Characterization of a Binding Site for Template Competitive Inhibitors of HIV-1 Reverse Transcriptase Using Photolabeling Derivatives

AbstractReverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC–nevirapine, and RTIC–efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA–tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

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All-Atom Models for the Non-Nucleoside Binding Site of HIV-1 Reverse Transcriptase Complexed with Inhibitors: A 3D QSAR Approach†

Journal of Medicinal Chemistry ◽

10.1021/jm9508088 ◽

1996 ◽

Vol 39 (8) ◽

pp. 1645-1650 ◽

Cited By ~ 36

Author(s):

Rick Gussio ◽

Nagarajan Pattabiraman ◽

Daniel W. Zaharevitz ◽

Glen E. Kellogg ◽

Igor A. Topol ◽

...

Keyword(s):

Reverse Transcriptase ◽

Binding Site ◽

3D Qsar ◽

Hiv 1

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Oxygen binding isotope effects of triazole-based HIV-1 reverse transcriptase inhibitors indicate the actual binding site

Archives of Biochemistry and Biophysics ◽

10.1016/j.abb.2017.10.017 ◽

2017 ◽

Vol 635 ◽

pp. 87-95

Author(s):

Agnieszka Krzemińska ◽

Tomasz Frączek ◽

P. Paneth

Keyword(s):

Reverse Transcriptase ◽

Binding Site ◽

Isotope Effects ◽

Oxygen Binding ◽

Reverse Transcriptase Inhibitors ◽

Hiv 1

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Characterization of a Mutant HIV-1 Reverse Transcriptase Resistant to (+)-(5S)-4,5,6,7-tetrahydro-5-methyl-6-(3-methyl-2-butenyl)-imidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-thione (TIBO R82150)

Antiviral Chemistry and Chemotherapy ◽

10.1177/095632029400500410 ◽

1994 ◽

Vol 5 (4) ◽

pp. 278-281

Author(s):

H. Samanta ◽

R. Rose ◽

A. K. Patick ◽

C. M. Bechtold ◽

J. Trimble ◽

...

Keyword(s):

Reverse Transcriptase ◽

Nucleoside Reverse Transcriptase Inhibitor ◽

Serial Passage ◽

Transcriptase Inhibitor ◽

Viral Resistance ◽

Resistant Virus ◽

Reverse Transcriptase Inhibitor ◽

Hiv 1

A virus strain resistant to R82150, a non-nucleoside reverse transcriptase (NNRT) inhibitor (tetrahydro-imidazo [4,5, 1- jk] [1,4] benzodiazepine-2(1 H)-thione), was isolated following serial passage of HIV-1 RF in CEM-SS cells. The virus is cross-resistant to another non-nucleoside reverse transcriptase inhibitor, TGG-II-23A [1,4-dimethyl-1-[5,5-dimethyl-2-oxazoionyl]-naphthalen-2-one), but remains susceptible to AZT, DDI, D4T and phosphonoformate (PFA). DNA sequencing of reverse transcriptase genes from resistant virus indicated that R82150 selects for amino acid alterations Y181C and V108I. In vitro mutagenized reverse transcriptase and recombinant HIV-1 (pNL4-3) carrying either of the mutations have been generated. Genotypic and phenotypic analyses identified V108I as an unreported R82150-associated mutation. Both reverse transcriptase and viral resistance assays indicated that the resistance conferred by the V108I mutation is 7-fold less than that conferred by Y181C.

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