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

Posted on by Catherine Zandonella
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.

Putting two and two together to make unexplored chemicals (J. American Chemical Society)

Posted on by Catherine Zandonella
Schematic for cobalt-catalyzed [2pi+2pi] reaction.
Schematic for cobalt-catalyzed [2pi+2pi] reaction. Image credit: Chirik group, Princeton University
By Tien Nguyen, Department of Chemistry

Researchers at Princeton have developed a new catalyst that may give unprecedented access to cyclobutanes, four-membered ring-containing molecules that have been relatively unexplored. Held back by the limited scope of previous methods, called [2π+2π] reactions, many cyclobutanes compounds have been out of reach, along with any unique properties that may be of interest to the pharmaceutical or fine chemical industry.

Led by Paul Chirik, the Edwards S. Sanford Professor of Chemistry, the team published the new cobalt-catalyzed [2π+2π] reaction and a thorough investigation of its mechanism in the Journal of the American Chemical Society on June 1.

“Because examples of this reaction are so rare, we wanted to understand why these cobalt complexes were special and how they worked in the reaction,” said Valerie Schmidt, lead author on the article and a postdoctoral researcher in the Chirik lab.

The new cobalt-catalyzed reaction overcame limitations that have plagued other similar methods, such as poor selectivity or requiring very reactive alkenes, which are chemical structures composed of two carbons joined by a double bond, as starting materials. The research team suspected their success came from certain molecules, called bis(imino)pyridine ligands, that are attached to the cobalt center and which are capable of passing electrons to and from the metal.

The Chirik group has used these redox active ligands previously, attached instead to iron to catalyze a [2π+2π] reaction reported in 2006. But the iron catalyst is highly sensitive to air and moisture, an issue that could be mitigated by switching to a less reactive metal like cobalt.

Replacing iron with cobalt presented a unique challenge in analysis because it altered the complex’s overall magnetic state from diamagnetic to paramagnetic. Unlike diamagnetic compounds, paramagnetic compounds can be difficult to identify by nuclear magnetic resonance (NMR) spectroscopy, a technique that uses a strong magnet to pulse atomic nuclei to reveal their environments, and a primary tool for characterizing molecules.

“We really had to be creative in finding ways to confirm our hypotheses about the catalyst,” Schmidt said. One extremely useful tool, analogous to nuclear magnetic resonance but that pulses electrons instead of nuclei, was electron paramagnetic resonance (EPR). This technique allowed the researchers to track the unpaired electrons, called radicals, throughout the reaction.

Additional data gathered from theoretical calculations, kinetic studies and x-ray crystal structure elucidation allowed the research team to sketch out a detailed reaction mechanism. They proposed that the cycle begins with successive coordination of the two tethered alkenes to the metal center.

Coordination of the second alkene was crucial, Schmidt explained, because it changed cobalt’s geometry, from square planar to tetrahedral, and effectively moved the unpaired electron from the ligand to the metal. Only then can the metal based radical promote the carbon-carbon forming event and push the reaction forward.

This action leads to the formation of a metallacycle—a pentagon shaped ring of four carbons and one cobalt atom. Cobalt is then squeezed out of the ring to release the final four-membered cyclobutane product in a process called reductive elimination. After testing a series of catalysts with varying size and electronic properties, the researchers suggested that reductive elimination was the turnover-limiting step, essentially the bottleneck of the reaction.

Armed with a deeper understanding of the cobalt catalyst system, the researchers hope to continually enhance its performance. “We want to make it as easy as possible to access cyclobutane containing molecules, because without this ability, we really have no idea what we are missing out on,” Schmidt said.

Read the abstract.

Schmidt, V. A.; Hoyt, J. M.; Margulieux, G. W.; Chirik, P. J. “Cobalt-Catalyzed [2π+2π] Cycloadditions of Alkenes: Scope, Mechanism and Elucidation of Electronic Structure of Catalytic Intermediates.” Journal of the American Chemical Society 2015, Just Accepted Manuscript.

This work was supported by the National Institutes of Health Ruth L. Kirschstein National Research Service Award (F32 GM109594) and Princeton University Intellectual Property Accelerator Fund.

 

Computational clues into the structure of a promising energy conversion catalyst (J. Physical Chemistry Letters)

Posted on by Catherine Zandonella
Mosaic structure
Representation of the mosaic texture of β-NiOOH and its possible structures.

By Tien Nguyen, Department of Chemistry

Hydrogen fuel is a promising source of clean energy that can be produced by splitting water into hydrogen and oxygen gas with the help of a catalyst, a material that can speed up the process. Although most known catalysts are inefficient, one called iron-doped nickel oxide is promising but not well understood.

Now researchers at Princeton University have reported new insights into the structure of an active component of the nickel oxide catalyst, known as β-NiOOH, using theoretical calculations. Led by Annabella Selloni, professor of chemistry at Princeton, the findings were published in The Journal of Physical Chemistry Letters on October 28.

“Understanding the structure is the basis for any further study of the material’s properties. If you don’t know the material’s structure you can’t know what it’s doing,” Selloni said. Nickel oxide’s exact structure has been difficult to determine experimentally because it is constantly changing during the reaction.

The research team took a theoretical approach and employed a “genetic algorithm” to search for the structure. Genetic algorithms operate under a set of parameters that draw inspiration from evolution by creating generation after generation of structures to arrive at the most “fit” or most likely candidates.

Taking the results of the genetic algorithm search in combination with computational techniques known as hybrid density functional theory calculations—which estimate a molecule’s electronic structure—co-author Ye-Fei Li, a former postdoctoral researcher at Princeton who is now at Fudan University, and Selloni were able to identify structures of nickel oxide that supported existing observations.

One such observation is the material’s mosaic texture, composed of tiny grain-like microstructures. The researchers propose that these microstructures are stable tunnel structures that relieve stress between layers. Another observed feature is the doubling of the distance between layers made of the same material, referred to as its c axis periodicity, which represents the alternating layers of Ni(OH)2 and NiO2 formed during the reaction.

Armed with a better understanding of the material’s structure, the scientists hope to further map out its activity in the reaction. “I’m interested in the microscopic mechanisms, what are the electrons and atoms doing?” Selloni said.

Read the abstract

Li, Ye-Fei and Annabella Selloni. “Mosaic Texture and Double c-Axis Periodicity of β–NiOOH: Insights from First-Principles and Genetic Algorithm Calculations.” J. Phys. Chem. Lett. 2014, 5, 3981.

This work was supported by the US Department of Energy, Division of Chemical Sciences, Geosciences and Biosciences under award DE-FG0212ER16286.