I am working with a particular extract which is cytotoxic to a particular cell line as well as HEK293. Is it possible to get a fraction that will only be cytotoxic to this cancer cell line from my crude extract?
Basically you are trying to find an anti-cancerous fraction from your extract. For cytotoxicity or anticancer property, you have to collect all the fractions of your extract of what methods you are following eg. precipitation, solvent separation or gel filtration or more specifically HPLC, HPTLC for fine tuning of your interested fraction and assay for it.
In am not fully sharing Sabry's and Bibhas' responses ...
If you want to have a "bioselective" compound in hands, you must identify the most active growth inhibitory pure compounds from your fraction and see how it (they) behave against the growth of normal versu cancer cells.
You have nevertheless to keep in mind that it is not because a compound kills normal cells in vitro that it cannot be further developed.