Plenty of reasons this is not a good idea.

There are no where near enough rapists and pedophiles to conduct enough clinical studies on. The US prison population is 2.3 million, of which a small fraction will be convicted rapists or pedophiles. By contrast, 111 million mice and rats are killed in US laboratories every year. So before long you'd get pressure to expand which prisoners can experimented upon and then which crimes result in a custodial sentence.

Second, for many drug trials you need to inflict a condition to see how the drug effects that condition. That is, every year loads of mice are given cancer to see if a drug is effective at treating that cancer. Not that many rapists in jail with lung cancer.

Thirdly, when testing drugs you need to properly test on a representative sample of the population. Otherwise you get skewed results. This is already a problem for women, especially pregnant women. Very little testing has done on them, so out knowledge of how drugs effect women is much more limited and can often lead to adverse health outcomes for women. Using prisoners, who are mostly male, would only exacerbate this problem.

Overall it's a terrible idea that is focused primarily on punishment of prisoners, not on rigorous clinical trials and good science.