Fragment-Based Screening and Drug Design

The last Monday seminar of the Summer term at Birkbeck was given by Dr Rob van Montfort of the Institute of Cancer Research. Van Montfort, a former postdoc in the School of Crystallography here, spent six years in industry, at the biotech company Astex Therapeutics before joining the ICR two years ago. There, he is developing high throughput, structure-based drug screening techniques and using them to design novel compounds as candidate anti-cancer drugs.

Van Montfort first described the problem that techniques such as his have been designed to solve: that of attrition in drug discovery. Not only does it often take well over 10 years to move a potential drug compound "from the bench to the bedside", but the attrition rate is immense and not sustainable. A typical drug discovery programme will involve the testing of millions of compounds, and result in, say, half a dozen candidates for Phase I clinical trials and, if all goes well, a single registered drug. And even if a compound reaches the clinic, it may well not recoup the millions of dollars that have been spent on its development.

Drug companies and adacemic groups have been turning to novel technologies to help address this problem and reduce the time and cost of drug development. The technique de Montfort described, fragment-based screening, is one of these. It was originally developed by Wim Hol's group at the University of Groningen, the Netherlands, and developed for commercial use by companies including Astex and Plexxikon.

Historically, X-ray crystallography has been used mainly in the mid stages of drug development, in modify promising lead compounds into drug candidates. Now - thanks largely to high-throughput crystallography or structural genomics programmes - X-ray technology has improved to the point where it can be used at a much earlier stage. In fragment-based screening, groups of small molecules taken from a "fragment library" are soaked into protein crystals and the resulting structures examined by X-ray crystallography to see which fragments have bound to which parts of the protein's ligand-binding sites. These fragment hits generally bind very weakly but may be "joined together", if they bind into different pockets within the binding site, and modified further to generate tight-binding inhibitors and, eventually, candidate drugs.

De Montfort went on to describe a few published case studies of Astex' protein drug targets, including the P38a MAP kinase. This kinase is involved in cellular responses to stress, and its inhibitors may be therapeutically useful in a variety of inflammatory and auto-immune diseases. Fragment-based screening identified a lipophilic fragment that bound into the selectivity pocket of this kinase (Hartshorn et al. (2005), J. Med. Chem. 48, 403-413; PDB 1W7H) and modified it to produce a larger, tight-binding inhibitor (Gill et al. (2005), J. Med. Chem. 48, 414-426; PDB 1W82 & 7 others).

Thrombin, a serine protease involved in blood coagulation, is an important therapeutic target for stroke and deep vein thrombosis (DVT). Van Montfort was involved in the development of thrombin inhibitors, a process that was particularly hard because the thrombin active site is charged, and the charged compounds that would be expected to bind there are unlikely to work as oral drugs. Howard et al. (2006) published a fragment-based screen against thrombin using a library of uncharged compounds, finding small fragments that bound to one pocket within the substrate-binding site and larger ones that bound to a different one (J. Med. Chem. 49, 1346-55; PDB 1WBG). Combining the chemistry of these fragments into a single, larger molecule produced a potent series of uncharged, non-peptide inhibitors with structures that had not previously been seen in protease inhibitors.

Kinases are signalling proteins that control many biochemical and physiological processes, including the cell cycle, and cell-cycle kinases are very important as targets for anti-cancer drugs. Both Astex and the ICR have extensive programmes developing kinase inhibitors, and thehe two organisations have collaborated on the discovery of compounds that inhibit protein kinase B (see e.g. Saxty et al. (2007), J. Med. Chem. 50, 2293-6; PDB 2UW3).

Van Montfort has now set up a fragment-based screening lab at the ICR and developed a library of over 1800 fragments. His group is investigating potential protein targets for drugs against cancer, including kinases.

All the journal references in this blog post are in the Journal of Medicinal Chemistry, which should be available via the Birkbeck e-library.