Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues

J Med Chem. 2021 Jan 14;64(1):782-796. doi: 10.1021/acs.jmedchem.0c01747. Epub 2020 Dec 23.


Nucleotide analogues are used for treating viral infections such as HIV, hepatitis B, hepatitis C, influenza, and SARS-CoV-2. To become polymerase substrates, a nucleotide analogue must be phosphorylated by cellular kinases which is rate-limiting. The goal of this study is to develop dNTP/NTP analogues directly from nucleotides. Tenofovir (TFV) analogues were synthesized by conjugating with amino acids. We demonstrate that some conjugates act as dNTP analogues and HIV-1 reverse transcriptase (RT) catalytically incorporates the TFV part as the chain terminator. X-ray structures in complex with HIV-1 RT/dsDNA showed binding of the conjugates at the polymerase active site, however, in different modes in the presence of Mg2+ versus Mn2+ ions. The adaptability of the compounds is seemingly essential for catalytic incorporation of TFV by RT. 4d with a carboxyl sidechain demonstrated the highest incorporation. 4e showed weak incorporation and rather behaved as a dNTP-competitive inhibitor. This result advocates the feasibility of designing NTP/dNTP analogues by chemical substitutions to nucleotide analogues.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry*
  • Binding Sites
  • COVID-19 / virology
  • COVID-19 Drug Treatment
  • Catalytic Domain
  • Drug Design
  • HIV Reverse Transcriptase / chemistry
  • HIV Reverse Transcriptase / metabolism
  • Humans
  • Magnesium / chemistry
  • Molecular Docking Simulation
  • Nucleotides / chemistry*
  • Nucleotides / metabolism
  • Phosphorylation
  • SARS-CoV-2 / isolation & purification
  • Substrate Specificity
  • Tenofovir / chemistry*
  • Virus Diseases / drug therapy*
  • Virus Diseases / virology


  • Amino Acids
  • Nucleotides
  • Tenofovir
  • reverse transcriptase, Human immunodeficiency virus 1
  • HIV Reverse Transcriptase
  • Magnesium