Elucidating Heterocyclic Chemistry in Pharmaceuticals

June 2, 2013
Patricia Van Arnum
Pharmaceutical Technology

Volume 37, Issue 6

Researchers at the Scripps Research Institute advance heteorcylic chemistry trhough new reagents and reaction-tracking techniques.

Heterocyclic compounds play an important role in medicinal chemistry and drug synthesis. Like any important functional class of compounds, developments that facilitate their production or elucidate their reaction mechanisms are significant for process chemists in the pharmaceutical industry. In two separate developments, researchers at The Scripps Research Institute (TSRI) in La Jolla, California recently reported on the use of zinc sulfinates as reagents for the direct chemical functionalization of nitrogen-based heterocycles and on reaction-tracking tools to better elucidate copper-catalyzed reactions in making triazoles.

Patricia Van Arnum

A toolkit for synthesizing heterocycles

In the first development, scientists at TSRI developed a set of chemical tools to simplify the synthesis of nitrogen-based heterocycles through more time- and cost-efficient chemical modifications of these compounds. In their work, the researchers pointed out that although advances in transition-metal-mediated cross-coupling have simplified the synthesis of such heterocycles, the carbon–hydrogen functionalization of medicinally important heterocycles that does not rely on prefunctionalized starting materials was an area requiring further research (1). Although the properties of heterocycles, such as their aqueous solubility and their ability to act as ligands, are desirable for biological applications, these properties also make such heterocycles challenging as substrates for direct chemical functionalization (1). To address that problem, the researchers used zinc sulfinate salts to transfer alkyl radicals to heterocycles, thereby allowing for the mild (i.e., moderate temperature, 50 °C or less), direct, and simple formation of carbon–carbon bonds while reacting in a complementary fashion to other carbon–hydrogen functionalization methods (i.e., Minisci, borono-Minisci, electrophilic aromatic substitution, transition-metal-mediated carbon–hydrogen insertion, and carbon–hydrogen deprotonation) (1). The researchers prepared a toolkit of these reagents and studied their reactivity across a range of heterocycles (natural products, drugs, and building blocks) without recourse to protecting-group chemistry. The reagents could be used in tandem in a single pot in the presence of water and air (1).

"Feedback from companies that have started to use this toolkit indicates that it solves a real problem for them by boosting their chemists' productivity and by expanding the realm of compounds that they can feasibly generate," said Phil S. Baran, PhD, a professor in the Department of Chemistry and a member of the Skaggs Institute for Chemical Biology at TSRI who led the study, in a Nov. 28, 2012 TSRI press release. The resistance of nitrogen heterocycles to modification by traditional techniques has slowed drug discovery and has put potential modifications out of reach, notes TSRI.


The genesis behind the toolkit began with the goal for a more a simplified approach. "The ideal for discovery chemists would be a method that works in water, in an open flask, [and] with procedures that are simple enough to be automated," said Baran. His group's previous work in synthesizing a natural product heterocycle, palau'amine, a toxin made by sea sponges in the Western Pacific that has shown anticancer, antibacterial and antifungal pharmaceutical promise, was a helpful beginning.

"As we developed an understanding of how that compound reacts, we recognized that it might help us solve this larger problem that discovery chemists face," said Baran in the release. In that synthesis, palau'amine was made by a route featuring highly chemoselective transformations, cascade reactions, and a transannular cyclization to produce the trans-5,5 ring junction (2) and led the researchers to examine reagents that would modify heterocycles directly.

Although direct methods exist, they often require extreme temperatures as well as expensive and hazardous reagents. During 2010 and 2011, Baran's laboratory experimented with several comparatively safe chemical reagents that work in mild conditions to make commonly desired heterocycle modifications, such as the addition of a difluoromethyl group, according to the TSRI 2012 release. One of these new reagents, a zinc dialkylsulfinate salt (DFMS), which was designed to transfer the difluoromethyl group, turned out to work particularly well. "We quickly realized that we might be able to make related zinc sulfinate salts that would attach other functional groups to heterocycles," Baran said.

In their recent work, Baran and his team developed an initial toolkit consisting of 10 of these zinc-based salts, each of which attaches a different functional group to a heterocycle framework. "We selected these groups because they are commonly used by medicinal chemists," said Fionn O'Hara, PhD, a postdoctoral researcher in the Baran laboratory and a co-author of the recent study (1). In many cases, these reagents can be used to sequentially make more than one modification to a starting compound. The groups that can be attached with the new reagents include trifluoromethyl, difluoromethyl, trifluoroethyl, monofluoromethyl, isopropyl and triethylene glycol monomethyl ether.

To show the ability of the reagents to work in biological media, Baran's team used the reagents to difluoromethylate or trifluoromethylate heterocycles in a solution of cell lysate as well as to serve as a buffer medium (i.e., tris), which is commonly used in laboratory-dish tests.

