title: Differential binding of tenofovir and adefovir to reverse transcriptase of hepatitis B virus.
abstract: BACKGROUND
  Resistance of the reverse transcriptase (RT) of hepatitis B virus (HBV) to the tenofovir nucleotide drug has not been observed since its introduction for treatment of hepatitis B virus (HBV) infection in 2008. In contrast, frequent viral breakthrough and resistance has been documented for adefovir. Our computational study addresses an inventory of the structural differences between these two nucleotide analogues and their binding sites and affinities to wildtype (wt) and mutant RT enzyme structures based on in silico modeling, in comparison with the natural nucleotide substrates.
  
  
  RESULTS
  Tenofovir and adefovir only differ by an extra CH3-moiety in tenofovir, introducing a center of chirality at the carbon atom linking the purine group with the phosphates. (R)-Tenofovir (and not (S)-tenofovir) binds significantly better to HBV-RT than adefovir. "Single hit" mutations in HBV-RT associated with adefovir resistance may affect the affinity for tenofovir, but to a level that is insufficient for tenofovir resistance. The RT-Surface protein gene overlap in the HBV genome provides an additional genetic constraint that limits the mutational freedom required to generate drug-resistance. Different pockets near the nucleotide binding motif (YMDD) in HBV-RT can bind nucleotides and nucleotide analogues with different affinities and specificities.
  
  
  CONCLUSIONS
  The difference in binding affinity of tenofovir (more than two orders of magnitude in terms of local concentration), a 30x higher dosage of the (R)-tenofovir enantiomer as compared to conformational isomeric or rotameric adefovir, and the constrained mutational space due to gene overlap in HBV may explain the absence of resistance mutations after 6 years of tenofovir monotherapy. In addition, the computational methodology applied here may guide the development of antiviral drugs with better resistance profiles.
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Formijn J
authors.initials: FJ
authors.lastname: van Hemert
authors.affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Ben
authors.initials: B
authors.lastname: Berkhout
authors.affiliation: Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Hans L
authors.initials: HL
authors.lastname: Zaaijer
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D001665:Binding Sites; D016000:Cluster Analysis; D018360:Crystallography, X-Ray; D003848:Deoxyguanine Nucleotides / Q000378:metabolism; D024882:Drug Resistance, Viral / Q000235:genetics; D006515:Hepatitis B virus / Q000201:enzymology*; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D063065:Organophosphonates / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism*; D000068698:Tenofovir; D013816:Thermodynamics
chemical_list: D003848:Deoxyguanine Nucleotides; D008024:Ligands; D009711:Nucleotides; D063065:Organophosphonates; C053001:adefovir; C029603:deoxyguanosine triphosphate; D000255:Adenosine Triphosphate; D000068698:Tenofovir; D012194:RNA-Directed DNA Polymerase; D000225:Adenine