Doxorubicin (Red devil)

As I mentioned in the previous entries on HF, mercury fulminate, and phosphine, I really like Breaking Bad.

As an astute commenter noted yesterday, they sometimes make some mistakes:

Like pentavalent carbon (green dots).

But they usually do a pretty good job and even sneak in some real chemistry:

See Walter fill orbitals!

During Walter's chemo last week, you saw some red stuff flowing into his IV. This was likely doxorubicin:

Doxorubicin is a DNA-binding molecule, like proflavine, ethidium, or paraquat.

Proflavine and ethidium are intercalators - they slip between the bases in DNA. Paraquat is a groove binder - it nestles itself in the crevice between the two strands of DNA. Doxorubicin is a little bit of both. The central aromatic bit intercalates a base pair, and the amino sugar hits the groove.

DNA-binding drugs are common in cancer chemotherapy: Cisplatin is yet another. The general toxicity of these compounds is why chemo is such a miserable experience, and medchem is always on the lookout for new targets. Another class of ligands targets DNA, but only a special structure that plays some roles in cancer called a quadruplex. The hope is that such strategies will make for less-toxic treatments.

Interestingly, that positively charged sugar on doxorubicin binds in the same places metal ions bind in the groove.