We are getting into some hard science here*, but the way most gene knockdown techniques work (there are lots of different methods) is to reduce the level of the targeted protein in the cell - for example, if there are 1000 molecules of the particular protein in the cell, then knocking it down might reduce the number to 100 (90% reduction). The enzymatic activity would then be 10% of the normal level (all things being equal).
If the targeted protein is an enzyme (like FTO) then the result is effectively the same as directly inhibiting the enzyme with a drug - for example, if the drug binds to the active site of 90% of the 1000 enzyme molecules at a particular concentration, the end result is only 100 enzyme molecules are active in the cell. The enzymatic activity would be 10% of the normal level also.
The end result is both approachs achieve the same outcome inside the cell. This means if we have data that using a gene knockdown that reduce an enzyme’s concentration in the cell causes a particular effect, then we can be pretty sure that inhibiting the same enzyme with a specific drug will cause the same effect in the cell. To put it simply, gene knockdown == specific drug inhibition.
*For the hard core science nerds this entire description is a gross simplification of the biology, but I am trying to answer the question not write a molecular biology textbook.
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