Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening.

HIV-1 reverse transcriptase (RT) plays an essential role in viral replication and is an attractive target for antiretroviral therapy. RT, a p66/p51 heterodimer, is a multi-domain protein that undergoes a series of conformational changes during the replication of the HIV-1 genome. The intrinsic flexibility of RT can provide novel allosteric sites for inhibition. Crystals of RT that diffract X-rays to better than 2 Å resolution facilitated the probing of RT for new druggable sites using X-ray crystallographic fragment screening. A total of 775 fragments were grouped into 143 cocktails, which were soaked into crystals of RT in complex with the non-nucleoside drug Edurant (TMC278/rilpivirine). Fragment binding was observed at seven new binding sites. These include the incoming nucleotide binding, Knuckles, NNRTI Adjacent, and 399 sites, located in the polymerase region of RT, and the 428, RNase H primer grip adjacent, and 507 sites, located in the RNase H region. Three of these sites-Knuckles, NNRTI adjacent, and the incoming nucleotide binding-are inhibitory and provide opportunities for discovery of new anti-AIDS drugs.