Posts Tagged ‘Drug Design’

Have a nap and let your computer cure cancer

// October 18th, 2010 // 2 Comments » // Drugs, How Things Work, Recent Research, Science Communication

computer doing science

Image by John Watson

While waiting for inspiration to strike a solid introduction into my head, my computer screen went blank. Good ol’ MacBook conserving energy! But letting your computer go idle doesn’t mean you have to waste its processing power. Why not cure cancer with grid computing?

It’s a kind of parallel computing, which breaks up complex problems into smaller calculations and then solves them at the same time. Instead of one processor working on one calculation a time, a group of processors work on different calculations together. Dual-core computers is one way to do it. Grid computing is another.

Grid computing is like a massive virtual computer whose processors are computers linked by a central software.

World Community Grid is one group which utilises the personal computers of over half a million volunteers around the globe. Their software switches on when the computer is idle and runs virtual experiments, calculating and number crunching its way through chemical simulations. They provide this public grid to humanitarian research projects.

Childhood cancer
One of the projects they are running is helping to solve childhood cancer by finding potential new drugs for neuroblastoma, one of the most common solid tumors in children. In some people the tumors do not respond well to chemotherapy. This research is hoping to turn this around by targeting three proteins which are important to the cancer’s survival. Knock out those proteins and the cancer will in turn be knocked out by chemo.

Good plan, but how to knock out the proteins? That’s where the grid comes in.

There are three million potential drug candidates who MIGHT bind to one of the proteins and knock them out. Of course, that’s a lot of laboratory time right there. A computer would be better, but to run these nine million virtual experiments would take 8000 years. By working with the public grid they expect the project to be finished in just two years. Possibly less.

That’s a big saving on time and grant money. It’s rational based drug design (which I blogged about here) taken to a crowd sourcing extreme. They are trying a similar thing to discover dengue fever drugs.

Carbon Nanotubes

Image by Mstroeck

Clean Water
Drug design isn’t the only industry using the World Community Grid. Last month universities in Australia and China announced they are running simulations through the grid to find out how to filter water using nanotubes.

Nanotubes are small tubes that only water molecules can fit through. Not bacteria, not even viruses. It’s a great way to get rid of water dwelling nasties and desalinate sea water. But with such small pores you would expect the pressure and energy needed to force water through the filter to be incredible. And incredibly expensive. But in 2005 experiments showed that actually the water flowed pretty fast through the filters.

Why? Possibly the water molecules touching the nanotubes act more like ice and reduce friction. But who knows? To find out exactly what’s happening they’re running realistic simulations using the grid. The outcome could lead to huge improvements in water availability, potentially saving millions of lives a year in the developing world.

Like the idea of grid computing? Sign up to the World Community Grid here, and let your down time make a difference.

Mac for 3D Molecular Visualisation. Apple makes Drug Design Sexy

// November 23rd, 2009 // 3 Comments » // Drugs, How Things Work

Drug design seems a glamorous industry full of coloured liquids, crystal bottles and incredibly expensive machines, but the reality involves a lot of repetitive experimentation and number crunching. Taking a lot of data and making it something you can imagine and understand is a freaking hard thing to do! Mac has made it easier (oh mac, how I love thee *hugs*) with sexy 3D visualisations for drug design.

scientist drawing molecule structure

Oh for the days when we could take a natural product and improve it by trial and error! Okay, we still do it a bit, but the trend at the moment is for a premeditated plan of attack – you need to track down active areas on target molecules and imagine a molecule that will fit in the active area, and then find out a way to make that molecule. It’s aptly called rational drug design, computer-assisted drug design or computer-assisted molecular design (CADD and CAMD).

Rational drug design is taking something that works a little bit and creating something else that works better. Identifying that initial “lead” molecule can be done by either using the natural product in the body (if it is known), studying cultural leads (old wives tales often have some truth to them), or by running a big ol’ experiment with a massive library of drugs. OH YEAH!

So we take the lead molecule and find out how well it binds to the molecule to make a benchmark. Then we change it. Add in a bit more positive charge on one end might make it stick better to a negative pocket in the active site. Adding a bit of bulk will make it fit nice and tight, less likely to fall out but if you make it too big then it won’t fit at all. Maybe your active site has two pockets and they need to be linked together a certain distance apart. This is where good old experimenting comes in, and each new trial reveals a little more about how the active site binds to a drug.

Following the molecules down the rabbit hole like this is called QSAR – quantitative structure-activity relationships – measuring the level of activity the drug has (or how well it binds to the target) against changes in structure. In the end we make a fancy-pants equation and use that to create the most effective drug POSSIBLE TO MAN with the least amount of side effects. It takes a long time, but the results include many of the drugs on the market today.

But what about 3D technology?

Imagine the time you can save by having a picture of the active site already! Rather than run hundreds of different drugs for your QSAR, you can pretty much paint a molecule in and try a few variations. By actually having that picture in front of us we can design drugs much more effectively, targeting them to the areas we already know are there. Plus it looks HOT. Check out Tamiflu.

Tamiflu Tamiflu

You can click on it and open up a 3D structure that you can rotate and zoom in on.

3D small molecules aren’t exactly new, but big-ass complex proteins are harder! I know of two journals that are using interactive 3D images of molecular structures: The journal of Biological Chemistry and PloS ONE are using software called iSee to make models of proteins and small molecules that you can move around and zoom in on. The Structural Genomics Consortium (SGC) are a non-for-profit organisation who are creating 3D structures of proteins and releasing them into the public domain for unrestricted use. It’s like open-source science! Having a ready-made starting point like this opens up a massive chunk of lab time and budget, and it’s for freeeeeee! You can download it for freeeeeee here, and have a look at their library. These pictures have come from which is easy-peasy if you just want to click and enjoy.

The only thing cooler than 3D molecules are 3D molecules that actually look like they’re jumping out the screen at you, like the amazing graphics of Coraline or Up (seriously, 3D movies are way cooler than I remember them! I remember those dodgy red and blue glasses, and thinking that was the best thing since ships biscuits even though it gave me a headache. These movies kick those old ones ASSES!) Seeing a molecule in true 3D is even more amazing, and it’s easier to see all the details. We did it once or twice at Uni in a special mini-cinema they had set up, I think to help people find the best place to drill for oil (under the X, duh). It was awesome seeing all the little enzymes supersized! If you’ve got some of those 3D glasses lying around, check Tamiflu out now! Guess those red and blue glasses were good for something after all!

Tamiflu in 3D

My boyfriend SexyMan blogged about all this here on his site Emerging 3D, albeit sans the science. What he does have is details on how to trick out a mac so it can do stereoscopic 3D and a link to some Mac scientific software. Mac’s are sexy enough, but a tricked out 3D displaying new iMac with the cool new touch-mouse? My mouth is watering just THINKING about it!

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