‘Radiolabeling’ lets scientists track the breakdown of drugs (Nature)

Graduate student Renyuan Pony Yu
Renyuan Pony Yu, a graduate student working with Princeton Professor Paul Chirik, has discovered a new way to radiolabel compounds for use in drug development.

By Tien Nguyen, Department of Chemistry

A new method for labeling molecules with radioactive elements could let chemists more easily track how drugs under development are metabolized in the body.

Chemists consider thousands of compounds in the search for a new drug, and a candidate’s metabolism is a key factor that must be evaluated carefully and quickly. Researchers at Princeton University and pharmaceutical company Merck & Co., Inc. report in the journal Nature that scientists can selectively replace hydrogen atoms in molecules with tritium atoms — a radioactive form of hydrogen that possesses two extra neutrons — to “radiolabel” compounds. This technique can be done in a single step while preserving the biological properties of the parent compound.

While current state-of-the-art techniques are quite reliable, they only work when dissolved in specific solvents, ones that aren’t always capable of dissolving the drug compound of interest. The researchers’ method, however, used an iron-based catalyst that is tolerant to a wider variety of solvents, and it labels the molecules at the opposite positions as compared to existing methods.

“The fact that you can access other positions is what makes this reaction really special,” said corresponding author Paul Chirik, the Edwards S. Sanford Professor of Chemistry at Princeton. Previous methods only incorporate radioactive tritium atoms into the molecule directly next to an atom or a group of atoms called a directing group. The new iron-catalyzed method does not require a directing group, and instead places tritium at whatever positions in the molecules are the least crowded.

“Radiolabeled compounds help medicinal chemists get a better picture of what actually happens to the drug by showing how the drug is metabolized and cleared,” said David Hesk, a collaborator at Merck and co-author on the work. By rapidly assessing the compounds’ metabolism early on, scientists can shorten the time it takes to develop and bring a drug to market. “Having another labeling reaction is very powerful because it gives radiochemists another tool in the toolbox,” he said.

This unique reactivity was actually discovered unexpectedly. Renyuan Pony Yu, a graduate student in the Chirik lab, had originally set out to use their iron catalyst for a different reaction that they were collaborating on with Merck. To study the iron catalyst’s capabilities, Yu subjected it to a technique called proton nuclear magnetic resonance spectroscopy (NMR), which allows chemists to deduce the positions of hydrogen atoms in molecules.

“We started seeing this beautiful, very systematic pattern of signals in the NMR, but we didn’t really know what they were,” said Yu, who is first author on the new study. Particularly puzzling was the fact that the pattern of signals would disappear over time.

The researchers turned to Istvan Pelczer, Director of the NMR Facility at Princeton chemistry and co-author on the work, who developed a special technique that helped them analyze the signals with much greater confidence. Using this method, they realized that the iron catalyst was reacting with the liquid solvent used to dissolve the NMR sample. The solvent’s deuterium atoms, another form of hydrogen that has one extra neutron and is not radioactive, were replacing the hydrogen atoms.

It wasn’t until Yu presented his findings to Matt Tudge, the Princeton authors’ collaborator at Merck, that the catalyst’s potential to introduce tritium atoms into radiolabeled molecules was recognized. “This is a classic example where you really need both partners,” Chirik said. “We were the catalyst experts, but they were the applications experts.”

Though tritium-labeled compounds are used mostly in metabolism studies, they can also be helpful at the very outset of a drug-discovery project to identify a biological target that the potential drugs can be tested against. The biological target could be an enzyme or protein associated with a certain disease. For example, statins are a well-known class of cholesterol-lowering drugs that target a specific enzyme in the body called HMG-CoA reductase.

To explore the scope of the reaction, Yu first optimized the reaction to incorporate deuterium atoms, which is commonly accepted as a model system for tritium. He found that the iron catalyst was surprisingly robust and successfully labeled many different types of compounds, including some from Merck’s library of past drug candidates.

“It was a very exciting project for me because I got to work with real drugs that are fully functionalized and useful,” Yu said. One of their test substrates was Claritin, which Yu bought from a local store; he extracted its active ingredient back in the lab.

Finally, Yu traveled to Merck’s campus in Rahway, where he received radioactivity training — Chirik’s laboratory isn’t equipped to handle radioactivity — and performed the reactions using tritium gas. The reactions were run in a special apparatus that looks like a steel-lined box and releases radioactive tritium gas. The apparatus can capture any unspent gas to limit the amount of radioactive waste produced.

