In this chapter, we provide a series of selected examples that demonstrate how molecular modelling and simulations can be used effectively to dissect the function and inhibition of challenging targets of pharmaceutical interest. Targets such as membrane proteins, RNA, metalloproteins, and intrinsically disordered proteins are often involved in the development and progression of diseases like cancer and neurodegenerative disorders. All these targets present challenging aspects related to their complex structure, which often hampers the use of traditional in silico drug discovery tools. We will show how computations can, nowadays, tackle these challenges returning useful insights that can aid the design of probes and potent inhibitors for drug discovery.