Baran's laboratory collaborated with scientists from Pfizer. "They provided insight into the types of compounds that would be valuable, assistance with optimization, and, most importantly, testing of the chemistry in their drug-discovery laboratories, where it is meant to be used," Baran said.

The first of the zinc sulfinate salts, DFMS, also known as Baran difluoromethylation reagent, is being manufactured in bulk and marketed by chemical suppliers, according to the TSRI release. Baran is working to expand his initial toolkit to provide more heterocycle-modifying choices.

Click chemistry

Other researchers at TSRI recently reported on reaction-tracking techniques used to elucidate the mechanism behind the copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction. This reaction involves the use of copper compounds to catalyze the linkage of two functional groups, a nitrogen-containing azide and a hydrocarbon alkyne, to make a stable five-membered heterocycle, 1,2,3-triazole. The CuAAC process is an example of click chemistry, a term coined in 2001 by Nobel Laureate K. Barry Sharpless to describe a set of bond-forming reactions useful for the rapid assembly of molecules with desired function (3). Click transformations are easy to perform, give rise to their intended products in high yields with little or no byproducts, and work well under many conditions (3). Organic azides, as highly energetic and selective functional groups, were used in organic dipolar cycloadditions with olefins and alkynes among the reactions fulfilling the click criteria, but the low reaction rate of the azide–alkyne cycloaddition did not make them useful in the click context until the copper-catalyzed reaction (3). The copper-catalyzed reaction was reported separately by Sharpless et al. in the United States and Melda et al. in Denmark (3). It transforms organic azides and terminal alkynes into the corresponding 1,4-disubstituted 1,2,3-triazoles, in contrast to the uncatalyzed reaction, which requires higher temperatures and provides mixtures of 1,4- and 1,5-triazole regioisomers (3).

The simplicity and reliable performance of CuAAC under diverse conditions, including in water and in the presence of oxygen, has made it a useful method whenever covalent stitching of small molecules or large biopolymers is needed, exemplified by protein and nucleic-acid labeling, in vitro and in vivo imaging, and drug synthesis, according to an Apr. 4, 2013 TSRI press release.

"Despite its many uses, the nature of the copper-containing reactive intermediates that are involved in the catalysis had not been well understood, in large part due to the promiscuous nature of copper, which rapidly engages in dynamic interactions with other molecules," said Valery Fokin, an associate professor at TSRI, who was principal investigator for the new study examining the reaction-tracking techniques of CuAAC, in the TSRI April 2013 release.

The researchers explained that despite the widespread use of copper-catalyzed cycloaddition reactions, the mechanism of these processes was difficult to establish due to multiple equilibria between several reactive intermediates (4). They reported that real-time monitoring of a representative cycloaddition process by means of heat-flow reaction calorimetry showed that monomeric copper acetylide complexes are not reactive toward organic azides unless an exogenous copper catalyst was added. Additional experiments with an isotopically enriched exogenous copper source showed the stepwise nature of the carbon–nitrogen bond-forming sequence and the equivalence of the two copper atoms within the cycloaddition steps (4).

The research revealed that in the CuAAC reaction, two copper-containing catalytic units—copper centers—are needed to help build the new triazole structure. "By monitoring the reaction in real time, we showed that both copper atoms are needed and established the involvement of copper-containing intermediates that could not be isolated or directly observed," said Brady Worrell, a co-author in the study in the TSRI April 2013 release. The researchers used isotopic copper as one of the copper centers to track the reaction. "We hypothesized that the two copper centers would have distinct roles, but found unexpectedly that their functions during key steps in the reaction are effectively interchangeable," said Jamil Malik, also a co-author, in the TSRI 2013 release.

The research not only provides insight into the CuAAC reaction, but also enables development of new reactions that exploit weak interactions of copper catalysts with carbon–carbon triple bonds. Fokin and his team have begun to devise new reactions in which one copper center can be replaced with a different element, to pursue complementary biocompatible and efficient techniques, notes TSRI.

Patricia Van Arnum is a executive editor of Pharmaceutical Technology, 485 Route One South, Bldg F, First Floor, Iselin, NJ 08830 tel. 732.346.3072, pvanarnum@advanstar.com.


1. P.S. Baran et al., Nature 492 (7427), 95-99 (2012).

2. I.B. Seiple et al., Angew. Chemie Int. Ed. Engl. 49 (6), 1095-1098 (2010).

3. J. Hason and V.V. Fokin, Chem. Soc. Rev. 39 (4), 1302-1315 (2010).

4. B. T. Worrell, J. A. Malik, and V.V. Fokin, Science 340 (6131), 457-460 (2013).