Phosphonoformic acid (PFA, foscarnet) belongs to a class of antiviral drugs that inhibit the human cytomegalovirus DNA polymerase (UL54) by mimicking the pyrophosphate leaving group of the nucleotide transfer reaction. Difficulties expressing UL54 have hampered investigation of the precise structural requirements rendering inhibition by this drug. However, a previously engineered chimeric DNA polymerase, constructed by mutating the homologous polymerase from bacteriophage RB69 (gp43) to express several variable elements from UL54, can bypass this obstacle because of its favorable expression and acquired sensitivity to PFA (Tchesnokov, E. P., Obikhod, A., Schinazi, R. F., and Götte, M. (2008) J. Biol. Chem. 283, 34218 -34228). Here, we compare two crystal structures that depict the chimeric DNA polymerase with and without PFA bound. PFA is visualized for the first time in the active site of a DNA polymerase, where interactions are resolved between the PP i mimic and two basic residues absolutely conserved in the fingers domain of family B polymerases. PFA also chelates metal ion B, the cation that contacts the triphosphate tail of the incoming nucleotide. These DNA complexes utilize a primer-template pair enzymatically chain-terminated by incorporation of acyclo-GMP, the phosphorylated form of the anti-herpes drug acyclovir. We postulate that the V478W mutation present in the chimera is critical in that it pushes the fingers domain to more readily adopt the closed conformation whether or not the drug is bound. The closed state of the fingers domain traps the variant polymerase in the untranslocated state and increases affinity for PFA. This finding provides a model for the mechanism of UL54 stalling by PFA.
The human cytomegalovirus (HCMV)3 belongs to the herpesviridae family, into which several important human pathogens are classified. A primary infection of this virus in pregnant mothers can be devastating to the developing fetus, resulting in several congenital disorders. Although a substantial portion of the global adult population is currently HCMV-seropositive, a functional immune system can hold the virus in check. For immunocompromised individuals, on the other hand, infection with HCMV presents a severe threat (1-3). Accordingly, antiviral therapy is used as both prophylaxis and therapeutic strategies in solid organ transplant recipients, who receive concomitant immunosuppressants. In this setting, infection with the virus is a major cause of morbidity and mortality.The limited pharmacological options available for treatment of HCMV largely consist of nucleoside analog inhibitors that target the gene product of UL54, a family B DNA polymerase. Although some inhibitors, such as cidofovir, are chemically synthesized as acyclic nucleoside phosphonates, most nucleoside analogs require monophosphorylation by a viral kinase, such as UL97 in HCMV, before other cellular kinases convert these drugs into triphosphorylated substrates of the DNA polymerase (4). Following incorporation into the viral DNA, these non-n...