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Multimodal mechanism of action of allosteric HIV-1 integrase inhibitors

  • Kellie Ann Jurado (a1) (a2) and Alan Engelman (a1) (a2) (a3)

Abstract

Integrase (IN) is required for lentivirus replication and is a proven drug target for the prevention of AIDS in HIV-1-infected patients. While clinical strand transfer inhibitors disarm the IN active site, allosteric inhibition of enzyme activity through the disruption of IN–IN protein interfaces holds great therapeutic potential. A promising class of allosteric IN inhibitors (ALLINIs), 2-(quinolin-3-yl) acetic acid derivatives, engage the IN catalytic core domain dimerisation interface at the binding site for the host integration co-factor LEDGF/p75. ALLINIs promote IN multimerisation and, independent of LEDGF/p75 protein, block the formation of the active IN–DNA complex, as well as inhibit the IN–LEDGF/p75 interaction in vitro. Yet, rather unexpectedly, the full inhibitory effect of these compounds is exerted during the late phase of HIV-1 replication. ALLINIs impair particle core maturation as well as reverse transcription and integration during the subsequent round of virus infection. Recapitulating the pleiotropic phenotypes observed with numerous IN mutant viruses, ALLINIs provide insight into underlying aspects of IN biology that extend beyond its catalytic activity. Therefore, in addition to the potential to expand our repertoire of HIV-1 antiretrovirals, ALLINIs afford important structural probes to dissect the multifaceted nature of the IN protein throughout the course of HIV-1 replication.

Copyright

Corresponding author

*Corresponding author: Alan Engelman, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, 450 Brookline Avenue, CLS-1010, Boston, MA 02215, USA. E-mail: alan_engelman@dfci.harvard.edu

