Reflections on a Copenhagen–Minneapolis Axis in Bioorganic Chemistry
Abstract
:1. Introduction
2. Motivations
3. Orthogonal Chemistry
4. Dithiasuccinoyl (Dts) Chemistry: Synthesis and Mechanisms
5. Dithiasuccinoyl (Dts) Chemistry: Thiolytic Deprotection and Applications to SPPS
6. Invention of PEG–PS Graft Resin Supports for SPPS and Other Applications
7. A Watershed Visit
8. Invention of PEGA Resin for SPPS and Other Applications31
9. Dts Chemistry in the Service of Glycopeptide Synthesis
10. Additional Results in Glycopeptide Synthesis (Minneapolis)34
11. Invention of Further PEG-Based Supports for SPPS and Other Applications
12. Dts Chemistry in the Service of PNA Synthesis
13. Peptides for the New Millennium: Minneapolis 1999
14. Summary and Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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1 | By necessity, the literature cited herein cannot be comprehensive, and is skewed considerably to refereed papers reported out of Copenhagen (Meldal) and Minneapolis (Barany). For more details on the backgrounds and prior investigations—including preliminary results communicated at scientific meetings—in areas of interest to us, please refer to our original publications and review articles, in which we have tried to be conscientious and comprehensive with respect to proper attributions to precedents and/or independently pursued similar lines of inquiry. |
2 | “An orthogonal system is defined as a set of completely independent classes of protecting groups. In a system of this kind, each class of groups can be removed in any order and in the presence of all other classes” (verbatim footnote 4 from ref. [9]). |
3 | GB’s mentor, R. B. Merrifield, used the word “orthogonal” in a lecture at the 5th American Peptide Symposium in 1977 in San Diego; a “note added in proof” to our proceedings report [10] states “During the discussion period for this paper we learned that the term ‘orthogonal’ has been used in a similar way in the laboratory of Dr. D. S. Kemp”. GB recalls being electrified by Dan Kemp’s lecture at the 4th American Peptide Symposium in 1975 in New York City, but does not believe the word came up then, nor does it appear anywhere in Kemp’s proceedings report [11]. |
4 | The anecdote that follows was recently confirmed by GB’s long-time friend and scientific confidante, Jed Fisher, who was in the conference room at the same time. |
5 | |
6 | While carrying out his first-ever SPPS in 1971, as part of the 6-week independent project phase of the legendary Rockefeller University summer biochemistry course, GB had the privilege to be informally mentored by Bernd Gutte, who was then wrapping up his postdoctoral studies. The resultant peptide proved to bind adenosine triphosphate (ATP), as reported at the 1972 Cold Spring Harbor Symposium on Muscle Contraction [36]. |
7 | In a recent search (accessed 26 October 2023) of the Web of Science database (https://www.webofscience.com/), the word “orthogonal” appeared over 3400 times in the titles of chemistry articles. |
8 | |
9 | |
10 | Because this compound (1) is formally a thioanhydride of O-ethyl xanthate (the product of ethanol and carbon disulfide), we refer to it colloquially as “ethyl xanthic anhydride” (EXA). |
11 | An alternative to the ZWK reaction starts with 1,2,4-dithiazolidine-3,5-dione (DtsNH) [89,95], which reacts with alkyl halides in the presence of base to provide Dts-amines. This Dts variation of the classical Gabriel synthesis was elegantly pioneered by Wood and coworkers [96], although it should be noted that GB pursued such approaches (never published) while still at The Rockefeller University and later with undergraduates carrying out directed studies at the University of Minnesota. |
12 | In 2005, we finally achieved [97] a long-elusive goal [9] to introduce the Dts group in a single step by reaction of bis(chlorocarbonyl)disulfane [Cl(C=O)SS(C=O)Cl] [9,98,99] with bis(trimethylsilyl)amines [TMS2NR]. For this method, the TMS group acts as a “large proton”, in the sense that two equiv of TMSCl are formed as co-products, rather than HCl (or HCl salts, if the reactions are carried out in the presence of base). |
13 | Point of personal privilege: The first author (MJB) of our 2005 J. Am. Chem. Soc. communication [97], currently an eminent historian of mathematics at the University of Edinburgh in Scotland, was at the time a Minnesota high school student competing in the nationwide Intel Science Talent Search. The two enabling ideas, namely the use of Cl(C=O)SS(C=O)Cl and the use of TMS2NR, date back respectively to GB’s graduate studies with RBM in the mid-1970s and to RPH’s graduate studies with GB in the late 1980s. The Nobel laureate coauthor (RBM) enthusiastically signed off on the manuscript, which turned out to be the final one of his illustrious career. |
