4′-Ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) Inhibits HIV-1 Reverse Transcriptase with Multiple Mechanisms

Michailidis, Eleftherios; Huber, Andrew D.; Ryan, Emily M.; Ong, Yee Tsuey; Leslie, Maxwell D.; Matzek, Kayla B.; Singh, Kamalendra; Marchand, Bruno; Hagedorn, Ariel N.; Kirby, Karen A.; Rohan, Lisa C.; Kodama, Eiichi N.; Mitsuya, Hiroaki; Parniak, Michael A.; Sarafianos, Stefan G.

doi:10.1074/jbc.m114.562694

Cited by 90 publications

(96 citation statements)

References 49 publications

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“…4A). Such extensive interactions of EFdA-TP at the N site are consistent with the previously reported high k on and low k off rates that result in RT binding EFdA-TP even better than dNTP substrates (15). These interactions contribute to the inhibition mechanism of EFdA-TP as an ICT or translocation-defective RT inhibitor as they would favor binding of the EFdA-MP-terminated primer at the pretranslocation N site.…”

Section: Resultssupporting

confidence: 72%

“…This hypothesis is supported by hydroxyl radical footprinting experiments showing that, at template sites favoring ICT, EFdA-MP-extended primers are overwhelmingly bound with EFdA-MP positioned at the N site (EFdA-MP N ) (15). At template sites where EFdA acts as a DCT, EFdA-MP N is extended to EFdA-MP P •dN-MP N ; in this case, we propose that inhibition occurs because of steric crowding between the 4′-E of EFdA-MP and the main chain of Y183, leading to localized primer distortions (Fig.…”

Section: Resultsmentioning

confidence: 52%

“…dG-dC-specific interactions at the P site (with the 2-amino of dG and 2-carbonyl of dC; Fig. 4C) may further stabilize pretranslocation complexes and explain the reported preference for the ICT rather than DCT mechanism of inhibition for such nucleic acid substrates (15).…”

Section: Resultsmentioning

confidence: 99%

“…terminator (ICT) or as a delayed chain terminator (DCT) that allows incorporation of a single nucleotide following EFdA-monophosphate (MP) and slows nucleotide extension after incorporation into the nascent primer (15). Moreover, RT misincorporates EFdA-MP more efficiently than dA-triphosphate (TP), resulting in mismatched primers that are difficult to extend.…”

mentioning

confidence: 99%

“…Moreover, RT misincorporates EFdA-MP more efficiently than dA-triphosphate (TP), resulting in mismatched primers that are difficult to extend. Finally, when EFdA acts as a DCT, EFdA-MP-terminated primers are protected from the phosphorolytic excision that can lead to NRTI resistance (15).…”

mentioning

confidence: 99%

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

Salie

Kirby

Michailidis

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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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/DNA EFdA-MP P •dT-MP N), or (iii) after incorporation of two EFdA-MPs (RT/DNA EFdA-MP P •EFdA-MP N); (iv) the latter was also solved with EFdA-MP mismatched at the N site (RT/DNA EFdA-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.EFdA | HIV-1 reverse transcriptase | inhibitors | NRTIs | X-ray crystallography

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Section: Resultssupporting

confidence: 72%

Section: Resultsmentioning

confidence: 52%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Salie

Kirby

Michailidis

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen

Agnello¹,

Brand²,

Chellat³

et al. 2019

Angewandte Chemie

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Das natürliche Phänomen der Wirkstoffresistenz stellt eine universelle Beeinträchtigung des Nutzens von pharmazeutischen Wirkstoffen in vielen klinischen Indikationen dar. Antibakterielle und antifungale Wirkstoffe sind dabei ebenso betroffen wie Wirkstoffe zur Behandlung von Krebs, Virusinfektionen oder durch Parasiten hervorgerufene Erkrankungen. Trotz der unterschiedlichen biologischen Zielstrukturen und Organismen, die bei der Entwicklung von Wirkstoffresistenzen involviert sind, konnten grundlegende molekulare Prozesse identifiziert werden, die zum Verständnis des Auftretens von Resistenzen beitragen und die Bekämpfung dieser nachteiligen Mechanismen erlauben. Strukturelle Informationen über die Prinzipien von Wirkstoffresistenzen sind heute vielfältig vorhanden, sodass neue Wirkstoffe entwickelt werden können, die weniger anfällig gegenüber einer Resistenzbildung sein werden. Dieser wissensbasierte Ansatz ist eine Grundlage für den Kampf gegen das unvermeidbare Auftreten von Wirkstoffresistenzen.

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A Structural View on Medicinal Chemistry Strategies against Drug Resistance

et al. 2019

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The natural phenomenon of drug resistance represents a generic impairment that hampers the benefits of drugs in all major clinical indications. Antibacterials and antifungals are affected as well as compounds for the treatment of cancer, viral infections or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, underlying molecular processes have been identified to understand the emergence of resistance and to overcome this detrimental mechanism. Detailed structural information of the root causes for drug resistance is nowadays frequently available to design next generation drugs anticipated to suffer less from resistance. This knowledge-based approach is a prerequisite in the fight against the inevitable occurrence of drug resistance to secure the achievements of medicinal chemistry in the future.

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4′-Ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) Inhibits HIV-1 Reverse Transcriptase with Multiple Mechanisms

Cited by 90 publications

References 49 publications

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

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

Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen

A Structural View on Medicinal Chemistry Strategies against Drug Resistance

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