Can someone suggest a way to solve this problem? Is it a normal phase or a reverse phase the problem with sugar interference exists. My compound of interest in the extract is a water soluble one and it is even very difficult to see in TLC plate due to the high concentration of sugars which happened to be matching with my compound's Rf. In normal phase my compound can be eluted out at EtoAc:MeOH (8.5:1.5) in which sugars also being eluted together. In RP-Cosmosil column my compound of interest is eluted with 100% water, along with sugars obviously. Is there any other way I can get good resolution between water soluble molecules?
At least reducting sugars are very easy to oxidize or condense to molecules that might not interfere, for non reducing sugars enzimatic hydrolysis may be necessary. You should consider that other interference than sugars may be operating, since sugar will be strongly bind to the stationary normal phase with the eluent you refer.
Did you attempt ion-exchange column chromatography? If your compound gets bound to either a cationic or anionic ion exchanger, you could easily wash (elute) out the sugars which do not bind to ion-exchange resins.
Good luck
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