No magic show: Real-world levitation to inspire better pharmaceuticals

ORIGINAL: Argonne National Lab

BY JARED SAGOFF 
SEPTEMBER 12, 2012

It’s not a magic trick and it’s not sleight of hand – scientists really are using levitation to improve the drug development process, eventually yielding more effective pharmaceuticals with fewer side effects.

Scientists at the U.S. Department of Energy’s (DOE) Argonne National Laboratory have discovered a way to use sound waves to levitate individual droplets of solutions containing different pharmaceuticals. While the connection between levitation and drug development may not be immediately apparent, a special relationship emerges at the molecular level.

At the molecular level, pharmaceutical structures fall into one of two categories: amorphous or crystalline. Amorphous drugs typically are more efficiently taken up by the body than their crystalline cousins; this is because amorphous drugs are both more highly soluble and have a higher bioavailability, suggesting that a lower dose can produce the desired effect.

“One of the biggest challenges when it comes to drug development is in reducing the amount of the drug needed to attain the therapeutic benefit, whatever it is,” said Argonne X-ray physicist Chris Benmore, who led the study.

“Most drugs on the market are crystalline – they don’t get fully absorbed by the body and thus we aren’t getting the most efficient use out of them,” added Yash Vaishnav, Argonne Senior Manager for Intellectual Property Development and Commercialization.

Getting pharmaceuticals from solution into an amorphous state, however, is no easy task. If the solution evaporates while it is in contact with part of a vessel, it is far more likely to solidify in its crystalline form. “It’s almost as if these substances want to find a way to become crystalline,” Benmore said. 

In order to avoid this problem, Benmore needed to find a way to evaporate a solution without it touching anything. Because liquids conform to the shape of their containers, this was a nearly impossible requirement -- so difficult, in fact, that Benmore had to turn to an acoustic levitator, a piece of equipment originally developed for NASA to simulate microgravity conditions.

Levitation or “containerless processing” can form pristine samples that can be probed in situ with the high-energy X-ray beam at Argonne’s Advanced Photon Source. “This allows amorphization of the drug to be studied while it is being processed,” said Rick Weber, who works on the project team at the synchrotron.

The acoustic levitator uses two small speakers to generate sound waves at frequencies slightly above the audible range – roughly 22 kilohertz. When the top and bottom speakers are precisely aligned, they create two sets of sound waves that perfectly interfere with each other, setting up a phenomenon known as a standing wave.

At certain points along a standing wave, known as nodes, there is no net transfer of energy at all. Because the acoustic pressure from the sound waves is sufficient to cancel the effect of gravity, light objects are able to levitate when placed at the nodes.

Although only small quantities of a drug can currently be “amorphized” using this technique, it remains a powerful analytical tool for understanding the conditions that make for the best amorphous preparation, Vaishnav explained.

Argonne researchers have already investigated more than a dozen different pharmaceuticals, and the laboratory’s Technology Development & Commercialization Division is currently pursuing a patent for the method. Technology Development & Commercialization is also interested in partnering with the pharmaceutical industry to develop the technology further as well as to license it for commercial development.

After adapting the technology for drug research, the Argonne scientists teamed up with Professors Stephen Byrn and Lynne Taylor at the Department of Industrial and Physical Pharmacy at Purdue University and Jeffery Yarger of the Department of Chemistry and Biochemistry at Arizona State University. The group is now working on identifying which drugs the levitation instrumentation will impact most strongly.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy'sOffice of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Molecular machine could hold key to more efficient manufacturing

ORIGINAL: U Manchester

11 Jan 2013

An industrial revolution on a minute scale is taking place in laboratories at The University of Manchester with the development of a highly complex machine that mimics how molecules are made in nature.

The artificial molecular machine developed by Professor David Leigh FRS and his team in the School of Chemistry is the most advanced molecular machine of its type in the world. Its development has been published in the journal Science.

Professor Leigh explains: “The development of this machine which uses molecules to make molecules in a synthetic process is similar to the robotic assembly line in car plants. Such machines could ultimately lead to the process of making molecules becoming much more efficient and cost effective. This will benefit all sorts of manufacturing areas as many man made products begin at a molecular level. For example, we’re currently modifying our machine to make drugs such as penicillin.” 

The machine is just a few nanometres long (a few millionths of a millimetre) and can only be seen using special instruments. Its creation was inspired by natural complex molecular factories where information from DNA is used to programme the linking of molecular building blocks in the correct order. The most extraordinary of these factories is the ribosome, a massive molecular machine found in all living cells.

Professor Leigh’s machine is based on the ribosome. It features a functionalized nanometre-sized ring that moves along a molecular track, picking up building blocks located on the path and connecting them together in a specific order to synthesize the desired new molecule. 

First the ring is threaded onto a molecular strand using copper ions to direct the assembly process. Then a “reactive arm” is attached to the rest of the machine and it starts to operate. The ring moves up and down the strand until its path is blocked by a bulky group. The reactive arm then detaches the obstruction from the track and passes it to another site on the machine, regenerating the active site on the arm. The ring is then free to move further along the strand until its path is obstructed by the next building block. This, in turn, is removed and passed to the elongation site on the ring, thus building up a new molecular structure on the ring. Once all the building blocks are removed from the track, the ring de-threads and the synthesis is over.

Professor Leigh says the current prototype is still far from being as efficient as the ribosome: “The ribosome can put together 20 building blocks a second until up to 150 are linked. So far we have only used our machine to link together 4 blocks and it takes 12 hours to connect each block. But you can massively parallel the assembly process: We are already using a million million million (10¹⁸) of these machines working in parallel in the laboratory to build molecules.”