14 | To the best of our knowledge, the first examples for conversion of R’O(C=S)NHR to their thermodynamically more stable R’S(C=O)NHR isomers were discovered toward the end of the 19th century. Experienced organosulfur chemists are well familiar with this transformation, which can occur spontaneously, or upon heating, or with catalysis, all depending on the precise nature of the substrate. In the "name game" of organic chemistry, the rearrangement is variously associated with Alexander Schönberg, or Melvin Newman with Howard Kwart, or (tangentially) Derek Barton with Stewart McCombie. |
15 | Specifically, “when you are on the ground, pick something up”. |
16 | Aqueous hydroxide under ambient conditions removes primary and secondary alkyl esters, although not tertiary alkyl esters—these latter require TFA (or moderate acids of comparable strength) under mostly anhydrous conditions (sometimes, a relatively small amount of water is added as a carbocation scavenger). |
17 | An anecdote from the 1970s might be instructive to young scientists nowadays. As a graduate student learning about peptide synthesis, GB admired the work of the Merck group on the “controlled polymerization” of N-carboxyanhydrides (NCAs) [104,105] for stepwise synthesis of small peptide fragments. The NCA approach is uniquely problematic with respect to the amino acid glycine (equilibration with its isocyanate isomer), so the sulfur analogue N-thiocarboxyanhydride (NTA) has to be applied to incorporate this residue [105,106]. Just as the Dts group is established in one more step beyond creating an Etc-amine derivative, so too are NTAs. Upon re-reading the classic review by Zumach and Kühle [89] in which he had first encountered a drawing of the lead heterocycle that he was to later reconfigure to Dts, GB realized that it was inevitable that the Merck group would also be aware of that same heterocyle—this realization resulted in several years of low-level anxiety and worrying about being “scooped”. GB’s preliminary Dts work was presented for the very first time in 1975 as a poster at the 4th American Peptide Symposium in New York City [a crosstown bus ride away from the Rockefeller campus]. Dan Veber of Merck visited the poster, and was gracious with his praise. As an aside, he remarked, “…you know, we actually made Dts-Gly-OEt and had it sitting in a vial in the laboratory, but were unable to proceed further because nobody could figure out how to remove the ester without destroying the heterocycle” (paraphrased, not exact quote). GB concluded that certain scientific problems succumb only to a single-minded focus, and that even outstanding and experienced scientists can miss something that is entirely obvious in hindsight. |
18 | Later, when Dts-amino acid derivatives were needed for SPPS (next section of this perspective), the free acids were released in situ from their DCHA salts by brief but vigorous agitation of the latter, dissolved or suspended in CH2Cl2, with Dowex 50 (hydrogen form) ion-exchange resin, followed by filtration. |
19 | As a counterpoint that directly ties in with our concept of orthogonality, Dts-amines are unusually stable under acidic conditions. We believe that this is due to the planarity of the heterocyclic ring, which allows for electron delocalization (evidenced by shorter bond lengths), and imparts a certain level of aromatic stabilization. |
20 | Use of trialkyl- and triarylphosphines [109,110,111,112] in the presence of water is a well-known method to reduce disulfides to the corresponding thiols. When we carried out the obvious control experiment under anhydrous conditions, we discovered that Dts-amines were converted to the corresponding isocyanates, along with COS and the appropriate phosphine sulfide. This observation led directly to novel and highly efficient procedures for the generation of phosphorothioates using first 1,2,4-dithiazolidine-3,5-dione (DtsNH) and then later 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH) [113,114]. |
21 | A somewhat surprising way to achieve Dts removal is under the acidic reductive conditions (pH 5.2) of color development in a standard amino acid analyzer. Specifically, the hydrindantin removes Dts, at least partially, and the ninhydrin reacts with the released amines to provide the purple chromophore (570 nm) that allows detection and quantification of the parent compounds [43,46]. |
22 | Application of MAc exemplifies a more “potent” thiol balanced by NMM, which is a weaker base. Interestingly, MAc is a “high κ” thiol, insofar as Dts cleavage is rate-limiting and no carbamoyl disulfide intermediate was ever isolated (see Scheme 4 as well as ref. [43]). In the more polar solvent DMF, no base is needed, and in fact the reaction is rapid in the presence of HOBt [which is a weak acid; it is included in the deprotection cocktail so as to neutralize any trace of amine impurities in DMF]. |
