Yes, there are a few. Mostly they are designed in combination with X-ray crystallography of the target which should be inhibited. Then molecules are designed which fit specifically into these targets.
The oldest example I could find is Dorzolamide which acts as a carbonic anhydrase inhibitor. See here: "Application of the three-dimensional structures of protein target molecules in structure-based drug design." Some more examples are names in the Wikipedia article on drug design.
While looking for an example, I found these articles, which also look interesting:
* Molecular Modeling and Computer Aided Drug Design. Examples of their Applications in Medicinal Chemistry
* Computer-based de novo design of drug-like molecules
* Recent advances in computer-aided drug design
I am also not sure, to what extent the modern small molecule inhibitors like Vemurafenib (PLX4032) and others are designed using computers. At least to some extent this should be true.