Navigation Links
New drug design technique could dramatically speed discovery process
Date:4/13/2010

COLUMBUS, Ohio Scientists here are taking the trial and error out of drug design by using powerful computers to identify molecular structures that have the highest potential to serve as the basis for new medications.

Most drugs are designed to act on proteins that somehow malfunction in ways that lead to damage and disease in the body. The active ingredient in these medicines is typically a single molecule that can interact with a protein to stop its misbehavior.

Finding such a molecule, however, is not easy. It ideally will be shaped and configured in a way that allows it to bind with a protein on what are known as "hot spots" on the protein surface and the more hot spots it binds to, the more potential it has to be therapeutic.

To accomplish this, many drug molecules are composed of units called fragments that are linked through chemical bonds. An ideal drug molecule for a specific protein disease target should be a combination of fragments that fit into each hot spot in the best possible way.

Previous methods to identify these molecules have emphasized searching for fragments that can attach to one hot spot at a time. Finding structures that attach to all of the required hot spots is tedious, time-consuming and error-prone.

Ohio State University researchers, however, have used computer simulations to identify molecular fragments that attach simultaneously to multiple hot spots on proteins. The technique is a new way to tackle the fragment-based design strategy.

"We use the massive computing power available to us to find only the good fragments and link them together," said Chenglong Li, assistant professor of medicinal chemistry and pharmacognosy at Ohio State and senior author of a study detailing this work.

Li likens the molecular fragments to birds flying around in space, looking for food on the landscape: the protein surface. With this technique, he creates computer programs that allow these birds or molecular fragments to find the prime location for food, or the protein hot spots. The algorithm is originated from a computation technique called particle swarm optimization.

"Each bird can see the landscape individually, and it can sense other birds that inform each other about where the foods are," Li said. "That's how this method works. Each fragment is like a bird finding food on the landscape. And that's how we place the fragments and obtain the best fragment combination for specific protein binding sites."

Li verified that the technique works by comparing a molecular structure he designed to the molecular base of an existing cancer medication that targets a widely understood protein.

"My method reconstructed what pharmaceutical companies have already done," he said. "In the future, we'll apply this technique to protein targets for diseases that remain challenging to treat with currently available therapies."

The research appears online and is scheduled for later print publication in the Journal of Computational Chemistry.

Li said this new computer modeling method of drug design has the potential to complement and increase efficiency of more time-consuming methods like nuclear magnetic resonance and X-ray crystallography. For example, he said, X-ray fragment crystallography can be hard to interpret because of "noise" created by fragments that don't bind well to proteins.

With this new computer simulation technique, called multiple ligand simultaneous docking, Li instructs molecular fragments to interact with each other before the actual experimental trials, removing weak and "noisy" fragments so only the promising ones are left.

"They sense each other's presence through molecular force. They suppress the noise and go exactly where they are supposed to go," he said. "You find the right fragment in the right place, and it's like fitting the right piece into a jigsaw puzzle."

Before he can begin designing a molecule, Li must obtain information about a specific protein target, especially the protein structures. These details come from collaborators who have already mapped a target protein's surface to pinpoint where the hot spots are, for example, through directed mutations or from databases.

Li starts the design process with molecular fragments that come from thousands of existing drugs already on the market. He creates a computer image of those molecules, and then chops them up into tiny pieces and creates a library of substructures to work with typically more than a thousand possibilities.

That is where computational power comes into play.

"To search all of the possibilities of these molecular combinations and narrow them down, we need a massive computer," he said. Li uses two clusters of multiple computers, one in Ohio State's College of Pharmacy and the other in the Ohio Supercomputer Center, to complete the simulations.

The results of this computation create an initial molecular template that can serve as a blueprint for later stages of the drug discovery process. Medicinal chemists can assemble synthetic molecules based on these computer models, which can then be tested for their effectiveness against a given disease condition in a variety of research environments.

Li already has used this technique to identify molecules that bind to known cancer-causing proteins. He said the method can be applied to any protein that is a suspected cause of diseases of any kind, not just cancer.


'/>"/>

Contact: Chenglong Li
cli@pharmacy.ohio-state.edu
614-247-8786
Ohio State University
Source:Eurekalert

Related biology news :

1. IGERT fellows to design biodevices using flexible electronics
2. Researchers successfully simulate photosynthesis and design a better leaf
3. Synaptics SecurePad(TM) Selected as CES Innovations 2008 Design and Engineering Award Honoree
4. Singulex Teams With Wyeth Pharmaceuticals to Translate Pre-Clinical Biomarker Research Into Clinical Study Design
5. HIV isolate from Kenya provides clues for vaccine design
6. Book is the first high-resolution digital mouse brain atlas designed for Web applications
7. Carnegie Mellon scientists develop fluorescent proteins for live cell imaging, biosensor design
8. Specially-designed soils could help combat climate change
9. Popcorn-ball design doubles efficiency of dye-sensitized solar cells
10. Biodesigns Rittmann offers promising perspectives on societys energy challenge
11. Whales and dolphins influence new wind turbine design
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:4/13/2017)... 2017 UBM,s Advanced Design and Manufacturing event ... emerging and evolving technology through its 3D Printing and ... alongside the expo portion of the event and feature ... focused on trending topics within 3D printing and smart ... event will take place June 13-15, 2017 at the Jacob ...
(Date:4/11/2017)... , April 11, 2017 No two ... researchers at the New York University Tandon School ... Engineering have found that partial similarities between prints ... used in mobile phones and other electronic devices ... The vulnerability lies in the fact that ...
(Date:4/5/2017)... , April 5, 2017 Today HYPR ... that the server component of the HYPR platform is ... providing the end-to-end security architecture that empowers biometric authentication ... HYPR has already secured over 15 million users across ... manufacturers of connected home product suites and physical access ...
Breaking Biology News(10 mins):
(Date:6/28/2017)... MO (PRWEB) , ... June 28, 2017 , ... Supplies ... panel of leading experts gathered at the Society of Nuclear Medicine and Molecular Imaging ... isotope of technetium-99m (Tc-99m), which is used in 30 to 40 million nuclear medicine ...
(Date:6/27/2017)... ... June 27, 2017 , ... Biodex Medical Systems, Inc. announces the release ... device. This assistive aid lifts patients safely from a seated to a standing position ... The Mobility Assist is the latest in a line of Biodex products promoting safe ...
(Date:6/26/2017)... , ... June 26, 2017 , ... ... Melissa Kirkegaard, the former Associate Director of Product Development R&D at Allergan and ... pharmaceutical products at both start-up and established biopharma companies, has joined the firm ...
(Date:6/23/2017)... (PRWEB) , ... June 23, 2017 , ... Biova, LLC., ... Ph.D. has joined Biova’s Board of Directors. Dr. Henig will bring a wealth of ... Henig has served as the Chief Technical and Scientific Officer of four major global ...
Breaking Biology Technology: