How can I inactivate all secondary metabolites rather than alkaloids for its purification?
I think you mean you want to only have alkaloids for study?
I can think of 2 ways. One way is to partition the extract between dichloromethane and acidic water. Separate the water, and make it basic (pH 9 or 10) and partition again in dichloromethane. The alkaloids will in the dichloromethane as a free base. You can Use C18 to purify them.
The other way is to use a strong cation exchange resin (SCX). This captures the alkaloids, and you may be able to resolve some of them from each other at this step.
See: http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Isolation_and_Purification_of_Alkaloids_with_SCX_Columns.pdf
http://www.isco.com/WebProductFiles/Applications/101/Application_Notes/AN98_Hints%20for%20Strong%20Ion%20Exchange%20Resins.pdf
http://www.isco.com/WebProductFiles/Applications/101/Application_Notes/AN40_Purification_of_Alkaloids_with_RediSep_Rf_SCX_Columns.pdf
I hope the attached article will give better idea on different types of alkaloid isolation
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