Evidence map›Paper›PMID 27489345›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2016

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

Zhe Li Salie, Karen A Kirby, Eleftherios Michailidis, Bruno Marchand, Kamalendra Singh, Lisa C Rohan, Eiichi N Kodama, Hiroaki Mitsuya, Michael A Parniak, Stefan G Sarafianos

Open access · greenAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
61citing papers in PubMed, 1 pooled it
5.8field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

61 citing papers in PubMed, 1 synthesis or guideline pooled it, 101 citations in OpenAlex.

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1 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 4 institutions in 2 countries.

Zhe Li SalieC. S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211;ORCID 0000-0003-2063-1013
Karen A KirbyC. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211;
Eleftherios MichailidisC. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211;
Bruno MarchandC. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211;
Kamalendra SinghC. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211;
Lisa C RohanDepartment of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261; Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 15213;
Eiichi N KodamaDivision of Infectious Diseases, Tohoku University and Tohoku Medical Megabank Organization, Sendai 980-8575, Japan;
Hiroaki MitsuyaExperimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; Department of Infectious Diseases, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan; Department of Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan; Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan;
Michael A ParniakDepartment of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219.
Stefan G SarafianosC. S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO 65211; C. S. Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65211; sarafianoss@missouri.edu.
University of Missouri · USUniversity of Pittsburgh · USNational Institutes of Health · USTohoku University · JP

Funding

Project 9P50GM103368 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI ARNOLD, EDWARD · 2012 to 2016
$20.0M
Structural studies of HIV Capsid with host factors and Capsid-targeting antiviralsR01AI120860 · NIAID · UNIVERSITY OF MISSOURI-COLUMBIA · PI Stefan G Sarafianos, Zhengqiang Wang · 2015 to 2026
$6.0M
Ultrapotent Inhibitors of Wild-type and Multi-drug Resistant HIVR01AI076119 · NIAID · UNIVERSITY OF MISSOURI-COLUMBIA · PI SARAFIANOS, STEFAN G · 2008 to 2018
$4.1M
Hepatitis C antivirals: Mechanism of action, combination efficacy and resistanceR01AI099284 · NIAID · ROCKEFELLER UNIVERSITY · PI RICE, CHARLES M · 2012 to 2016
$3.6M
Ultrapotent Inhibitors of Wild-type and Multi-drug Resistant HIVR37AI076119 · NIAID · EMORY UNIVERSITY · PI Stefan G Sarafianos · 2020 to 2026
$3.6M
Novel antivirals targeting the RNase H activity of HIV reverse transcriptaseR01AI100890 · NIAID · UNIVERSITY OF MISSOURI-COLUMBIA · PI SARAFIANOS, STEFAN G, WANG, ZHENGQIANG · 2012 to 2016
$3.6M
Development of Novel Agents Active against Hepatitis B VirusZIABC011486 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI MITSUYA, HIROAKI · 2013 to 2025
$3.0M
Reverse Transcriptase Multi-Class Drug Resistance and Rilpivirine Susceptibility in Diverse HIV-1 SubtypesR01GM118012 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI SARAFIANOS, STEFAN G · 2016 to 2019
$1.6M
NIAID NIH HHS R01 AI076119NIAID NIH HHS R01 AI099284NIAID NIH HHS R01 AI100890NIAID NIH HHS R01 AI120860NIAID NIH HHS R37 AI076119NIGMS NIH HHS P50 GM103368NIGMS NIH HHS R01 GM118012
6 · The paper itself

Abstract

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-MP(P)• dT-MP(N) ), or (iii) after incorporation of two EFdA-MPs (RT/DNAEFdA-MP(P)• EFdA-MP(N) ); (iv) the latter was also solved with EFdA-MP mismatched at the N site (RT/DNAEFdA-MP(P)• 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. 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.

Indexed as

Anti-HIV AgentsCatalytic DomainCrystallography, X-RayDeoxyadenosinesEnzyme StabilityHIV Reverse TranscriptaseReverse Transcriptase InhibitorsAnti-HIV AgentsDeoxyadenosinesHIV Reverse TranscriptaseislatravirReverse Transcriptase InhibitorsEFdAHIV-1 reverse transcriptaseinhibitorsNRTIsX-ray crystallography

Identifiers

PMID27489345
PMCPMC4995989
OpenAlexW2486192779

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.