Professor Leigh continues: “The next step is to start using the machine to make sophisticated molecules with more building blocks. The potential is for it to be able to make molecules that have never been seen before. They’re not made in nature and can’t be made synthetically because of the processes currently used. This is a very exciting possibility for the future.” 

Notes for editors

A short video that illustrates the machine and how it works is available from the press office.

It can also be viewed on the university’s YouTube page here. 

Images can also be obtained from the press office. 

Professor David Leigh is available for interviews on Friday 11 January. 

The paper “Sequence-Specific Peptide Synthesis by an Artificial Small-Molecule Machine” will be published in Science on Friday 11 January. 

For more information and image or interview requests please contact: 

Morwenna Grills

Media Relations Officer

Faculty of Engineering and Physical Sciences

The University of Manchester 

Tel: 0161 275 2111

Mobile: 07920 087466

Email: Morwenna.Grills@manchester.ac.uk

Folding research recruits unconventional help

ORIGINAL: CELL - Current Biology

Michael Gross is a science writer based at Oxford. He can be contacted via his web page at www.michaelgross.co.uk

Summary
A denatured protein chain can find its well-ordered three-dimensional structure, the native state, in under a second, using only the information contained in the sequence. For researchers, however, the prediction of structures from sequences is a hard problem, so they are now recruiting all the help they can get, including idle computers and game consoles, game players, and little hints from evolution. Michael Gross reports.

MAIN TEXT

Protein folding is one of the miracles of nature that human technology finds quite difficult to follow. Ever since the classic ribonuclease A experiments of Christian Anfinsen in the 1960s it has been clear that the amino acid sequence of a polypeptide chain determines the unique three-dimensional folded conformation it will adopt under physiological conditions. Even though we now know that some proteins remain intrinsically disordered, and some may ‘fold around’ a ligand, it is still true that a protein's structure, and hence its function, is somehow encoded in the sequence of the amino acids. As the theoretician Cyrus Levinthal pointed out early on, there is an astronomical number of wrong conformations which the chain cannot possibly try out in a reasonable time, so there must be mechanisms that allow polypeptide chains to find the native state encoded in their sequence. Folding researchers have elucidated some of these mechanisms in the last decades, but so far haven't been able to decipher the code and therefore aren't generally able to read a sequence and predict what shape it will adopt.

An early approach to the problem was to build bigger computers dedicated to simulations of folding, a development that culminated in the development of IBM's Blue Gene, first announced in 1999 with the explicit target of tackling protein folding, but it didn't crack the prediction problem once and for all. By the turn of the millennium, computer simulations of the protein movements could only just cover a microsecond, while it was known from experimental studies that the relevant folding reactions happened on the millisecond timescale.

Folding at home

Based on that shortfall of computing power and the increasing availability of PCs connected via the internet, the group of Vijay Pande at Stanford University developed a distributed computing program called Folding@home, using the now widely adopted practice of chopping a problem into small parcels and farming them out to many computers that are online but idle (as, for instance, most computers in universities are, most of the time).

Since 2006, the lab also offers a version of the program that runs on games consoles, which enabled a dramatic increase in the processing power accessible to the program. In September 2007, the program achieved a consistent level above one petaFLOPS (10¹⁵ floating-point operations per second), as the first computing system of any kind to do so (the fastest supercomputer at the time was Blue Gene with just over a quarter of that power). In November 2011, Folding@home passed the milestone of six petaFLOPS.

Folding puzzle: The rearrangement of a linear polymer into a compact three-dimensional shape proceeds autonomously in nature but is still puzzling biochemists. (Photo: Michael Gross.)

The simulation of protein dynamics by the Folding@home software is based on the observation that protein chains populate certain free energy minima for a period of time, and then quickly move on to another minimum. Pande's group uses so-called Markov state models to find connections between these minima and map the likelihood of transitions. In 2010, the group used this approach combined with the distributed computing power of Folding@home to simulate the folding of the 39-residue protein NTL9, which takes about 1.5 milliseconds (J. Am. Chem. Soc. (2010), 132, 1526–1528). The time span of this simulation was a thousand times longer than that achieved by other methods.

Pande's group uses this approach to address a range of biomedically relevant issues around protein folding, including diseases that involve misfolded proteins (such as Alzheimer's, Parkinson's and Huntington's disease), the fundamental questions of protein folding mechanisms, and the prediction of unknown structures from sequences, which feed into commercial drug design. “Through the Folding@home distributed computing project, we have been able to muster an unparalleled computational resource for studying protein folding, allowing us to study complex systems on timescales thousands of times longer than would otherwise be possible,” says Pande. The group makes all datasets generated from the research available on request.

Folding game

Meanwhile, the group of David Baker at the University of Washington at Seattle had developed an algorithm called Rosetta for the prediction of small protein structures, and also set up distributed computing (Rosetta@home) to provide additional computing power for the prediction work. Participants who have this program installed on their computers can watch how the protein chain gradually finds its native conformation. It so happened that some participants watched the process and spotted possible arrangements that would improve the energy-efficient packing, but weren't able to interact with the program, finding themselves in the situation of someone watching a game show and shouting at their TV set.

Folding fun: Tens of thousands of online game players around the world have contributed to folding research via the game Foldit, developed at the University of Washington at Seattle. (Photo: Mohini Patel Glanz.)