I had some email from an undergraduate chemistry major who's interested in doing drug discovery work eventually. He was wondering if organic synthesis was still the way to go in graduate school, and my answer is "definitely." I've warned people away from too much of a medicinal chemistry focus in their graduate work before, and I'll be glad to do it again.
Let me be clear, though, that I'm talking about academic medicinal chemistry programs as they've usually been run. What you often end up doing in these is learning a fair amount about each of the major areas of drug discovery, but you generally don't get really good at any of them. And since there's no market for a one-man drug company, you're left in a bad situation. We don't need fair-to-middling chemists who are also fair-to-middling pharmacologists. Perhaps there are other ways to run a med-chem department at a university that won't lead to this problem, but the only one I can think of is to run it like a little drug company, which I don't think is going to work out very well.
The reason we like for people to do lots of organic chemistry before they join the drug industry is that we (the medicinal chemists) are the only ones who understand that stuff. Other departments have members (sometimes) with a reasonable knowledge of the main points of organic synthesis, but it's only the chemists who can really dive into it. Someone has to, and by golly, it's us. So we need people who really know what they're doing: people who can use the fastest and cleanest routes to making the most diverse analogs, who can think up structures that no one else has ever made and reduce them to practice, and who can find the cheapest, most reliable ways to scale up a synthesis for real world use. The wider the range of serious organic synthesis experience you have, the more we'd like to talk to you.
This might eventually become a problem for us in industry, as the field of organic synthesis continues to mature. Already, I think we have a bit less emphasis on people who've done total synthesis of natural products, because fewer groups are doing that these days. (And some of the groups who are, aren't doing it in a way that everyone in the group gets the kind of training we need - the "team of lab Sherpas" approach damages as many people as it improves, as far as I'm concerned).
But total synthesis, done right, is still the perfect sort of training for our needs, even though we don't do thirty-two step reaction sequences. It sends you all over the state of the synthetic art, gives you a varied problem-solving workout, and trains you to always look for alternatives to the chemistry you're doing. We couldn't ask for more. I find this state of affairs a bit irritating, though, since I think that total synthesis is a slowly dying art form, and rightfully so. There's less and less need, in my opinion, for those thirty-two step routes. I can almost imagine keeping it all going just to provide the drug industry with the kind of people it likes to hire, though. In fact, I can almost imagine that this is already happening right in front of us. . .
One of the major alternatives to total synthesis is working on new synthetic methods, which is a valuable service to the science. But while that can train people very well for drug research, it can also leave them partially crippled. It depends on how broad their experience of different reactions has been, and how general their approach to problem solving has had to be. If you come out of graduate school as the world's best set of hands for one particular reaction, my advice is to go do a completely different sort of post-doc, to prove that you have the hands to do something else. And that's because "do something else" is pretty much the job description of a working medicinal chemist.