Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening.
Abhimanyu K SinghSergio E MartinezWeijie GuHoai NguyenDominique ScholsPiet HerdewijnSteven De JongheKalyan DasPublished in: Nature communications (2021)
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.
Keyphrases
- circulating tumor
- cell free
- antiretroviral therapy
- single molecule
- hiv positive
- human immunodeficiency virus
- hiv testing
- hiv infected
- nucleic acid
- hepatitis c virus
- hiv aids
- men who have sex with men
- cerebral ischemia
- high resolution
- sars cov
- gold nanoparticles
- magnetic resonance
- drug delivery
- south africa
- magnetic resonance imaging
- structural basis
- molecular docking
- genome wide
- computed tomography
- gene expression
- high throughput
- subarachnoid hemorrhage
- dna methylation
- brain injury
- blood brain barrier
- quantum dots
- simultaneous determination
- tandem mass spectrometry