as X-ray diffraction, NMR or biochemical assays that, crucially, are not sensitive to the rapid fluctuations of the DNA architecture or the solvent molecule-driven dynamics that occur in solution. These dynamics directly influence both the shape and chemical environment of the binding site and it is therefore imperative that they are built into any models of DNA binding.
As a result of capital investment in ultrafast laser technology at the CLF and STFC-funded Programme Access research, the capability now exists for studying biomolecular processes in real time and at high spatial resolution using 2D-IR spectroscopy. We seek to establish that this technology can address key issues in the pharmaceutical sector by applying it to record the first 'molecular movie' of the DNA:ligand binding process of an MGB drug candidate. In doing so, we will reveal the influence of DNA fluctuations and water molecules upon binding in unprecedented detail and demonstrate that STFC-funded research can take a lead in transferring academic research to impact in this arena. The results of this work will demonstrably contribute to the design of MGB species for healthcare and we envisage integrating this new knowledge early into the drug design process, ultimately leading to next generation drug candidates with improved efficacy and selectivity for their particular target sequences. In addition, this demonstration of capability will provide a gateway both for future engagement between STFC research and the pharmaceutical sector and for exploitation of future funding routes from previously inaccessible sources such as MRC and the Wellcome Trust.

This proposal seeks to show that ultrafast laser technology developed at the STFC Central Laser Facility (CLF) can deliver a molecular-level understanding of the role of dynamic structural and solvation processes in DNA:ligand binding and that this knowledge can impact directly upon the design of new therapeutic small molecules for healthcare applications. As a result, this work will generate impact in a variety of ways, these are summarised here and discussed in more detail in the Pathways to Impact attachment.

i) The project team will benefit immediately from the new molecular insights that the project will provide and, through the team members and partners, a clear route is established for the data produced to drive new directions for MGB drug design.

ii) An in-depth understanding of DNA-ligand binding has the potential to generate impact in a wider sense than the specific outcomes of the project. Current applications of DNA-binding species encompass nanoscience and photonics-related technologies as well as the broader healthcare sector. In the latter, example routes to impact occur not only through the featured molecules with antibiotic capabilities but also via the potential for MGB-type compounds to play a role in the treatment of many other conditions. We will seek to exploit this both through the project team and new collaborative/KT ventures as appropriate.

iii) The broader outcomes of the project will be of significant interest to the pharmaceutical and biotechnology industries via both the molecular targets studied here and the tangible output in terms of data and platform technology developed. To exploit this, we will work with a number of potential beneficiaries and there are established links between Strathclyde and global pharmaceutical concerns to facilitate this.

iv) Demonstration of 2D-IR as a tool for biological applications will establish the CLF at the forefront of the global ultrafast bio-spectroscopy field. We will make the technology accessible to non-expert users including those in the pharmaceutical sector.

v) The project will contribute positively to future economic and academic impact through training early career researchers in the skills needed across the commercial and academic sectors.