FU-2 (Chemotherapy Revisited)-Model Kit Exercise-PDB files

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My family came over for dinner the other night. I prepared some nice pork chops. I should have served crow. It was the first time I’d seen them since my son-in-law started treatment for colorectal cancer. Said treatment involved an 8-week regimen of radiation and capecitabine chemotherapy. As I mentioned in the previous blog, capecitabine is a prodrug of the 5-fluorouracil (5-FU) and, in turn, 5-fluorodeoxyuridine monophosphate (FdUMP). 

About that crow. I speculated in the earlier blog that FdUMP is a competitive inhibitor of dUMP, which, being an organic chemist, I smugly assumed was the result of stronger hydrogen bonding between FdUMP and the active site of TS compared to that between dUMP and TS. In fact, the binding constants are 2.87 uM and 0.7 uM, respectively: dUMP binds to TS roughly 4 times more tightly than FdUMP. Gulp!

So why does FdUMP work? The enzyme thymidylate synthase (TS) converts deoxyuridine monophosphate (dUMP) into deoxythymidine monophosphate (dTMP). If you inhibit TS, you inhibit DNA synthesis. In addition to TS and dUMP, this conversion requires the cofactor 5,10-methylenetetrahydrofolate, (THF), which serves as the source of the methyl carbon in dTMP.  Here’s a snapshot of the mechanism for this transformation that I copied from an article entitled “Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design” by Robert M. Stroud et.al. in Science 235 4787, (448-455). 

Notice that the H atom is eliminated from C-5 during the conversion of intermediate 2 to intermediate 3. Replacing that H atom with an F atom, as is the case with FdUMP, eliminates the possibility of that elimination. No elimination…no methyl group…no dTMP…no DNA…no cancer!!!

Here’s a screenshot of the PDB file (5FCT) of the crystal structure of the enzyme thymidylate synthase (TS) with 5-fluorodeoxyuridine monophosphate (FdUMP) and the cofactor 5,10-methylenetetrahydrofolic acid (THF) in the active site. The sulfur atom of a cysteine residue (C190) is positioned directly over C6 of the FdUMP, while the methylene carbon atom of the THF lies directly below C5.

The active site of 5FCT

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