References

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1Sterne, J.A. et al. (2005) Long-term effectiveness of potent antiretroviral therapy in preventing AIDS and death: a prospective cohort study. Lancet 366, 378-384
2Engelman, A. and Cherepanov, P. (2012) The structural biology of HIV-1: mechanistic and therapeutic insights. Nature Review Microbiology 10, 279-290
3Frentz, D., Boucher, C.A. and van de Vijver, D.A. (2012) Temporal changes in the epidemiology of transmission of drug-resistant HIV-1 across the world. AIDS Reviews 14, 17-27
4Debouck, C. et al. (1987) Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor. Proceedings of the National Academy of Sciences of the USA 84, 8903-8906
5Pettit, S.C. et al. (2002) Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. Journal of Virology 76, 10226-10233
6Könnyű, B. et al. (2013) Gag-Pol processing during HIV-1 virion maturation: a systems biology approach. PLoS Computational Biology 9, e1003103
7Briggs, J.A. et al. (2004) The stoichiometry of Gag protein in HIV-1. Nature Structural and Molecular Biology 11, 672-675
8Lanman, J. et al. (2004) Key interactions in HIV-1 maturation identified by hydrogen-deuterium exchange. Nature Structural and Molecular Biology 11, 676-677
9Pornillos, O., Ganser-Pornillos, B.K. and Yeager, M. (2011) Atomic-level modelling of the HIV capsid. Nature 469, 424-427
10Zhao, G. et al. (2013) Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497, 643-646
11Sundquist, W.I. and Kräusslich, H.G. (2012) HIV-1 assembly, budding, and maturation. Cold Spring Harbor Perspective in Medicine 2, e006924
12McKee, C.J. et al. (2008) Dynamic modulation of HIV-1 integrase structure and function by cellular lens epithelium-derived growth factor (LEDGF) protein. Journal of Biological Chemistry 283, 31802-31812
13Bao, K.K. et al. (2003) Functional oligomeric state of avian sarcoma virus integrase. Journal of Biological Chemistry 278, 1323-1327
14Faure, A. et al. (2005) HIV-1 integrase crosslinked oligomers are active in vitro. Nucleic Acids Research 33, 977-986
15Li, M. et al. (2006) Retroviral DNA integration: reaction pathway and critical intermediates. EMBO Journal 25, 1295-1304
16Bera, S. et al. (2009) Molecular interactions between HIV-1 integrase and the two viral DNA ends within the synaptic complex that mediates concerted integration. Journal of Molecular Biology 389, 183-198
17Kotova, S. et al. (2010) Nucleoprotein intermediates in HIV-1 DNA integration visualized by atomic force microscopy. Journal of Molecular Biology 399, 491-500
18Hare, S. et al. (2010) Retroviral intasome assembly and inhibition of DNA strand transfer. Nature 464, 232-236
19Maertens, G.N., Hare, S. and Cherepanov, P. (2010) The mechanism of retroviral integration through X-ray structures of its key intermediates. Nature 468, 326-329
20Hare, S., Maertens, G.N. and Cherepanov, P. (2012) 3′-Processing and strand transfer catalysed by retroviral integrase in crystallo. EMBO Journal 31, 3020-3028
21Katzman, M. et al. (1989) The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. Journal of Virology 63, 5319-5327
22Pauza, C. (1990) Two bases are deleted from the termini of HIV-1 linear DNA during integrative recombination. Virology 179, 886-889
23Sherman, P.A. and Fyfe, J.A. (1990) Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. Proceedings of the National Academy of Sciences of the USA 87, 5119-5123
24Bushman, F.D. and Craigie, R. (1991) Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. Proceedings of the National Academy of Sciences of the USA 88, 1339-1343
25Engelman, A., Mizuuchi, K. and Craigie, R. (1991) HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell 67, 1211-1221
26Bushman, F.D., Fujiwara, T. and Craigie, R. (1990) Retroviral DNA integration directed by HIV integration protein in vitro. Science 249, 1555-1558
27Krishnan, L. and Engelman, A. (2012) Retroviral integrase proteins and HIV-1 DNA integration. Journal of Biological Chemistry 287, 40858-40866
28Li, L. et al. (2001) Role of the non-homologous DNA end joining pathway in the early steps of retroviral infection. EMBO Journal 20, 3272-3281
29Kilzer, J.M. et al. (2003) Roles of host cell factors in circularization of retroviral DNA. Virology 314, 460-467
30Munir, S. et al. (2013) Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle. Retrovirology 10, 87
31[No authors listed] (2007) FDA notifications. Accelerated approval for raltegravir tablets. AIDS Alert 22, 143-144
32Markowitz, M. et al. (2007) Rapid and durable antiretroviral effect of the HIV-1 integrase inhibitor raltegravir as part of combination therapy in treatment-naive patients with HIV-1 infection: results of a 48-week controlled study. Journal of Acquired Immune Deficiency Syndrome 46, 125-133
33Sichtig, N. et al. (2009) Evolution of raltegravir resistance during therapy. Journal of Antimicrobial Chemotherapy 64, 25-32
