Hello ! The separation of your active natural compounds from HCl could be carried out by subjecting the hydrochloric acid extract to ultrasound processes at 20 °C for 40 min. After that you can take out the extract from the ultrasonic bath and let it at room temperature for half an hour. Then centrifuge the extract at 3500 rpm for 25 min, then collect the supernatant and dilute with suitable solvent and store it in a refrigerator at 5 °C until further analysis.
I suggest that you add a base such as 0.1 N NaOH and extract with DCM or ether. If the natural products are alkaloids or phenol derivatives they will be dissolved in the organic layer and the HCl will react with NaOH to yield NaCl which will be dissolved in the aqueous layer.
It is advised that you repeat the extraction with DCM or ether 3 times, collect the organic layer, dry over MgSO4 anhydrous, filter and evaporate.
Add base. Then fractionally separate your active constituent with various solvent. Try to find out your bioactive in different solvent by TLC. By, this you can get confirmed solubility of your active compound, as well as future solvent of choice for isolation.
If the product is polar or if the product is water soluble or product is not alkaloids . In this case DCM, or Ethyl Acetate is not helpful. You have to make salt by adding base and pass through ion exchange resin. In this way HCl will remove out from your solution and you will free to purify it further.
Subject your acidic extract to Diaion HP-20 column and elute the column by water only until the acid disappear (check by litmus paper). Finally elute the column by MeOH and you will find all your compounds in the MeOH eluate
You can use suitable base like NaOH(2M) to neutralize the acid and then you can further extract with suitable organic solvent like Di-ethyl ether/ethyl acetate or DCM. Natural compound like flavonoids, poly phenols and other small molecules will dissolve in these organic solvents and the acid will get neutralize by base to form salt which will remain in the aqueous solution. After extraction you can check the spots in TLC and can perform further separation of compound based on your need.