I found in literature very few natural drugs used as orphan drugs (mainly enzymes)...the majority is synthetic drugs. is there an article which lists the natural orphan drugs.
Orphacol is a medicine containing cholic acid, a substance found in the bile which is used to digest fats.
It is used to treat adults and children from one month of age who have a genetic abnormality that makes them unable to produce bile. Orphacol is used in patients who do not have enough of two specific liver enzymes (3β-Hydroxy-Δ5-C27-steroid oxidoreductase or Δ4-3-Oxosteroid-5β-reductase). This makes their liver unable to produce enough of the main components of bile, called primary bile acids, such as cholic acid. When these primary bile acids are lacking, the body produces abnormal bile acids instead which can damage the liver, potentially leading to life-threatening liver failure.
Because the number of patients with inborn errors in primary bile acid synthesis is low, the condition is considered ‘rare’, and Orphacol was designated an ‘orphan medicine’ (a medicine used in rare diseases) on 18 December 2002.
You can look at EMA's and FDA's list of designated orphan products, and Orphanet's inventory of orphan drugs (if you haven't already done so). I'm not quite sure what you mean by "natural" products - the enzymes you mention are produced biologically in modified organisms.