Structural basis for strand-transfer inhibitor binding to HIV intasomes

Abstract

The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of antiretroviral drugs, integrase strand-transfer inhibitors (INSTIs). Challenges associated with lentiviral intasome biochemistry have hindered high-resolution structural studies of how INSTIs bind to their native drug target. Here, we present high-resolution cryo–electron microscopy structures of HIV intasomes bound to the latest generation of INSTIs. These structures highlight how small changes in the integrase active site can have notable implications for drug binding and design and provide mechanistic insights into why a leading INSTI retains efficacy against a broad spectrum of drug-resistant variants. The data have implications for expanding effective treatments available for HIV-infected individuals.

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

“…The ɑ1 helix of this NTD is shortened in the first HIV-1 tetrameric intasome structure where it begins with Asp 3 [24]. The ɑ1 helix is extended in four of five recent intasome structures, with only one structure showing partial disruption [23]. The second NTD does not interact with the viral DNA and is distant from the active site.…”

“…Four NTDs in two structurally distinct positions exist in the HIV-1 core intasome complex cryo-EM structures determined with Sso7d-IN [23,24]. One NTD, positioned close to the viral DNA and the CCD responsible for catalysis, forms NTD-NTD interactions in the dodecameric HIV-1 intasome and the hexadecameric MVV intasome [25].…”

“…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].…”

“…In contrast to PFV IN [26,41], study of HIV-1 IN is challenging due to poor solubility and a propensity to aggregate [42,43], along with inefficient catalysis in vitro [44][45][46][47][48][49][50]. Fusion of a small DNA-binding protein, Sso7d, that mimics the N-terminal extension domain of PFV to the N-terminus of HIV-1 IN improved catalysis and the solubility of HIV-1 intasomes [51], and enabled structural determination of the HIV-1 core intasome complex by cryo-electron microscopy (cryo-EM) [23,24]. However, a native HIV-1 intasome structure remains elusive.…”

CRYO-EM STRUCTURE OF THE DELTA-RETROVIRAL INTASOME IN COMPLEX WITH THE PP2A REGULATORY SUBUNIT B56γ

“…Thus, interaction with PP2A may allow the virus to locate chromatin loci that are bookmarked for expression soon after completion of cell division (33). Our structural work, presented here, will be instrumental to fully characterize the role of PP2A-B56 in HTLV-1 infection, and given that small changes in the active site between different retroviral INs significantly impact drug binding (34), forms the foundation to develop highly specific inhibitors of HTLV-1 integration.…”