23 | The adjective “difficult” gained traction in the 1980s through the work of Charles Deber, Stephen Kent, and Bob Sheppard [119,120,121,122,123,124], who documented that some couplings during stepwise SPPS, regardless of protecting group (Boc, Fmoc, or Dts), were reproducibly slow and/or did not go to completion despite lengthier coupling times, higher temperatures, microwave irradiation, more reactive activation methods, and/or addition of chaotropic agents to the coupling milieus. The consensus view, developed by the aforementioned pioneers and still held today, is that these couplings are difficult due to the formation of secondary structure (aggregation) in the resin-bound peptides. |
24 | The preceding paragraph used the “Achilles heel” metaphor from Greek mythology. In a different vein, GB recalls being admonished by his mother with words to the effect “Dts may have started out as your brainchild, but it has now grown into an unruly teenager!” |
25 | This approach accepts a modest level of additional crosslinking, readily quantified, whenever a bifunctional diacid is coupled on both sides to the resin-bound amines. Typically, about two-thirds of the PEG chains retain an accessible end group that can be modified further to eventually initiate SPPS or SPOS. The ultimate properties of such statistically hetero-diverse PEG–PS do not appear to be adversely affected by the added crosslinking. |
26 | When the starting PS component of commercial PEG–PS is MBHA–PS, the resin material is labile to anhydrous HF, and therefore not suitable for stepwise SPPS by Boc chemistry. However, PEG–PS is easily reformulated starting from aminomethyl–PS, whereupon it is entirely suitable for Boc chemistry with a final HF cleavage step. |
27 | The Twins were on their way to their second World Series championship in four years. A box score for this particular game can be found at https://www.baseball-reference.com/boxes/MIN/MIN199110090.shtml. |
28 | GB’s opening joke was a tongue-in-cheek apology for appearing tired, on account of not being accustomed to staying up so late. |
29 | See: https://www.facebook.com/abeautifulequation/photos/a.632898940054321/5368004756543692/ For more about Bohr, see: https://www.nobelprize.org/prizes/physics/1922/bohr/biographical/ To celebrate the 100th anniversary of the Bohr model of the atom, GB collaborated with Alex Vratsanos on “Great Dane”, a crossword puzzle published in the 20 September 2013 issue of The Chronicle of Higher Education, as reproduced and discussed at: http://www1.chem.umn.edu/groups/baranygp/puzzles/greatdane/. |
30 | Live broadcast of a Joe Biden-led committee hearing of the United States Senate concerning confirmation of Clarence Thomas in light of explosive allegations of sexual harassment from Professor Anita Hill. |
31 | In the section that follows, as well as a later section entitled “Invention of Further PEG-based Supports …”, we highlight novel support materials (PEGA, POEPS, POEPOP, POEPS-3, and SPOCC) invented by Meldal and coworkers. No attempt has been made to name the monomers leading to these materials in a manner entirely consistent with how we have described the chemistry leading to various generations of PEG–PS and CLEAR supports. |
32 | Shortly after PRH presented preliminary findings from Minneapolis in 1994 at the 23rd European Peptide Symposium in Braga, Portugal, Morten Meldal let us know that work along the same lines was already underway in Copenhagen and had been presented seven weeks earlier at the XVIIth International Carbohydrate Symposium in Ottawa, Canada. In a cordial conversation, GB suggested that the first full paper on this topic should be submitted by the Copenhagen group, followed soon thereafter by a paper from Minneapolis. |
33 | The auxiliary nucleophile forms a yellow ion-pair with unreacted amino groups on the resin, thereby allowing visual monitoring of the progress of the reaction. In addition, the active species for coupling is likely to be the more reactive Dhbt ester, formed in situ by transesterification that displaces the pentafluorophenyl (Pfp) ester. |
34 | In keeping with the title of this perspective, we have already described innovative work in the field of glycopeptide synthesis where there was some synergy or overlap from the efforts in Copenhagen and Minneapolis. Meldal’s many additional contributions and successes in the field fall outside our scope, but the interested reader can easily find them summarized elsewhere [148,149]. Methodologies developed at Carlsberg were readily extended to combinatorial libraries, for example in a paper by St. Hilaire et al. [150] which described carboxylic acid-encoded glycopeptide libraries. |
