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Title: Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
ORCiD logo [1];  [2];  [2];  [2];  [2];  [3];  [4];  [5];  [6];  [7]
  1. Univ. of Missouri, Columbia, MO (United States)
  2. Univ. of Missouri, Columbia, MO (United States). School of Medicine
  3. Univ. of Pittsburgh, PA (United States)
  4. Tohoku Univ., Sendai (Japan); Tohoku Medical Megabank Organization, Sendai (Japan)
  5. 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)
  6. Univ. of Pittsburgh, Pittsburgh, PA (United States). School of Medicine
  7. Univ. of Missouri, Columbia, MO (United States); Univ. of Missouri, Columbia, MO (United States). School of Medicine
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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
Citation Metrics:
Cited by: 58 works
Citation information provided by
Web of Science

References (23)

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Cited By (10)

Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen journal January 2019
A Structural View on Medicinal Chemistry Strategies against Drug Resistance journal January 2019
Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV‐1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine journal August 2019
HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir journal January 2018
Where are we with injectables against HIV infection and what are the remaining challenges? journal January 2018
A Subcutaneous Implant of Tenofovir Alafenamide Fumarate Causes Local Inflammation and Tissue Necrosis in Rabbits and Macaques journal December 2019
CMCdG, a Novel Nucleoside Analog with Favorable Safety Features, Exerts Potent Activity against Wild-Type and Entecavir-Resistant Hepatitis B Virus journal January 2019
Long-Acting Anti-HIV Drugs Targeting HIV-1 Reverse Transcriptase and Integrase journal April 2019
The evolution of antiviral nucleoside analogues: A review for chemists and non-chemists. Part II: Complex modifications to the nucleoside scaffold journal February 2019
Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine journal February 2020

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
X-ray crystallography
NRTIs
inhibitors
HIV-1 reverse transcriptase
EFdA