The research in our laboratory focuses on the molecular mechanisms for retroviral integration into the host genome, discovery of HIV-1 integrase inhibitors with allosteric mechanisms of action and virus-host interactions. We employ innovative and complementary biochemistry, biophysics, structural biology, pharmacology, molecular biology and virology approaches.
Structure and function of HIV-1 integrase. We are investigating structural determinants for how a key HIV-1 enzyme integrase carries out concerted integration of reverse transcribed viral cDNA into chromatin of infected cells (1,2). Furthermore, we have recently discovered an unexpected, non-catalytic role of integrase in HIV-1 biology, which includes its ability to bind and localize the viral RNA genome within the protective cone-shaped capsid core during virion maturation (3). Our current efforts are focused on dissecting structural and mechanistic basis for highly specific interactions of integrase with select sites on the viral RNA genome.
Allosteric HIV-1 integrase inhibitors (ALLINIs). Evolution of HIV-1 strains resistant to current therapies is a major clinical problem in the fight against AIDS. Therefore, new inhibitors with unexploited mechanisms of action are needed. One such mechanism investigated by our group is to allosterically modulate HIV-1 integrase multimerization. In proof-of-concept studies (4,5) we reported a compound that binds at the IN dimer interface, “locking” interacting subunits into an inactive conformation. More recently, we have elucidated the mechanism of action of ALLINIs, which are currently in clinical trials (6-8). These inhibitors potently blocked HIV-1 replication by inducing hyper- or aberrant- integrase multimerization in virions and resulted in eccentric particle maturation with the ribonucleoprotein complex being mislocalized between the capsid core and the particle membrane. These studies have delineated the significance of correctly ordered integrase structure for HIV-1 particle morphogenesis and demonstrated the feasibility of exploiting integrase multimerization as a therapeutic target. Our current efforts are centered on developing novel integrase inhibitors with unique structural scaffolds for their potential clinical use.
Virus-host interactions. Host cell factors regulate retroviral replication. We have identified bromodomain and extraterminal domain (BET) proteins (Brd2, 3, 4) as principal cellular-binding partners of gammaretroviral murine leukemia virus (MLV) integrase and demonstrated their importance for targeting MLV integration to transcription start sites (9). These findings inform ongoing efforts to develop safer retroviral vectors for human gene therapy. In addition, we are studying how LEDGF/p75, a key cellular binding partner of lentiviral integrases, navigates HIV-1 preintegration complexes to active genes during integration (10,11). Furthermore, we have recently discovered and are currently investigating molecular mechanisms of novel critical co-factors for HIV-1 infection.
1. Passos, D. O., Li, M., Yang, R., Rebensburg, S. V., Ghirlando, R., Jeon, Y., Shkriabai, N., Kvaratskhelia, M., Craigie, R., and Lyumkis, D. (2017) Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science 355, 89-92
2. Kessl, J. J., Li, M., Ignatov, M., Shkriabai, N., Eidahl, J. O., Feng, L., Musier-Forsyth, K., Craigie, R., and Kvaratskhelia, M. (2011) FRET analysis reveals distinct conformations of IN tetramers in the presence of viral DNA or LEDGF/p75. Nucleic Acids Res. 39, 9009-9022
3. Kessl, J. J., Kutluay, S. B., Townsend, D., Rebensburg, S., Slaughter, A., Larue, R. C., Shkriabai, N., Bakouche, N., Fuchs, J. R., Bieniasz, P. D., and Kvaratskhelia, M. (2016) HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis. Cell 166, 1257-1268 e1212
4. Shkriabai, N., Patil, S. S., Hess, S., Budihas, S. R., Craigie, R., Burke, T. R., Jr., Le Grice, S. F., and Kvaratskhelia, M. (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 United States of America 101, 6894-6899
5. Kessl, J. J., Eidahl, J. O., Shkriabai, N., Zhao, Z., McKee, C. J., Hess, S., Burke, T. R., Jr., and Kvaratskhelia, M. (2009) An allosteric mechanism for inhibiting HIV-1 integrase with a small molecule. Mol. Pharmacol. 76, 824-832
6. Jurado, K. A., Wang, H., Slaughter, A., Feng, L., Kessl, J. J., Koh, Y., Wang, W., Ballandras-Colas, A., Patel, P. A., Fuchs, J. R., Kvaratskhelia, M., and Engelman, A. (2013) Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation. Proceedings of the National Academy of Sciences of the United States of America 110, 8690-8695
7. Sharma, A., Slaughter, A., Jena, N., Feng, L., Kessl, J. J., Fadel, H. J., Malani, N., Male, F., Wu, L., Poeschla, E., Bushman, F. D., Fuchs, J. R., and Kvaratskhelia, M. (2014) A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase. PLoS Pathog 10, e1004171
8. Koneru, P. C., Francis, A. C., Deng, N., Rebensburg, S. V., Hoyte, A. C., Lindenberger, J., Adu-Ampratwum, D., Larue, R. C., Wempe, M. F., Engelman, A. N., Lyumkis, D., Fuchs, J. R., Levy, R. M., Melikyan, G. B., and Kvaratskhelia, M. (2019) HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. Elife 8
9. Sharma, A., Larue, R. C., Plumb, M. R., Malani, N., Male, F., Slaughter, A., Kessl, J. J., Shkriabai, N., Coward, E., Aiyer, S. S., Green, P. L., Wu, L., Roth, M. J., Bushman, F. D., and Kvaratskhelia, M. (2013) BET proteins promote efficient murine leukemia virus integration at transcription start sites. Proceedings of the National Academy of Sciences of the United States of America 110, 12036-12041
10. Eidahl, J. O., Crowe, B. L., North, J. A., McKee, C. J., Shkriabai, N., Feng, L., Plumb, M., Graham, R. L., Gorelick, R. J., Hess, S., Poirier, M. G., Foster, M. P., and Kvaratskhelia, M. (2013) Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res. 41, 3924-3936
11. Singh, P. K., Plumb, M. R., Ferris, A. L., Iben, J. R., Wu, X., Fadel, H. J., Luke, B. T., Esnault, C., Poeschla, E. M., Hughes, S. H., Kvaratskhelia, M., and Levin, H. L. (2015) LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes. Genes Dev. 29, 2287-2297