A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase

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

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Abstract

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.

Original languageEnglish (US)
Article numbere1004171
JournalPLoS Pathogens
Volume10
Issue number5
DOIs
StatePublished - 2014

Fingerprint

Integrases
Integrase Inhibitors
HIV-1
HIV Integrase Inhibitors
p31 integrase protein, Human immunodeficiency virus 1
Virus Replication
Morphogenesis
Virion
Antiviral Agents
Molecular Biology
Chromosomes
Genome
lens epithelium-derived growth factor
quinoline

ASJC Scopus subject areas

  • Microbiology
  • Parasitology
  • Virology
  • Immunology
  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Sharma, A., Slaughter, A., Jena, N., Feng, L., Kessl, J. J., Fadel, H., ... Kvaratskhelia, M. (2014). A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase. PLoS Pathogens, 10(5), [e1004171]. https://doi.org/10.1371/journal.ppat.1004171

A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase. / Sharma, Amit; Slaughter, Alison; Jena, Nivedita; Feng, Lei; Kessl, Jacques J.; Fadel, Hind; Malani, Nirav; Male, Frances; Wu, Li; Poeschla, Eric; Bushman, Frederic D.; Fuchs, James R.; Kvaratskhelia, Mamuka.

In: PLoS Pathogens, Vol. 10, No. 5, e1004171, 2014.

Research output: Contribution to journalArticle

Sharma, A, Slaughter, A, Jena, N, Feng, L, Kessl, JJ, Fadel, H, Malani, N, Male, F, Wu, L, Poeschla, E, Bushman, FD, Fuchs, JR & Kvaratskhelia, M 2014, 'A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase', PLoS Pathogens, vol. 10, no. 5, e1004171. https://doi.org/10.1371/journal.ppat.1004171
Sharma, Amit ; Slaughter, Alison ; Jena, Nivedita ; Feng, Lei ; Kessl, Jacques J. ; Fadel, Hind ; Malani, Nirav ; Male, Frances ; Wu, Li ; Poeschla, Eric ; Bushman, Frederic D. ; Fuchs, James R. ; Kvaratskhelia, Mamuka. / A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase. In: PLoS Pathogens. 2014 ; Vol. 10, No. 5.
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abstract = "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.",
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