Research Article: A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase

Date Published: May 29, 2014

Publisher: Public Library of Science

Author(s): Amit Sharma, Alison Slaughter, Nivedita Jena, Lei Feng, Jacques J. Kessl, Hind J. Fadel, Nirav Malani, Frances Male, Li Wu, Eric Poeschla, Frederic D. Bushman, James R. Fuchs, Mamuka Kvaratskhelia, Bryan R. Cullen.


The quinoline-based allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are promising candidates for clinically useful antiviral agents. Studies using these compounds have highlighted the role of IN in both early and late stages of virus replication. However, dissecting the exact mechanism of action of the quinoline-based ALLINIs has been complicated by the multifunctional nature of these inhibitors because they both inhibit IN binding with its cofactor LEDGF/p75 and promote aberrant IN multimerization with similar potencies in vitro. Here we report design of small molecules that allowed us to probe the role of HIV-1 IN multimerization independently from IN-LEDGF/p75 interactions in infected cells. We altered the rigid quinoline moiety in ALLINIs and designed pyridine-based molecules with a rotatable single bond to allow these compounds to bridge between interacting IN subunits optimally and promote oligomerization. The most potent pyridine-based inhibitor, KF116, potently (EC50 of 0.024 µM) blocked HIV-1 replication by inducing aberrant IN multimerization in virus particles, whereas it was not effective when added to target cells. Furthermore, KF116 inhibited the HIV-1 IN variant with the A128T substitution, which confers resistance to the majority of quinoline-based ALLINIs. A genome-wide HIV-1 integration site analysis demonstrated that addition of KF116 to target or producer cells did not affect LEDGF/p75-dependent HIV-1 integration in host chromosomes, indicating that this compound is not detectably inhibiting IN-LEDGF/p75 binding. These findings delineate the significance of correctly ordered IN structure for HIV-1 particle morphogenesis and demonstrate feasibility of exploiting IN multimerization as a therapeutic target. Furthermore, pyridine-based compounds present a novel class of multimerization selective IN inhibitors as investigational probes for HIV-1 molecular biology.

Partial Text

HIV-1 integrase (IN) is an important therapeutic target as its function is essential for viral replication. A tetramer of IN assembles on the viral DNA ends to form the stable synaptic complex (SSC) and catalyzes two reactions necessary for the integration of linear viral DNA into the host chromatin [1]. IN initially removes a GT dinucleotide from the 3′-terminus of each viral DNA end (3′-processing), and then integrates recessed viral DNA ends into the target DNA in a staggered fashion through concerted transesterification reactions (DNA strand transfer). IN is comprised of three domains: the N-terminal domain (NTD) which contains the Zn-binding motif (HH-CC type), the catalytic core domain (CCD) which contains the DDE catalytic triad that coordinates essential Mg2+ ions, and the C-terminal domain (CTD) which contains an SH3-like fold (reviewed in [2]). Each of these domains contributes to protein multimerization [3]–[6].




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