Link Prediction in Bipartite Networks between biological pathways and drugs
I am not sure if I understood correctly how you classify  the drugs. But what you attempt to do is similar to what they do here but in that article they use the drugs targeted to a molecule/pathway to find combination of drugs that are better for the disease (not an alternative drug), see the first image:

In that article they mention the pathway cross-talk inhibition (PCI), you might want to calculate it for your pathways to assess the relative reduction of the pathway efficiency.