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

DOI: 10.1038/s41467-021-27409-y DOI Help

Authors: Abhimanyu Singh (KU Leuven) , Sergio E. Martinez (KU Leuven) , Weijie Gu (KU Leuven) , Hoai Nguyen (KU Leuven) , Dominique Schols (KU Leuven) , Piet Herdewijn (KU Leuven) , Steven De Jonghe (KU Leuven) , Kalyan Das (KU Leuven)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nature Communications , VOL 12

State: Published (Approved)
Published: December 2021
Diamond Proposal Number(s): 22010

Open Access Open Access

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 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.

Journal Keywords: Cryoelectron microscopy; Structure-based drug design; Target identification; Virtual drug screening; X-ray crystallography

Diamond Keywords: Viruses; Human Immunodeficiency Virus (HIV)

Subject Areas: Biology and Bio-materials, Medicine

Diamond Offline Facilities: XChem
Instruments: I04-1-Macromolecular Crystallography (fixed wavelength)

Added On: 15/12/2021 10:02


Discipline Tags:

Pathogens Infectious Diseases Health & Wellbeing Structural biology Drug Discovery Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX) Fragment Screening