34Steigbigel, R.T. et al. (2008) Raltegravir with optimized background therapy for resistant HIV-1 infection. New England Journal of Medicine 359, 339-354
35Olin, J.L., Spooner, L.M. and Klibanov, O.M. (2012) Elvitegravir/cobicistat/emtricitabine/tenofovir disoproxil fumarate single tablet for HIV-1 infection treatment. Annals of Pharmacotherapy 46, 1671-1677
36Metifiot, M. et al. (2011) Elvitegravir overcomes resistance to raltegravir induced by integrase mutation Y143. AIDS 25, 1175-1178
37Eron, J.J. et al. (2013) Safety and efficacy of dolutegravir in treatment-experienced subjects with raltegravir-resistant HIV type 1 infection: 24-week results of the VIKING Study. Journal of Infectious Diseases 207, 740-748
38Wells, J.A. and McClendon, C.L. (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450, 1001-1009
39Li, X. et al. (2011) Structural biology of retroviral DNA integration. Virology 411, 194-205
40Dyda, F. et al. (1994) Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266, 1981-1986
41Molteni, V. et al. (2001) Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain. Acta Crystallography D Biological Crystallography 57, 536-544
42Lin, Z. et al. (1999) Chicoric acid analogues as HIV-1 integrase inhibitors. Journal of Medicinal Chemistry 42, 1401-1414
43Shkriabai, N. et al. (2004) Identification of an inhibitor-binding site to HIV-1 integrase with affinity acetylation and mass spectrometry. Proceedings of the National Academy of Sciences of the USA 101, 6894-6899
44Kessl, J.J. et al. (2009) An allosteric mechanism for inhibiting HIV-1 integrase with a small molecule. Molecular Pharmacology 76, 824-832
45Du, L. et al. (2008) Symmetrical 1-pyrrolidineacetamide showing anti-HIV activity through a new binding site on HIV-1 integrase. Acta Pharmacologica Sinica 29, 1261-1267
46Turlure, F. et al. (2004) Human cell proteins and human immunodeficiency virus DNA integration. Frontiers in Bioscience 9, 3187-3208
47Van Maele, B. et al. (2006) Cellular co-factors of HIV-1 integration. Trends in Biochemical Science 31, 98-105
48Vandegraaff, N. and Engelman, A. (2007) Molecular mechanism of HIV integration and therapeutic intervention. Expert Reviews in Molecular Medicine 9, 1-19
49Engelman, A. (2007) Host cell factors and HIV-1 integration. Future HIV Therapy 1, 415-426
50Nishizawa, Y. et al. (2001) Spatial and temporal dynamics of two alternatively spliced regulatory factors, lens epithelium-derived growth factor (ledgf/p75) and p52, in the nucleus. Cell Tissue Research 305, 107-114
51Ge, H., Si, Y. and Roeder, R.G. (1998) Isolation of cDNAs encoding novel transcription coactivators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation. EMBO Journal 17, 6723-6729
52Engelman, A. and Cherepanov, P. (2008) The lentiviral integrase binding protein LEDGF/p75 and HIV-1 replication. PLoS Pathogens 4, e1000046
53Poeschla, E.M. (2008) Integrase, LEDGF/p75 and HIV replication. Cellular and Molecular Life Sciences 65, 1403-1424
54Cherepanov, P. et al. (2003) HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells. Journal of Biological Chemistry 278, 372-381
55Emiliani, S. et al. (2005) Integrase mutants defective for interaction with LEDGF/p75 are impaired in chromosome tethering and HIV-1 replication. Journal of Biological Chemistry 280, 25517-25523
56Cherepanov, P. et al. (2004) Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase. Journal of Biological Chemistry 279, 48883-48892
57Izumoto, Y. et al. (1997) Hepatoma-derived growth factor belongs to a gene family in mice showing significant homology in the amino terminus. Biochemical and Biophysical Research Communications 238, 26-32
58Vanegas, M. et al. (2005) Identification of the LEDGF/p75 HIV-1 integrase-interaction domain and NLS reveals NLS-independent chromatin tethering. Journal of Cell Science 118, 1733-1743
59Cherepanov, P. et al. (2000) High-level expression of active HIV-1 integrase from a synthetic gene in human cells. FASEB Journal 14, 1389-1399
60Maertens, G. et al. (2003) LEDGF/p75 is essential for nuclear and chromosomal targeting of HIV-1 integrase in human cells. Journal of Biological Chemistry 278, 33528-33539
61Llano, M. et al. (2004) LEDGF/p75 determines cellular trafficking of diverse lentiviral but not murine oncoretroviral integrase proteins and is a component of functional lentiviral preintegration complexes. Journal of Virology 78, 9524-9537
62Vandegraaff, N. et al. (2006) Biochemical and genetic analyses of integrase-interacting proteins lens epithelium-derived growth factor (LEDGF)/p75 and hepatoma-derived growth factor related protein 2 (HRP2) in preintegration complex function and HIV-1 replication. Virology 346, 415-426
63Vandekerckhove, L. et al. (2006) Transient and stable knockdown of the integrase cofactor LEDGF/p75 reveals its role in the replication cycle of human immunodeficiency virus. Journal of Virology 80, 1886-1896
64Llano, M. et al. (2006) An essential role for LEDGF/p75 in HIV integration. Science 314, 461-464