Chemists take care to handle radioactive compounds and waste very carefully, but tritium’s radioactivity is so weak that the particles it emits cannot penetrate simple glassware. For this reason, tritium-labeled compounds can’t be used in any human imaging studies such as PET scans, which require radiolabeled compounds that emit high-energy particles.

This past summer, Yu presented the preliminary results of the iron-catalyzed reaction at the 2015 International Isotope Society Symposia to researchers in the radiolabeling and pharmaceutical community. They were very excited about the research and eager to use the catalyst in their own studies, Yu said.

But the major challenge for the researchers is that the iron catalyst is extremely air and moisture sensitive, and it can only be handled inside a glovebox, a special chamber in which oxygen and water vapor have been excluded. The Chirik group is working to develop a more stable catalyst that can be made commercially available, and have recently entered into a partnership with Green Center Canada, a company that helps bring academic research to market.

In the meantime, the Chirik group has found that the iron catalyst can replace hydrogen atoms with other groups besides deuterium and tritium atoms and is extending this chemistry into many other projects in the lab.

“This project is always going to be a special one for me because it’s kind of a pivot point for the type of chemistry that our group can do,” Chirik said, “and there’s this really cool application.”

Read the abstract.

Yu, R. P.; Hesk, D.; Rivera, N.; Pelczer, I.; Chirik, P. J. “Iron-Catalyzed Tritiation of Pharmaceuticals.” Nature, 2016, DOI: 10.1038/nature16464.

This work was supported by Merck & Co. and Princeton University’s Intellectual Property Accelerator Fund.

In rainforests, battle for sunlight shapes forest structure (Science)

New finding helps explain rainforests’ influence on global climate

Rainforest photo
Rainforests around the globe have a remarkably consistent pattern of tree sizes. Now researchers have found that the reason for this structure has to do with the competition for sunlight after a large tree falls and leaves an opening in the canopy. Image credit: Caroline Farrior

By Catherine Zandonella, Office of the Dean for Research

Despite their diversity, the structure of most tropical rainforests is highly predictable. Scientists have described the various sizes of the trees by a simple mathematical relationship called a power law.

In a new study using data from a rainforest in Panama, researchers determined that competition for sunlight is the underlying cause of this common structure, which is observed in rainforests around the globe despite differences in plant species and geography. The new finding can be used in climate simulations to predict how rainforests absorb excess carbon dioxide from the atmosphere.

The study, conducted by researchers at Princeton University, the National Institute for Mathematical and Biological Synthesis, the Smithsonian Tropical Research Institute and collaborating institutions, was published Jan. 8 in the journal Science. The investigation was supported in large part by the National Science Foundation.

Diagram of rainforest trees
After a large tree falls, many small individuals are able to grow due to an increase in available sunlight (T=1). Once they have grown to touch one another (T=2), they begin to overtop one another and leave individuals behind in the understory (T=3). Image courtesy of Caroline Farrior.

The researchers found that the rainforest structure stems from what happens after a tall tree falls and creates a gap in the canopy. The gap enables sunlight to reach the forest floor and fuel the rapid growth of small trees. Over time, the trees’ crowns grow to fill the gap until the point where not all of the trees can fit in the sunlit patch. Some will be left behind in the shade of their competitors.

“This process of moving from fast growth in the sun to slow growth in the shade sets up this characteristic size structure that is common across tropical rainforests, despite the differences in their environments,” said Caroline Farrior, first author of the study who is a postdoctoral fellow at the National Institute for Mathematical and Biological Synthesis and will soon be an assistant professor of integrative biology at the University of Texas-Austin.

Farrior, who earned her Ph.D. in ecology and evolutionary biology from Princeton University in 2012, completed most of the work as a postdoctoral researcher in the Princeton Environmental Institute with co-author Stephen Pacala, Princeton’s Frederick D. Petrie Professor in Ecology and Evolutionary Biology.

(View a video interview with Dr. Farrior courtesy of the National Institute for Mathematical and Biological Synthesis.)

“Rainforests store about twice as much carbon as other forests,” Pacala said. “About half of that is due to huge trees, but the other half is all that stuff in the middle. It is not possible to build an accurate climate model without getting that right.”

To gain an understanding of how rainforests grow, Farrior and colleagues analyzed decades of tree census data from a 50-hectare plot on Barro Colorado Island in the Panama Canal. From these data, they identified the mechanism most important in driving the observed size structure in tropical rainforests.

