Just reiterating what Joe Tulsa said - Nattokinase is to be taken on an empty stomach ... at least one hour before eating or 2-3 hours after eating.
It is my understanding that you get the best results when taken on an empty stomach because when you take it with food, the enzymes will work on breaking down any protein you have just eaten instead of the problem proteins you want it to work on.
I take it along with Serrapeptase and I leave them on my bathroom counter so I can take them when I wake up in the night to use the restroom. That way, by the time I wake up the hour has passed and I can eat my breakfast without worrying! It is great that it's working for you - it will probably work even better on an empty stomach :-)