Pronounced Inhibition Shift from HIV Reverse Transcriptase to Herpetic DNA Polymerases by Increasing the Flexibility of α-Carboxy Nucleoside Phosphonates

J Med Chem. 2015 Oct 22;58(20):8110-27. doi: 10.1021/acs.jmedchem.5b01180. Epub 2015 Oct 9.


Alpha-carboxynucleoside phosphonates (α-CNPs) are novel viral DNA polymerase inhibitors that do not need metabolic conversion for enzyme inhibition. The prototype contains a cyclopentyl linker between nucleobase and α-carboxyphosphonate and preferentially (50- to 100-fold) inhibits HIV-1 RT compared with herpetic DNA polymerases. A synthesis methodology involving three steps has been developed for the synthesis of a series of novel α-CNPs, including a Rh(II)-catalyzed O-H insertion that connects the carboxyphosphonate group to a linker moiety and an attachment of a nucleobase to the other end of the linker by a Mitsunobu reaction followed by final deprotection. Replacing the cyclopentyl moiety in the prototype α-CNPs by a more flexible entity results in a selectivity shift of ∼ 100-fold in favor of the herpetic DNA polymerases when compared to selectivity for HIV-1 RT. The nature of the kinetic interaction of the acyclic α-CNPs against the herpetic DNA polymerases differs from the nature of the nucleobase-specific kinetic interaction of the cyclopentyl α-CNPs against HIV RT.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / chemical synthesis*
  • Antiviral Agents / pharmacology*
  • DNA Polymerase I / antagonists & inhibitors
  • DNA Polymerase beta / antagonists & inhibitors
  • DNA Primers
  • Drug Design
  • HIV Reverse Transcriptase / antagonists & inhibitors*
  • HIV-1 / drug effects
  • HIV-1 / enzymology
  • Herpesvirus 3, Human / drug effects
  • Herpesvirus 3, Human / enzymology
  • Humans
  • Molecular Conformation
  • Nucleic Acid Synthesis Inhibitors / chemical synthesis*
  • Nucleic Acid Synthesis Inhibitors / pharmacology*
  • Organophosphonates / chemical synthesis*
  • Organophosphonates / pharmacology*
  • Plasmids / genetics
  • Reverse Transcriptase Inhibitors / chemical synthesis*
  • Reverse Transcriptase Inhibitors / pharmacology*
  • Simplexvirus / drug effects
  • Simplexvirus / enzymology*
  • Structure-Activity Relationship


  • Antiviral Agents
  • DNA Primers
  • Nucleic Acid Synthesis Inhibitors
  • Organophosphonates
  • Reverse Transcriptase Inhibitors
  • HIV Reverse Transcriptase
  • DNA Polymerase I
  • DNA Polymerase beta