I'm a first year PhD student who is struggling a little with one of my first synthesis problems, which seems like it should
be straightforward but ...er....i'm running into quite a few problems.
My issue is with the efficacy of amide bond formation where whilst I do get desired product, both my HPLC and ESI-MS show side products.https://ibb.co/5vRzLNz
I'm working with a cyclic octapeptide (Lysine (unprotected side chain) - Leu- Trp- Leu - Lysine (Boc)-Leu-Trp-Leu) which has a lysine residue -NH2 group, which I wish to conjugate to the carboxylic acid terminal of flumequine.
HATU/HCTU conjugation didn't work and led to desired conjugate, plus a lysine/guanidinium side product
My supervisor advised me to try DMTMM.BF4 coupling or PyBOP coupling which i've attempted by dissolving my cyclic peptide in DMF (only solvent it dissolves into), activating with base. Separately activating my flumequine with the coupling reagent and small amount of base for 30 mins. Then adding the two solutions together. Once again there is desired product (around 1548 positive mode ESI), plus an unknown side product (this time based on mass spectra i really can't determine what the peak corresponds to based on the reagents i've used and the mechanism). (its' at 1432 in positive mode ESI)
I should note I use 1eq cyclic peptide to 1.2 eq flumequine/1.2 coupling agent.
I thought perhaps the nature of flumequine itself, having an extended delocalisation of electrons possible, it makes flumequine to some extent a better leaving group than intermediate moieties in either of the coupling agent mechanisms?
Is there something fundamental in how I set my reactions up that i'm not doing properly because i've tried all these reactions multiple times and they aren't working, and i'm about close to losing the plot after several weeks of this
I wanted to try EDC/NHS coupling but i'm told this can also give side products fairly easily (?)
Many Thanks and apologies if i've not gone into enough detail, i'd be happy to give more