The simplest approach would be to use an ODS (C18) column. Apply your metanol extract to the column and wash the column 5-6 times with ultra pure distilled water followed by a 60-100% methanol gradient.

Thank you very much Vijay Singh and Erkan Halay.

Most of free sugars are completely soluble in water. You can simply macerate your dried total extract with distilled water and remove all free sugars.

Dear Khanavi, 

But how can I confirm that my bioactive compound will not dissolve in water?

Dear Khanavi, only if your Bioactive compounds are very polar glycosides containing many sugars could be soluble in water, if not they won't be 

A very simple method is to dry  your extract and use liquid liquid extraction with water/ ethylacetate mixture. If your bioactive compounds are not very polar they will dissolve in ethyacetate and your sugars to ethylacetate. To accomplish that you should completely remove methanol. By this method you can not be sure for the proportion of your compound that ends up in water..  

correction your sugars to water

My extracts containing more polar compounds I guess. i tried this method by yield is very less and ethyle acetate fraction not showing any significant pharmacological applications.

You said your ethyl acetate fraction has not significant pharmacological applications. And have you tried the remanent fraction, it means the aqueous fraction??. By other side which bio assays you did for the organic fraction?.