Cyclin-dependent kinases (CDKs) are key regulators of cell growth and proliferation. Impaired regulation of their activity leads to various diseases such as cancer and heart hypertrophy. Consequently, a number of CDKs are considered as targets for drug discovery. We review the development of inhibitors of CDK2 as anti-cancer drugs in the first part of the paper and in the second part, respectively, the development of inhibitors of CDK9 as potential therapeutics for heart hypertrophy. We argue that the above diseases are systems biology, or network diseases. In order to fully understand the complexity of the cell growth and proliferation disorders, in addition to experimental sciences, a systems biology approach, involving mathematical and computational modelling ought to be employed.