Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)
- Univ. of Missouri, Columbia, MO (United States)
- Univ. of Missouri, Columbia, MO (United States). School of Medicine
- Univ. of Pittsburgh, PA (United States)
- Tohoku Univ., Sendai (Japan); Tohoku Medical Megabank Organization, Sendai (Japan)
- National Inst. of Health (NIH), Bethesda, MD (United States). National Cancer Inst.; Kumamoto Univ. Graduate School of Medical Sciences (Japan); National Center for Global Health and Medicine, Tokyo (Japan)
- Univ. of Pittsburgh, Pittsburgh, PA (United States). School of Medicine
- Univ. of Missouri, Columbia, MO (United States); Univ. of Missouri, Columbia, MO (United States). School of Medicine
4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is the most potent nucleoside analog inhibitor of HIV reverse transcriptase (RT). It retains a 3'-OH yet acts as a chain-terminating agent by diminishing translocation from the pretranslocation nucleotide-binding site (N site) to the posttranslocation primer-binding site (P site). Also, facile misincorporation of EFdA-monophosphate (MP) results in difficult-to-extend mismatched primers. To understand the high potency and unusual inhibition mechanism of EFdA, we solved RT crystal structures (resolutions from 2.4 to 2.9 Å) that include inhibition intermediates (i) before inhibitor incorporation (catalytic complex, RT/DNA/EFdA-triphosphate), (ii) after incorporation of EFdA-MP followed by dT-MP (RT/DNAEFdA-MPP•dT-MPN), or (iii) after incorporation of two EFdA-MPs (RT/DNAEFdA-MPP•EFdA-MPN); (iv) the latter was also solved with EFdA-MP mismatched at the N site (RT/DNAEFdA-MPP•EFdA-MP*N). We report that the inhibition mechanism and potency of EFdA stem from interactions of its 4'-ethynyl at a previously unexploited conserved hydrophobic pocket in the polymerase active site. Furthermore, the high resolution of the catalytic complex structure revealed a network of ordered water molecules at the polymerase active site that stabilize enzyme interactions with nucleotide and DNA substrates. Finally, decreased translocation results from favorable interactions of primer-terminating EFdA-MP at the pretranslocation site and unfavorable posttranslocation interactions that lead to observed localized primer distortions.
- Research Organization:
- Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
- Sponsoring Organization:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Mizzou Advantage; Trail to a Cure
- Grant/Contract Number:
- AC02-05CH11231; AC02-06CH11357; AI076119; AI099284; AI100890; AI120860; GM103368; GM118012
- OSTI ID:
- 1349117
- Journal Information:
- Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, Issue 33; ISSN 0027-8424
- Publisher:
- National Academy of SciencesCopyright Statement
- Country of Publication:
- United States
- Language:
- ENGLISH
Web of Science
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