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Mutant Proteins and Cancer Drugs the Possibilities of Metal Structures

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Mutant Proteins and Cancer Drugs the Possibilities of Metal Structures Autumn 2008 Mutant proteins and cancer drugs Towards the $1000 genome The possibilities of metal structures What’s next for the CCDC? As I see it... virtual screening, we try to filter out those mol - Colin Groom, the Cambridge Crystallographic Data Centre’s new ecules that can’t possibly bind and identify the director, talks to Sarah Houlton about the centre and its future ones that might. What uses does it have outside What’s the CCDC all about? information about molecular recognition than pharma? It was set up in 1965 from the chemistry any other database, and the recognition that goes While it is primarily used in pharma, it also has department, and became independent in 1989 on between a small molecule and a crystal is very potential in crystalline materials. These are used as a not-for-profit company. This gives us a nice similar to that between a small molecule and a in many applications and we would like to stable structure as a self-sustaining research protein in the body. This allows us to derive com - extend the database into this field. It’s also institution, where we’re not driven by max - putational descriptions of those interactions, being used by material scientists who are trying imising profit but by doing good science. Our which companies not only use to optimise the fit to understand crystal growth – this also has activities fall into three strands, and the main between the molecule and the protein, but also pharma applications where scientists are trying one is the structural database, which now con - between a molecule and a lattice of other mole - to find the best crystal form to use in a drug tains more than 450,000 small molecule crystal cules in the materials science area. product. As well as organic molecules, the data - structures. It’s used by well over a thousand In terms of molecular docking software, base contains metal organic compounds, for institutions and companies around the world, although some companies have gone down the example, and these are of interest to material including 100 or so commercial organizations. route of screening millions of compounds scientists in areas such as catalysis, gas storage It’s not just a repository – it also contains con - against a target protein, this can only be done and carbon capture. There’s a huge range of textual data and software that helps scientists with compounds that already exist. With virtual possibilities for the database – and we’re begin - make proper use of the crystal structures. screening, we can look at compounds that ning to make people in those scientific commu - The second strand is other software, devel - might exist but don’t, opening up a whole new nities aware of what the database can offer oped primarily in the pharma area. The most area of science. them. We don’t yet know all its possible uses – well known is Gold, a ligand docking program. It also reduces the need for physical testing – we’re hoping that people in other fields will be It is heavily used by industry, but also in acade - a company may have millions of compounds in able to tell us as they know their science better mia, and we’re continuing to develop it so that their libraries but for a complex system they than we possibly could. it allows much better virtual screening for can only realistically test several thousand. We active compounds. And the third strand is the can direct them towards the most appropriate So what does the future hold for research we do in the broad area of molecular ones to test. There are two issues here – one is CCDC? interactions. identifying whether a compound has the The primary thing, of course, is to ensure the potential to bind to a protein, and the other database stays up-to-date, and available for sci - Why is the database important? defining the most probable binding mode. And entists to use. And the secondary one, which is I think it has become an essential tool for com - these are really quite different problems, as in also essential, is to make sure it is used for the panies in developing new pharmaceuticals, the latter you have to look very closely at the best scientific good. We do our own research reflected in the fact that all the major pharma geometry of the ligand and the energetics of with the database and collaborate with others, companies use our database. It contains more interaction between it and the protein. With and we want to encourage users to get as much benefit as possible from the database. So we will He’d been sponsored by the RAF at school continue to develop new tools to help scientists m and for his degree, but realised that science in their research, and the revenue we generate o was for him and he stayed on to do a PhD o from providing the database allows us to r with Sandy Giddes. ‘It was expensive as I had develop these tools. G to pay the RAF back!’ he says. n i Career: After a postdoc in Leeds with Simon l Is the idea is that it will remain self- o Philips, Tony North and John Findlay, he went sustaining? C to New Zealand for a second postdoc at Absolutely. I think it is the most stable model Massey University – the outdoor lifestyle was for the centre, as we are not reliant on applying a definite draw! Pfizer came calling in 1994 as V for grants every few years, which would leave C they were setting up a protein crystallography the research community uncertain about the group, so he returned to the UK and the future of the database. Ultimately, someone has company’s Sandwich site, also spending a year to pay, and I guess the taxpayer could pay for it helping set up a new research site in through the research councils, but this way, Cambridge, US. In 2002, he moved to with the funding coming from the current Celltech to lead the computational group in users, it is much more predictable. Cambridge. He took up his new role at CCDC in October. So you’re looking forward to the Interests: Much of his time is taken up with future, then? his family and other animals – his wife rescues Absolutely. This is a fantastic place, and after 15 Born: Telford, Shropshire, when it was sick creatures and there are chickens running years in industry it’s great to come somewhere still a collection of little villages and round the garden. He’s also a frustrated that’s a mixture of academia, biotech and indus - before it became a New Town climber – Cambridge is far too flat for his try, full of people who are really motivated by Status: His wife, Kerrie, was a molecular liking, so he likes to travel to less flat places as what they do. It’s a great blend of academia with biologist, and now works for various often as possible. commercial reality. I also think the structure and charities. They have two children – Did you know? He’s also a big footy fan – ethos of the organisation encourages people to Thomas, who’s 12, and 11-year-old Ellen. supporting both Telford United and Leeds work with us – we’re a charity and we exist to Education: After the local comprehensive United. And his choice of university was made do great science. People like that and want to and sixth form college, he went to Leeds on the strength of its proximity to Elland work with us. Industry doesn’t just see us as a University to study biotechnology – one of Road… ‘I had a big club and a local club profit-driven software company – they see us as the first universities to offer the subject as when I was a kid. The way things are going, a research organisation with a great scientific a degree course. Telford will soon be the big club!’ pedigree which can help them with their own science. And that’s really refreshing. 2 Chem@Cam Autumn 2008 Reluctant reactions Letters Not just old girls! scheme, for which I am increasingly grateful! Dear Editor Yours sincerely Your article ‘The class of 1946 remi - Reg Lewis nisces’ prompted by Mary Ashworth’s 93 Buryfield Road, Solihull, letter and photograph produced letters W Midlands B91 2DQ from four other ‘old girl’ students. This letter is just to prove that at least one ‘old boy’ student still survives, Wonder and delight thought Jennifer Turner’s letter suggests that Peter Gray also survives. Dear Editor I enjoy Chem@Cam , because it keeps I was recently made aware of the article me up-to-date on what the chemistry in the Autumn 2007 edition of department is doing, but I do not pre - Chem@Cam about pictures from the tend to understand the more advanced 1950s, which included a rather fine one work – when we were students there of my father, Sandy Ashmore. were only 92 known elements. I partic - Ah, that picture of RGW Norrish. ularly enjoy the Puzzle Corner, and was One of my friends at Emmanuel lucky enough to win a prize a couple of recounts still how he came across him years ago. One of your puzzle setters, in November 1968 (or so) flat on his Keith Parsons, is a former colleague of back in the garden, saying to himself mine at Bakelite. ‘I’ve got a *@&*ing Nobel prize’ in After graduating, I decided to go into tones of wonder and delight! And I the chemical industry.
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