a unique opportunity!


by Ms Lara Malins, PhD candidate

 

Receiving the 2012 Feutrill Prize for the best student
presented lecture at ICOS19.

During my years as an undergraduate, I recall spending late nights cramming for organic chemistry exams, which almost always meant learning to recognise various “named reactions,” in which you identify and associate a certain chemical transformation with the name of its discoverer: the Brooke rearrangement, the Finkelstein reaction, the Luche reduction, to name a few. I remember talking extensively about the synthetic importance of forming new carbon-carbon bonds in the form of metal catalysed “cross-coupling reactions;” the names that immediately come to mind are Heck, Sonogashira, Miyaura, Negishi, and Suzuki — many of whom shared the Nobel Prize in Chemistry in 2010. At the time I committed these named reactions to memory, however, they were truly just names — I could not picture the person behind the reaction, and certainly never thought I would have the opportunity to get close enough to try. But as I sat down with Nobel Laureate Ei-ichi Negishi at the 19th International Conference on Organic Synthesis (ICOS19) over a sandwich and a cup of tea, I was amazed to learn of the stories behind his discovery. I enjoyed his honesty about the challenges of research, his willingness to acknowledge others for their important contributions, and even his self-professed penchant for predicting future winners of the Nobel Prize. For the first time, I could place a face and a personal experience behind the famous name and reaction. It was truly an inspiring moment.

Meeting with a chemistry Nobel Laureate was just one of the many unique opportunities I had at this year’s ICOS19 in Melbourne, Australia. As a third-year organic chemistry PhD student under the supervision of Dr Richard Payne, I have had the opportunity to attend numerous conferences over the years, some as close as University of New South Wales, and others as far away as Hawaii and the island of Crete in Greece. The ICOS meeting, however, was truly exceptional in the breadth of outstanding speakers present — many of whom will no doubt live on as future undergraduates commit their names and reactions to memory. Additionally, ICOS19 was my first opportunity to give an oral presentation at an international conference and in front of leaders in my field. It was an honour to be selected as one of twenty student speakers tasked with providing an overview of the results of their PhD research.

In the Payne group, a major research focal point is the synthesis of complex peptide and glycopeptides fragments with the aim of understanding their biological significance and exploiting their unique properties for the purpose of developing therapeutic agents, such as cancer vaccines. In order to understand the biological function of a protein or peptide, particularly those with additional layers of complexity, such as the attachment of carbohydrate chains, it is increasingly important to be able to access these compounds synthetically in the laboratory. My research focuses on the development of novel methods for the synthesis of large peptide and glycopeptide fragments to aid in this goal.

The most common method for synthesising peptide fragments is called solid phase peptide synthesis (SPPS), which involves anchoring amino acids to a solid resin or bead and growing the peptide chain through an iterative process, one amino acid at a time. Though robust and highly efficient, SPPS has significant limitations. Long (> 50 amino acids) peptide chains tend to be difficult to synthesise using SPPS due to the tendency of peptide chains to form aggregates and develop more complex secondary and tertiary structures in much the same manner that large proteins may fold and dimerise. One solution to this problem lies in the synthesis of large peptide fragments and small proteins via ligation methodologies. If we synthesise two medium-sized peptide chains by SPPS and then link the two fragments together in an efficient and selective manner, like two complimentary pieces of a jigsaw puzzle, we can quickly grow the length of our peptide chain (Scheme 1a).

Scheme 1. A) Model ligation reaction for the synthesis of large peptide fragments. B) Native chemical ligation reaction between a Cys-containing peptide (Peptide 2) and a thioester-containing fragment (Peptide 1). C) Ligation-desulfurisation chemistry utilising unnatural thiol-containing amino acid residues.