65Shun, M.C. et al. (2007) LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. Genes and Development 21, 1767-1778
66Marshall, H.M. et al. (2007) Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS One 2, e1340
67Cherepanov, P. et al. (2005) Solution structure of the HIV-1 integrase-binding domain in LEDGF/p75. Nature Structural and Molecular Biology 12, 526-532
68Cherepanov, P. et al. (2005) Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proceedings of the National Academy of Sciences of the USA 102, 17308-17313
69Rahman, S. et al. (2007) Structure-based mutagenesis of the integrase-LEDGF/p75 interface uncouples a strict correlation between in vitro protein binding and HIV-1 fitness. Virology 357, 79-90
70Busschots, K. et al. (2007) Identification of the LEDGF/p75 binding site in HIV-1 integrase. Journal of Molecular Biology 365, 1480-1492
71Al-Mawsawi, L.Q. et al. (2008) Inhibitory profile of a LEDGF/p75 peptide against HIV-1 integrase: insight into integrase-DNA complex formation and catalysis. FEBS Letters 582, 1425-1430
72De Rijck, J. et al. (2006) Overexpression of the lens epithelium-derived growth factor/p75 integrase binding domain inhibits human immunodeficiency virus replication. Journal of Virology 80, 11498-11509
73Hombrouck, A. et al. (2007) Virus evolution reveals an exclusive role for LEDGF/p75 in chromosomal tethering of HIV. PLoS Pathogens 3, e47
74Mazumder, A. et al. (1996) Antiretroviral agents as inhibitors of both human immunodeficiency virus type 1 integrase and protease. Journal of Medicinal Chemistry 39, 2472-2481
75Al-Mawsawi, L.Q. et al. (2006) Discovery of a small-molecule HIV-1 integrase inhibitor-binding site. Proceedongs of the National Academy of Sciences of the USA 103, 10080-10085
76Hou, Y. et al. (2008) Screening for antiviral inhibitors of the HIV integrase-LEDGF/p75 interaction using the AlphaScreen luminescent proximity assay. Journal of Biomolecular Screening 13, 406-414
77Du, L. et al. (2008) D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75. Biochemical and Biophysical Research Communications 375, 139-44
78De Luca, L. et al. (2009) Pharmacophore-based discovery of small-molecule inhibitors of protein-protein interactions between HIV-1 integrase and cellular cofactor LEDGF/p75. ChemMedChem 4, 1311-1316
79Christ, F. et al. (2010) Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nature Chemical Biology 6, 442-448
80Fenwick, C.W. et al. (2011) Resistance studies with HIV-1 non-catalytic site integrase inhibitors. Antiviral Therapy 16 (Suppl 1), A9
81Peat, T.S. et al. (2012) Small molecule inhibitors of the LEDGF site of human immunodeficiency virus integrase identified by fragment screening and structure based design. PLoS One 7, e40147
82Tsantrizos, Y.S., Boes, M., Brochu, C., Fenwick, C., Malenfant, E., Mason, S., and Pesant, M. (November 22, 2007) Inhibitors of human immunodeficiency virus replication. International Patent Application WO 2007/131350 A1
83Tsiang, M. et al. (2012) New class of HIV-1 integrase (IN) inhibitors with a dual mode of action. Journal of Biological Chemistry 287, 21189-21203
84Svarovskaia, E.S. et al. (2004) Azido-containing diketo acid derivatives inhibit human immunodeficiency virus type 1 integrase in vivo and influence the frequency of deletions at two-long-terminal-repeat-circle junctions. Journal of Virology 78, 3210-3222
85Christ, F. et al. (2012) Small-molecule inhibitors of the LEDGF/p75 binding site of integrase block HIV replication and modulate integrase multimerization. Antimicrobial Agents and Chemotherapy 56, 4365-4374
86Kessl, J.J. et al. (2012) Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors. Journal of Biological Chemistry 287, 16801-16811
87Balakrishnan, M. et al. (2013) Non-catalytic site HIV-1 integrase inhibitors disrupt core maturation and induce a reverse transcription block in target cells. PLoS One 8, e74163
88Wang, H. et al. (2012) HRP2 determines the efficiency and specificity of HIV-1 integration in LEDGF/p75 knockout cells but does not contribute to the antiviral activity of a potent LEDGF/p75-binding site integrase inhibitor. Nucleic Acids Research 40, 11518-11530
89Jurado, K.A. et al. (2013) Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation. Proceedings of the National Academy of Sciences of the USA 110, 8690-8695
90Schrijvers, R. et al. (2012) LEDGF/p75-independent HIV-1 replication demonstrates a role for HRP-2 and remains sensitive to inhibition by LEDGINs. PLoS Pathogens 8, e1002558
91Schrijvers, R. et al. (2012) HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells. Retrovirology 9, 84
92Desimmie, B.A. et al. (2013) LEDGINs inhibit late stage HIV-1 replication by modulating integrase multimerization in the virions. Retrovirology 10, 57
93Engelman, A. (1999) In vivo analysis of retroviral integrase structure and function. Advances in Virus Research 52, 411-426
