Planting acetone within peptides

It is great to witness your students succeed, especially when you meet them at conferences some years after graduation and learn about their notable accomplishments. As Ved Srivastava and I were running the American Peptide Symposium in Florida last week, I ran across Naila Assem and heard about her recent work. Naila recently accepted a job at Novozymes in San Francisco (, which is excellent. I asked her to do a guest post on her recent work with Phil Dawson at Scripps. Here it is, verbatim:

After working on peptidomimetic ligation in the Yudin lab (, pursuing my post-doctorate with a pioneer in the peptide ligation field, such as Dr. Philip Dawson, seemed like the logical next step for me. Upon completing my Ph.D., I packed my bags and joined the Dawson lab at the Scripps Research Institute. One of the things I have greatly enjoyed about working in the Dawson lab is how multidisciplinary the projects have been. While working on synthesizing small peptide mimics of a highly conserved epitope on the Hepatitis C virus, I came across dichloroacetone (DCA), a cross-linking reagent. On today’s post I would like to highlight the utility of DCA, which is the subject of a recently published paper in Angewandte Chemie (

Since short peptides do not typically form stable secondary structures, the Dawson lab utilizes synthetic techniques to display small peptides in a biologically relevant manner. In our work with Hepatitis C we found that DCA was effective at cyclizing two cysteine side chains. From this observation we wondered if we could use DCA to stabilize helical secondary structure. What further attracted us to DCA was the ketone within the akyl chain that could potentially be used as a site for functionalization. We first tested to see if dichloroacetone could be used to cross-link two cysteine side chains, in the i and i+4 positions, to induce helical formation. Although the cross-linking reaction between two cysteine side chains proved to be selective and high yielding we found that it did not give enough slack for proper helix formation. On the other hand, cross-linking between two homo-cysteines gave proper helix-stabilization.

Once we were able to establish helicity we explored the ketone’s ability to undergo oxime ligation. We first tested typical aniline catalyzed oxime ligation conditions and found full conversion to the desired product after 16 hours. We were able to demonstrate the ability to tag the cross-linker with a diverse set of labels including fluorophores such a Alexafluor 647 and Alexafluor 488. We were also able to biotynilate or add peptide tags such as a poly-arginine or FLAG-tag. Additionally, we could dimerize the helical peptide with a bis-aminooxy linker or simply add an aminooxy functionality that can be used to conjugate on to the surface of carrier proteins or virus like particles.

The utility of DCA in a protein/peptide interaction setting was demonstrated when we synthesized an S-peptide analog and bound it to RNAse S. The DCA cross-linked peptide analog (Ac-KETAAhCKFEhCQHMDS-NH2) was successfully co-crystallized at 2.2 Å. The cross-linked peptide structure was found to be highly conserved when compared to the natural S-peptide in complex to RNAse S. Additionally, we were able to show that DCA can be used the make peptide cycles and bicycles.


On the heels of condensation

My lab has been interested in new ways to access uncommon substitution motifs in aromatic heterocycles. Here is our rationale: while there are countless examples of imaginative approaches to borylate an existing ring using directed ortho-metallation or C-H activation, the corresponding reactions are governed by the innate reactivity of a given heterocycle. The selectivity also depends on the reagent that effects the site-selective transformation.

We have been thinking about ways to assemble structures using different rules. As part of this undertaking, we placed our bets on amphoteric molecules and explored ways of controlling the selectivity of boron group transfer using simple condensation reactions.

In grey rectangles below you see some of the amphoteric species described by our lab in the past. In green you see a new and surprisingly stable class of compounds described by my postdoctoral fellow Piera Trinchera and graduate student Victoria Corless in a recent Angewandte paper. The dicarbonyl scaffold, prepared using photocatalysis and organocatalysis (special thanks to MacMillan, Stephenson, and Yoon for trailblazing this area) can be transformed into several types of heterocycles with unusual regiochemistry of the C-B bond. I think medicinal chemists might be interested in this technique as there are many molecules one can imagine making using dicarbonyls. I applaud Piera and Victoria’s efforts. I was also glad to see Chemical and Engineering News comment on their research. The next issue of Angewandte will have the cover designed by Piera and Victoria, which is a nice touch (although I am left with a bill for 2100 Euros for their beautiful artwork…).


I would end by pondering over a curious finding that most isomers accessible through our condensative approach are not easily accessible by alternative metal-based techniques. You might ask “Is there a reason for that?”. I would say – there ain’t one, although it is tempting to speculate on the innate selectivity of condensation reactions.