35 | This perspective will not delve into Knud Jensen’s highly creative independent idea of carbopeptides, which he brought with him to Minneapolis and devoted considerable time and effort to achieving proof-of-concept results. The goal was to use a sugar (specifically, d-galactopyranose) as a template to start four identical peptide strands (initially, six amino acid residues each, plus β-alanine “spacers”) that might interact with each other to achieve stable secondary or tertiary structures as protein models (4-helix bundles) or multiple antigenic peptides (MAPs). Because the expertise and resources of his laboratory facilitated progress towards this ambitious goal, GB was delighted to coauthor the first report in 2000 in the J. Pept. Sci. [151] but he then encouraged KJJ to elaborate on this work on his own to launch his independent academic career in the Department of Chemistry at the University of Copenhagen. Follow-up papers from Jensen and coworkers ultimately came out in the first few years of the 21st century [152,153,154,155]. |
36 | CLEAR supports are explained in a later section of this perspective. |
37 | Sweden and Denmark are close enough that people headed to the south of Sweden often fly into the Copenhagen airport, and then take a train or automobile across the Øresund Bridge. In the framing of this perspective’s title, one might say that Maria Kempe was an “honorary” member of Copenhagen’s scientific circle. |
38 | We may write about the “Barcelona–Minneapolis connection” at a different time for a different venue. For now, we interpret the title “Copenhagen–Minneapolis axis” of this perspective generously, so as to include Fernando Albericio’s important work on ChemMatrix. |
39 | This section deviates somewhat from our overall framing for this perspective, since to the best of our knowledge, Morten Meldal’s research programs never tackled PNA. Nonetheless, we include it because PNA originated from Copenhagen, and Meldal-trained Knud Jensen was one of the leaders of the Minneapolis effort in this area. Our discussion here is focused only on Dts chemistry; separate efforts from Minneapolis using Fmoc chemistry have been communicated elsewhere [180]. |
40 | If the end goal for the synthetic PNA is hybridization to target genomic DNA for mutational analysis, diagnostics, and myriad additional applications, then PNA that is assembled by a segment approach is far less likely to lead to false positive results, which would otherwise be a distinct risk whenever there are single-deletion “failure” sequences due to stepwise synthesis. In collaboration with Francis Barany and Robert Hammer, we began discussing these concepts in 1993; there is a straight line from those discussions to our invention of “universal zip-code arrays” which were first filed to the United States Patent and Trademark Office (USPTO) in 1997 and disclosed in a 2001 Journal of Molecular Biology paper [188]. |
41 | The previous footnote mentions a PNA segment approach. We began working toward this goal around 1996 under a grant from the National Institute of Science and Technology (NIST), in collaboration with Robert Hammer, who had graduated from our Minneapolis laboratory in 1990 and was by then an independent Assistant Professor at Louisiana State University (LSU) in Baton Rouge. In never-published work, Bob’s LSU postdoctoral fellow Kristofer Moffett used chemistry with three degrees of orthogonality [Nω-Fmoc/side-chain Z/Cω-allyl ester] to synthesize all 16 suitably protected Fmoc-PNA dimers, and made some progress towards combining these to create a few PNA tetramers. Since then, there have been several literature reports on short PNA oligomers [189,190,191]. |
42 | The two co-Chairs had been colleagues for several years at the University of Minnesota, respectively in the Department of Chemistry in the Institute of Technology (since renamed College of Science and Engineering) and the Department of Laboratory Medicine and Pathology in the Medical School. About a year before the 16th American Peptide Symposium, GBF moved to Florida Atlantic University. |
43 | A full photo gallery from the meeting can be found at http://www1.chem.umn.edu/16aps/Photoindex.html. |
44 | These various activities are outside of the scope of the present perspective, but may be the subject of future writings. |
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Barany, G.; Hansen, P.R. Reflections on a Copenhagen–Minneapolis Axis in Bioorganic Chemistry. Molecules 2024, 29, 1317. https://doi.org/10.3390/molecules29061317
Barany G, Hansen PR. Reflections on a Copenhagen–Minneapolis Axis in Bioorganic Chemistry. Molecules. 2024; 29(6):1317. https://doi.org/10.3390/molecules29061317
Chicago/Turabian StyleBarany, George, and Paul R. Hansen. 2024. "Reflections on a Copenhagen–Minneapolis Axis in Bioorganic Chemistry" Molecules 29, no. 6: 1317. https://doi.org/10.3390/molecules29061317
APA StyleBarany, G., & Hansen, P. R. (2024). Reflections on a Copenhagen–Minneapolis Axis in Bioorganic Chemistry. Molecules, 29(6), 1317. https://doi.org/10.3390/molecules29061317