It is not advisable to run water soluble plant extract directly In HPLC. It can damage the Column. You can follow following steps for your sample.
The brief steps are:
First of all you isolate the pure fraction from plant extracts using following techniques. First run TLC to know the type of fractions. After that Column Chromatography with HPLC, after isolated pure fraction run FT-IR, LC-MS, HNMR, CNMR for structure elucidation. You can read my papers too.