94Engelman, A. (2011) The pleiotropic nature of human immunodeficiency virus integrase mutations. In HIV-1 Integrase: Mechanism and Inhibitor Design (Neamati, N., ed.), pp. 67-81. John Wiley & Sons, Inc., Hoboken, NJ.
95Shin, C. et al. (1994) Genetic analysis of the human immunodeficiency virus type 1 integrase protein. Journal of Virology 68, 1633-1642
96Masuda, T. et al. (1995) Genetic analysis of human immunodeficiency virus type 1 integrase and the U3 att site: unusual phenotype of mutants in the zinc finger-like domain. Journal of Virology 69, 6687-6696
97Engelman, A. et al. (1995) Multiple effects of mutations in human immunodeficiency virus type 1 integrase on viral replication. Journal of Virology 69, 2729-2736
98Wiskerchen, M. and Muesing, M.A. (1995) Human immunodeficiency virus type 1 integrase: effects of mutations on viral ability to integrate, direct viral gene expression from unintegrated viral DNA templates, and sustain viral propagation in primary cells. Journal of Virology 69, 376-386
99Leavitt, A.D. et al. (1996) Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection. Journal of Virology 70, 721-728
100Wu, X. et al. (1999) Human immunodeficiency virus type 1 integrase protein promotes reverse transcription through specific interactions with the nucleoprotein reverse transcription complex. Journal of Virology 73, 2126-2135
101Zhu, K., Dobard, C. and Chow, S.A. (2004) Requirement for integrase during reverse transcription of human immunodeficiency virus type 1 and the effect of cysteine mutations of integrase on its interactions with reverse transcriptase. Journal of Virology 78, 5045-5055
102Hehl, E.A. et al. (2004) Interaction between human immunodeficiency virus type 1 reverse transcriptase and integrase proteins. Journal of Virology 78, 5056-5067
103Wilkinson, T.A. et al. (2009) Identifying and characterizing a functional HIV-1 reverse transcriptase-binding site on integrase. Journal of Biological Chemistry 284, 7931-7939
104Dobard, C.W., Briones, M.S. and Chow, S.A. (2007) Molecular mechanisms by which human immunodeficiency virus type 1 integrase stimulates the early steps of reverse transcription. Journal of Virology 81, 10037-10046
105Shehu-Xhilaga, M. et al. (2002) The conformation of the mature dimeric human immunodeficiency virus type 1 RNA genome requires packaging of pol protein. Journal of Virology 76, 4331-4340
106Allen, P., Worland, S. and Gold, L. (1995) Isolation of high-affinity RNA ligands to HIV-1 integrase from a random pool. Virology 209, 327-336
107Buxton, P., Tachedjian, G. and Mak, J. (2005) Analysis of the contribution of reverse transcriptase and integrase proteins to retroviral RNA dimer conformation. Journal of Virology 79, 6338-6348
108Moore, M.D. et al. (2008) Suboptimal inhibition of protease activity in human immunodeficiency virus type 1: effects on virion morphogenesis and RNA maturation. Virology 379, 152-160
109Kaplan, A.H. et al. (1993) Partial inhibition of the human immunodeficiency virus type 1 protease results in aberrant virus assembly and the formation of noninfectious particles. Journal of Virology 67, 4050-4055
110Ohishi, M. et al. (2011) The relationship between HIV-1 genome RNA dimerization, virion maturation and infectivity. Nucleic Acids Research 39, 3404-3417
111Cherepanov, P. et al. (1999) Activity of recombinant HIV-1 integrase on mini-HIV DNA. Nucleic Acids Research 27, 2202-2210
112Feng, L. et al. (2013) The A128T resistance mutation reveals aberrant protein multimerization as the primary mechanism of action of allosteric HIV-1 integrase inhibitors. Journal of Biological Chemistry 288, 15813-15820
113Shen, L., Rabi, S.A. and Siliciano, R.F. (2009) A novel method for determining the inhibitory potential of anti-HIV drugs. Trends in Pharmacological Sciences 30, 610-616
114Rosenbloom, D.I. et al. (2012) Antiretroviral dynamics determines HIV evolution and predicts therapy outcome. Nature Medicine 18, 1378-1385
115Shen, L. et al. (2008) Dose-response curve slope sets class-specific limits on inhibitory potential of anti-HIV drugs. Nature Medicine 14, 762-766
116Katlama, C. et al. (2010) Efficacy of darunavir/ritonavir maintenance monotherapy in patients with HIV-1 viral suppression: a randomized open-label, noninferiority trial, MONOI-ANRS 136. AIDS 24, 2365-2374
117Shen, L. et al. (2011) A critical subset model provides a conceptual basis for the high antiviral activity of major HIV drugs. Science Translational Medicine 3, 91ra63
118Rabi, S.A. et al. (2013) Multi-step inhibition explains HIV-1 protease inhibitor pharmacodynamics and resistance. Journal of Clinical Investigation 123, 3848-3860
119Engelman, A., Kessl, J.J. and Kvaratskhelia, M. (2013) Allosteric inhibition of HIV-1 integrase activity. Current Opinion in Chemical Biology 17, 339-345

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Multimodal mechanism of action of allosteric HIV-1 integrase inhibitors

  • Kellie Ann Jurado (a1) (a2) and Alan Engelman (a1) (a2) (a3)

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