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Interesting question by @Van_DeventerJim: Which electrophiles are most suitable to be introduced into complex (bio)molecules by click chemistry, while keeping the reactive group intact? I have no direct experience, but I want to give my two cents, on what I think could work(1/29) https://twitter.com/Van_DeventerJim/status/1381432430696001536
I think the two strategies that are most promising would be to 1) use a low reactivity electrophile that will survive the click conditions as is or 2) use a masked electrophile that can be activated, e.g. by light, after the click chemistry. (2/29)
Which of these strategies I would chose, depends on several factors. These include: How reactive is the final probe supposed to be (very specific vs. broad profiling)? Which amino acids do you intent to target? How well would a possible activation step be tolerated? (3/29)
Full disclosure at this point. I am not aiming to give a comprehensive overview and if I miss your work on this, I apologize in advance and encourage you to add to this thread. These are just a few thoughts of mine on what could be promising and were I would start. (4/29)
For using low reactivity electrophiles, acryl amides would be an obvious choice, if targeting cysteines is suitable. @Keribackus probably has one of the most comprehensive experiences on this reactive group from her @nature paper ( http://doi.org/10.1038/nature18002). (5/29)
Click chemistry has been done with acryl amides several times also on quite complex biomolecules like glycans #glycotime. E.g. by the group of Yoshiharu Kimura @KyotoU_News in this paper in @ACSMacroLett. (6/29) http://dx.doi.org/10.1021/mz500555x
As @nasufovic_v also pointed out as response to this tweet, even α-chloroacetamides seem to be feasible, if some more reactivity towards cysteines would be desired. This has e.g. been shown in this paper by the group of Yue Wang in J. Med. Chem. (7/29) http://doi.org/10.1021/acs.jmedchem.6b01237
Another alternative for cysteines might be polyfluorinated benzenesulfonamides. These have been thoroughly studied e.g. in this paper by the groups of Frederik Diness and Morten Meldal in @angew_chem. (8/29) http://doi.org/10.1002/anie.201712589
Furthermore, heteroaromatic sulfones could be feasible. Brent Martin @MichiganChem (sadly not on twitter as far as I know) would probably be one of the best persons to comment on this based on his group's paper in @J_A_C_S. (9/29) http://doi.org/10.1021/jacs.9b08831
If you are not in the luxurious situation to have a suitable cysteine in the target, things are of course getting a little more complicated. There are some reactive groups that I think should be suitable here. (10/29)
For targeting lysines, activated esters, which are hydrolytically stable enough, might work. Polyfluorinated phenols seem most suitable as leaving group. @SpringGroupChem even studied their stability to click conditions in this @ChemCommun paper (11/29) http://doi.org/10.1039/C9CC04022F
I could also imagine N-acyl-N-alkyl sulfonamides to work in this case, but I have not found click chemistry on them in the literature. The group of Itaru Hamachi @KyotoU_News just recently used them in complex molecules in this @J_A_C_S paper. (12/29) https://doi.org/10.1021/jacs.1c00703
Depending on what you want to do, it might also be feasible to bring in the unreactive N-acyl sulfonamide into the molecule by click chemistry and activate it later on by alkylation (see below). (13/29)
Phenyl glyoxals would also be feasible to target arginines, but @patrick_zanon in my group will probably agree that they can be tricky to handle. They have been clicked to give probes e.g. by the group of @Pthompsn1018 in this @ChemicalBiology paper(14/29) http://doi.org/10.1021/acschembio.5b00438
Last but certainly not least, for targeting different amino acid residues, the SuFEx chemistry pioneered by K. Barry Sharpless @scrippsresearch should be feasible. The group of Hua‐Li Qin published on clicking these compounds in this @EurJOC paper. (15/29) http://doi.org/10.1002/ejoc.201801825
If the reactive group needs to be more reactive and more tyrosine selective, Ku-Lung Hsu @Hsu_Lab_UVa could maybe comment, if his group's SuTEx chemistry, described e.g. in this @J_A_C_S paper, might also be feasible. (16/29) http://doi.org/10.1021/jacs.0c00648
A second strategy would be to use activatable electrophiles. These come in two flavors, as protected reactive group that are activated in a separate reaction or light-activatable electrophiles that are activated in situ. (17/29)
For protected reactive groups, I already hinted at the N-acyl-N-alkyl sulfonamides that could be introduced as N-acyl sulfonamides using click chemistry and then activated using alkylation. Another example of this is in this @NatureComms paper. (18/29) http://doi.org/10.1038/s41467-018-04343-0
I want to furthermore mention the work by the group of Eranthie Weerapana @BostonCollege. E.g. in this @J_A_C_S paper, they developed light-activatable, protected bromomethyl ketones for labeling of cysteine. (19/29) http://doi.org/10.1021/jacs.5b04350
While these can also be used for activation in situ as discussed below, I can also imagine to use this as a protection group strategy to liberate this highly reactive group in a separate reaction and then have the electrophile available without requiring in situ activation(20/29)
Directly activating electrophiles in situ for me has additional advantages as the initial compound will be unreactive. In this way, it is highly likely that it will not cause trouble during the click chemistry and that it will also enable in cell studies more easily. (21/29)
For lysines, o-nitrobenzyl alcohols are interesting light-activatable reactive groups. They have been recently applied e.g. by the group of Xiao-Hua Chen in this @NatureComms paper and are suitable also in complex biological systems. (22/29) http://doi.org/10.1038/s41467-020-19274-y
This reactive group has been stable towards click chemistry e.g. in this paper by the groups of Takashi Ito @KState and Yi Yi @IndianaUniv in @ACS_Langmuir. (23/29) http://doi.org/10.1021/acs.langmuir.0c01572
For targeting aspartates and glutamates, 2,5-disubstituted tetrazoles are a suitable light-activatable group also for applications in living cells. This has e.g. been investigated by Shao Q. Yao in this @angew_chem paper. (24/29) http://doi.org/10.1002/anie.201508104
We are also very excited about this chemistry and have recently used it to develop light-activatable probes to study aspartates and glutamates in a proteome-wide setup with residue-specific resolution. (25/29) http://doi.org/10.1021/acscentsci.9b01268
The 2,5-disubstituted tetrazole is stable to click chemistry as e.g. shown by the group of @doc_jlmeier in this paper in @ChemBioChem. (26/29) http://doi.org/10.1002/cbic.201800651
To wrap up, I will engage in some shameless self-promotion. If you want to learn more about the proteome-wide reactivity of most of these reactive groups and some more, also check out our @ChemRxiv with first author @patrick_zanon. (27/29) http://doi.org/10.26434/chemrxiv.14186561
These are my thoughts. I would be excited if others would add their thoughts or experimental experiences to this thread. As I mentioned, we have not tried this experimentally, so I would also be excited to hear if some of you disagree on some (hopefully not all) points. (28/29)
Thanks @Van_DeventerJim for bringing up this interesting question and making me do my homework on this topic that I wanted to look into for a while now (also for making me spent way too much time on it). I hope my thoughts are helpful and maybe even provoke some discussion(29/29)
