Structural basis of second-generation HIV integrase inhibitor action and viral resistance

Abstract

Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo–electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.

Influence of the amino-terminal sequence on the structure and function of HIV integrase

“…In IN GSH, the N-terminal amino group is oriented toward the C-terminal end of the ɑ2 helix, whereas in IN 1F, it is flipped ~ 180° and oriented toward the ɑ3 helix of a neighboring NTD. The same NTD–NTD interface is observed in dodecameric HIV-1, hexadecameric MVV, and SIV intasome structures [ 22 – 25 ], and the NTDs modeled at this position adopt extended ɑ1 helical structures in four of six structures (Additional file 3 : Figure S3). The NTDs that do not form an NTD–NTD interface show a variety of structures: disordered, partially unstructured, and extended (Additional file 3 : Figure S3).…”

“…This NTD does not form NTD-NTD interactions in dodecameric or hexadecameric intasomes and shows a range of ɑ1 helical structures: disordered, partially unstructured, and extended [23]. Intasomes of a closely-related simian immunodeficiency virus were prepared with IN purified with an N-terminal affinity tag and subsequent human rhinovirus 3C protease cleavage, leaving 3 residues (G-P-G-) preceding F1 [22]. The NTDs in these structures show extended ɑ1 helices.…”

“…IN carries out two catalytic reactions: 3′-processing and strand transfer [1], in a macromolecular complex consisting of multiple IN protomers, viral DNA, cofactors, and host cell proteins termed the intasome [14,[19][20][21][22][23][24][25]. Early intasome structures were determined with IN from the prototype foamy virus (PFV) [26][27][28][29][30], revealing the structural details of enzymatic activity and the mechanism of action of the strand-transfer inhibitors (STIs), which displace the 3′ viral DNA end from the active site, rendering the intasome nonfunctional [22,23,31,32]. STIs are in widespread clinical use [33], however, as with all antiretrovirals, development of resistance is a major barrier to durable inhibition of viral replication [34,35].…”

Systemic in Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server

“…And Bictegravir and Dolutegravir are integrase inhibitors used in combination with other drug for treatment of HIV infection. They are structurally related as the former is a derivation from the latter (75). And their binding energies to nsp5 are also very similar (-9.5 kcal/mol for Bictegravir and -8.9…”

Cryo-EM as a powerful tool for drug discovery

“…Recent cryo-EM studies have revealed how these compounds, as well as other related molecules, are bound to integrase ( Fig. 4 J) [98] , [99] , coordinating two Mg 2+ ions in the active site. The structure of a resistant mutant in complex with bictegravir provides insights into the mechanism of resistance.…”