scholarly journals Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer

2015 ◽  
Vol 25 (1) ◽  
pp. 46-55 ◽  
Author(s):  
Matthew T. Miller ◽  
Steve Tuske ◽  
Kalyan Das ◽  
Jeffrey J. DeStefano ◽  
Eddy Arnold
Keyword(s):  
Reverse Transcriptase ◽  
Dna Aptamer ◽  
Hiv 1

scholarly journals Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer

2020 ◽  
Vol 2 ◽  
pp. 116-129 ◽  
Author(s):  
Steve Tuske ◽  
Jie Zheng ◽  
Erik D. Olson ◽  
Francesc X. Ruiz ◽  
Bruce D. Pascal ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Structural Biology ◽  
Dna Aptamer ◽  
High Affinity ◽  
Integrative Structural Biology ◽  
Hiv 1

scholarly journals Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase

Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 285
Author(s):  
Siriluk Ratanabunyong ◽  
Supaphorn Seetaha ◽  
Supa Hannongbua ◽  
Saeko Yanaka ◽  
Maho Yagi-Utsumi ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Double Mutant ◽  
Binding Pocket ◽  
Drug Binding ◽  
Dna Aptamer ◽  
Hek293 Cells ◽  
Dna Aptamers ◽  
Ic50 Values ◽  
Methionine Residues ◽  
Hiv 1

The human immunodeficiency virus type-1 Reverse Transcriptase (HIV-1 RT) plays a pivotal role in essential viral replication and is the main target for antiviral therapy. The anti-HIV-1 RT drugs address resistance-associated mutations. This research focused on isolating the potential specific DNA aptamers against K103N/Y181C double mutant HIV-1 RT. Five DNA aptamers showed low IC50 values against both the KY-mutant HIV-1 RT and wildtype (WT) HIV-1 RT. The kinetic binding affinity forms surface plasmon resonance of both KY-mutant and WT HIV-1 RTs in the range of 0.06–2 μM and 0.15–2 μM, respectively. Among these aptamers, the KY44 aptamer was chosen to study the interaction of HIV-1 RTs-DNA aptamer complex by NMR experiments. The NMR results indicate that the aptamer could interact with both WT and KY-mutant HIV-1 RT at the NNRTI drug binding pocket by inducing a chemical shift at methionine residues. Furthermore, KY44 could inhibit pseudo-HIV particle infection in HEK293 cells with nearly 80% inhibition and showed low cytotoxicity on HEK293 cells. These together indicated that the KY44 aptamer could be a potential inhibitor of both WT and KY-mutant HIV-RT.

scholarly journals Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket − Targeting P-pocket by fragment screening

2021 ◽  
Author(s):  
Abhimanyu K Singh ◽  
Sergio E Martinez ◽  
Weijie Gu ◽  
Hoai Nguyen ◽  
Dominique Schols ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
High Throughput Screening ◽  
Dna Aptamer ◽  
Structural Elements ◽  
Resistance Mutations ◽  
Solution Structures ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Dna Complex ◽  
Hiv 1

HIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3′-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography and identified binding of two to P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized of which two showed noticeable RT inhibition. An engineered RT/DNA aptamer complex trapped the transient P-pocket in solution. Structures of the RT/DNA complex were determined with a fragment and a synthesized analog bound at P-pocket by single-particle cryo-EM. Identification of P-pocket and the devised structure-based platform provide an opportunity for designing new types of polymerase inhibitors.

scholarly journals Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – Targeting P-pocket by fragment screening

2021 ◽  
Author(s):  
Abhimanyu Singh ◽  
Sergio Martinez ◽  
Weijie Gu ◽  
Hoai Nguyen ◽  
Dominique Schols ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
High Throughput Screening ◽  
Dna Aptamer ◽  
Structural Elements ◽  
Resistance Mutations ◽  
Solution Structures ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Dna Complex ◽  
Hiv 1

Abstract HIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3’-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography and identified binding of two to P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized of which two showed noticeable RT inhibition. An engineered RT/DNA aptamer complex trapped the transient P-pocket in solution. Structures of the RT/DNA complex were determined with a fragment and a synthesized analog bound at P-pocket by single-particle cryo-EM. Identification of P-pocket and the devised structure-based platform provide an opportunity for designing new types of polymerase inhibitors.

scholarly journals Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – targeting P-pocket by fragment screening

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Abhimanyu K. Singh ◽  
Sergio E. Martinez ◽  
Weijie Gu ◽  
Hoai Nguyen ◽  
Dominique Schols ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
High Throughput Screening ◽  
Dna Aptamer ◽  
Structural Elements ◽  
Resistance Mutations ◽  
X Ray Crystallography ◽  
Fragment Screening ◽  
Hiv Rt ◽  
Dna Complex ◽  
Hiv 1

AbstractHIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3’-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography that identifies two leads that bind the P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized, two of which show noticeable RT inhibition. An engineered RT/DNA aptamer complex could trap the transient P-pocket in solution, and structures of the RT/DNA complex were determined in the presence of an inhibitory fragment. A synthesized analog bound at P-pocket is further analyzed by single-particle cryo-EM. Identification of the P-pocket within HIV RT and the developed structure-based platform provide an opportunity for the design new types of polymerase inhibitors.

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