Hello Aggie
It's a good idea to check out any supplements with your pharmacist and doctor to see if there are possible contraindications or interactions or warnings and to be aware of possible side effects.
You are quite right - it should not be assumed that just because something is natural it is harmless either in general or for you as an individual.
After all even normal foodstuffs can have effects in certain instances - grapefruit juice should not be taken while on certain medicines and sudden large quantities of plants containing Vitam K can interact with blood thinning medicines, not to mention the obvious issue of allergies.
On line research can be useful too as an initial check or further check.
I google ( St John's Wort contraindications) for example, and look for reputable, non commercial sites, noting what each one says to get a good overall picture. rxlist has mentions of medicines and plant remedies and I think supplements too.
I hope the Methotrexate helps you

Cheers
Clare