 

The most commonly used ligation technique is called native chemical ligation (NCL) and was discovered in 1994. It involves the reaction of one peptide bearing an N-terminal cysteine (Cys) amino acid residue and another complimentary peptide bearing a reactive C-terminal thioester moiety. In the course of the reaction, the thiol component of the Cys-containing peptide (Peptide 2 in Scheme 1b) attacks the thioester of the second peptide fragment (Peptide 1) in a transthioesterification reaction. A spontaneous rearrangement of the reaction intermediate then allows for the formation of a native peptide bond. Most importantly, the reaction proceeds in a very efficient and selective manner, in the presence of all naturally occurring amino acid residues. The one major drawback to this technique, however, is the requirement for a Cys residue in the target peptide chain; as Cys is relatively uncommon in naturally occurring peptides (1.8% abundance), this represents a severe limitation to the number of accessible peptides and proteins. In an effort to circumvent this issue, many groups have explored the synthesis of unnatural amino acid derivatives that bear the same reactive thiol group as Cys. These building blocks may be utilised in the ligation reaction but are able to be converted back into a natural amino acid residue (by removal of the sulfur-containing thiol group) following ligation. This motif is often referred to as ligation-desulfurisation chemistry (Scheme 1c).

My contributions to the area of ligation-desulfurisation chemistry as a part of the Payne group consist of the synthesis of an unnatural variant of the amino acid phenylalanine (Phe), bearing a reactive thiol group, and thereby enabling it to facilitate the linking of peptide chains via native chemical ligation. In my ICOS presentation, I discussed the synthesis of the Phe-derived building block (compound 1) from commercially available starting materials and demonstrated its application in ligation-desulfurisation chemistry by synthesising a variety of larger peptide fragments (Scheme 2).

Scheme 2. Unnatural thiol-derived phenylalanine (Phe) building block 1 and selenol-Phe building block 2, and their application in native chemical ligation-desulfurisation/deselenisation chemistry.

 

As a group, we have also become very interested in the role of selenium, an element lying just below sulfur in the periodic table and maintaining similar chemical properties, in facilitating native chemical ligation. Other research groups have recently shown that selenocysteine (Sec), a selenium analog of Cys, is also able to facilitate native chemical ligation. Following the ligation, the selenium moiety may be removed in a deselenisation reaction with much greater selectivity than the typical conditions used for desulfurisation (which remove any thiol present in the peptide chain — even those which are important to the overall structure and activity of the protein). Thus, having completed our synthesis of the thiol-containing Phe building block 1, we embarked upon the synthesis of an analogous selenium-derivative of Phe (compound 2) and demonstrated for the first time that this unnatural building block can be used to facilitate ligation (Scheme 2). Furthermore, the unnatural selenium appendage can be selectively removed after ligation without disturbing any native thiol-bearing amino acids in the peptide chain, enabling us to greatly increase the scope of peptides and proteins accessible via native chemical ligation. We were pleased to publish this work in late May, 2012, and it was a great opportunity to present these exciting results just a month later at the ICOS meeting. For this work, I was surprised and honoured to receive the 2012 Feutrill Prize, awarded by the Royal Australian Chemical Institute (RACI) for the best student presented lecture at the conference.

When I arrived back in Sydney after an amazing conference and a few days of exploring the sites and sounds of Melbourne, I found myself inspired and eager to continue my pursuits in the laboratory. Currently, we are in the process of applying our ligation-desulfurisation and ligation-deselenisation methodologies to the total synthesis of interferon gamma, a complex, 166 amino acid glycopeptide that is important in the function of the immune system and is implicated in the treatment and management of a variety of diseases, including chronic granulomatous disease (CGD), a rare, debilitating genetic disorder. In my last year as a PhD student at The University of Sydney, I hope to make considerable strides in this area and to ultimately seek a post-doctoral position that will enable me to further my research interests — implementing chemical tools to further understand biological function and aid in the management of diseases. I am confident that in utilising the “named reactions” and numerous other tools given to us by Nobel Laureates like Ei-ichi Negishi, we can use chemistry to answer some of the most important and fundamental biological questions.

 

Members of the Payne group at the ICOS19 conference dinner. From Left: Richard Payne, Robert Thompson, Anh Tran, Alexandra Manos-Turvey, Lara Malins.

 

Sydney Annual's recently ran an article on Lara Malin's research.
Please view article here

 

 

 

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