“With this new understanding of tropical forests, we can go on to build better models, we can make more accurate estimates of the carbon storage that’s currently in tropical forests, and we can go on to more accurately predict the pace of climate change in the future,” Farrior said.

The research included work by Stephanie Bohlman, an assistant professor at the University of Florida and a research associate at the Smithsonian Tropical Research Institute (STRI), and Stephen Hubbell, a staff scientist at STRI.

The study was supported by Princeton’s Carbon Mitigation Initiative and the National Institute for Mathematical and Biological Synthesis (NSF grant no. DBI-1300426) at the University of Tennessee-Knoxville. The Barro Colorado Island forest dynamics research project was founded by Stephen Hubbell, Robin Foster and Richard Condit of STRI.

The study, “Dominance of the suppressed: Power-law size structure in tropical forests,” by Caroline Farrior, Stephanie Bohlman, Stephen Hubbell and Stephen Pacala, appeared in the journal Science on Jan. 8, 2016.

PPPL physicists simulate innovative method for starting up tokamaks without using a solenoid (Nuclear Fusion)

Francesca Poli
PPPL Scientist Francesca Poli. Photo Credit: Elle Starkman / PPPL Office of Communications. PPPL, located on Princeton University’s Forrestal Campus and managed by the University, is devoted to developing practical solutions for the creation of sustainable energy from fusion and to creating new knowledge about the physics of ultra-hot, charged gases known as plasmas.

By Raphael Rosen, PPPL Office of Communications

Scientists at the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) have produced self-consistent computer simulations that capture the evolution of an electric current inside fusion plasma without using a central electromagnet, or solenoid.

The computer simulations of the process, known as non-inductive current ramp-up, were performed using TRANSP, the gold-standard code developed at PPPL. The results were published in October 2015 in the journal Nuclear Fusion. The research was supported by the DOE Office of Science.

In traditional donut-shaped tokamaks, a large solenoid runs down the center of the reactor. By varying the electrical current in the solenoid scientists induce a current in the plasma. This current starts up the plasma and creates a second magnetic field that completes the forces that hold the hot, charged gas together.

But spherical tokamaks, a compact variety of fusion reactor that produces high plasma pressure with relatively low magnetic fields, have little room for solenoids. Spherical tokamaks look like cored apples and have a smaller central hole for the solenoid than conventional tokamaks do. Physicists, therefore, have been trying to find alternative methods for producing the current that starts the plasma and completes the magnetic field in spherical tokamaks.

One such method is known as coaxial helicity injection (CHI). During CHI, researchers switch on an electric coil that runs beneath the tokamak. Above this coil is a gap that opens into the tokamak’s vacuum vessel and circles the tokamak’s floor. The switched-on electrical current produces a magnetic field that connects metal plates on either side of the gap.

Researchers next puff gas through the gap and discharge a spark across the two plates. This process causes magnetic reconnection — the process by which the magnetic fields snap apart and reconnect. This reconnection creates a magnetic bubble that fills the tokamak and produces the vital electric current that starts up the plasma and completes the magnetic field.

This current must be nurtured and fed. According to lead author Francesca Poli, the new computer simulations show that the current can best be sustained by injecting high-harmonic radio-frequency waves (HHFWs) and neutral beams into the plasma.

HHFW’s are radio-frequency waves that can heat both electrons and ions. The neutral beams, which consist of streams of hydrogen atoms, become charged when they enter the plasma and interact with the ions. The combination of the HHFWs and neutral beams increases the current from 300 kiloamps to 1 mega amp.

But neither HHFWs nor neutral beams can be used at the start of the process, when the plasma is relatively cool and not very dense. Poli found that HHFWs would be more effective if the plasma were first heated by electron cyclotron waves, which transfer energy to the electrons that circle the magnetic field lines.

“With no electron cyclotron waves you would have to pump in four megawatts of HHFW power to create 400 kiloamps of current,” she said. “With these waves you can get the same amount of current by pumping in only one megawatt of power.

“All of this is important because it’s hard to control the plasma at the start-up,” she added. “So the faster you can control the plasma, the better.”

PPPL is managed by Princeton University for the U.S. Department of Energy’s Office of Science.

Read the abstract.

F.M. Poli, R.G. Andre, N. Bertelli, S.P. Gerhardt, D. Mueller and G. Taylor. “Simulations towards the achievement of non-inductive current ramp-up and sustainment in the National Spherical Torus Experiment Upgrade.” Nuclear Fusion. Published October 30, 2015. DOI: 10.1088/0029-5515/55/12/123011