Guide to Nuclear Entry:
Novel Target for Anti-HIV Therapeutics

HIV-1 Virus Infection and Nuclear Entry

PIC: Preintegration complex: a structure of viral proteins surrounding the genetic material
α: Karyopherinα: a cellular protein that transports the viral genetic material into the cell nucleus
MA: Matrix protein: the virus component of the preintegration complex that connects the PIC to K
α thus allowing the virus genetic material to enter the cell nucleus
NLS: Nuclear Localization Sequence: amino acid sequence within MA that is the recognition site for K

Human cells consist of compartments. The largest compartment is the cytoplasm, where most biochemical processes occur. When the Human Immunodeficiency Virus Type-1 attacks human cells, (Fig. 1) the HIV-1 virus releases its genetic material (RNA) into the cytoplasm and makes DNA copies of each gene. (Fig. 2) Nuclear entry is the process of transporting this HIV-1 genetic material into another compartment of the cell, the nucleus, where DNA genetic material is duplicated. (Fig. 3) This process is critical for the HIV-1 virus to establish a productive infection. In the absence of nuclear entry, the viral DNA is degraded in the cytoplasm of the infected host cell. The infection is thereby aborted, meaning that the host cell remains uninfected.

In the cytoplasm, the HIV DNA is bound to a number of viral proteins in a complex called the pre-integration complex (PIC). (Fig. 2) The PIC specifically associates with a human protein called Karyopherin (K
α) and other cellular factors. (Fig. 4) Association of the PIC with Kα is mediated by specific amino acid sequences in a viral protein component of the PIC known as the matrix protein (MA). This binding region defines the nuclear localization sequences (NLS) responsible for targeting the viral DNA to the nucleus. After the PIC joins with the Kα, the HIV genes are imported into the nucleus of the cell, where multiple copies of the viral genome are made. Interrupting the MA-Kα binding inhibits nuclear entry and subsequent virus production. Thus, the MA-Kα binding region (a.k.a. NLS) represents a molecular target for drug development. (Fig. 5) Nuclear Entry Inhibition is the process by which this binding is blocked and represents a viable approach for managing HIV infection.

ITI has identified several Nuclear Entry inhibitors compounds that reduce the replication of HIV genes under laboratory conditions. These compounds are small, are easily synthesized, have been shown to be non-toxic in small animals, and may be taken orally. In addition, ITI continues to screen for new compounds and derivatives of existing leads using proprietary libraries synthesized at Albany Molecular Research Institute or the Tokyo Institute of Technology by Dr. Takashi Takahashi’s group.  To date, several new compounds have been identified with significant anti-HIV activity. The lead ITI compound is currently in pre-clinical development.

Nuclear Entry as a Platform Technology for Development of Anti-Viral Therapies

Platform Technology
Hepatitis B virus
Herpes viruses (e.g. HSV, CMV)
Influenza virus

Similar to HIV-1, several other RNA and DNA viruses replicate in the nucleus of target cells and require nuclear entry to establish productive infections. These viruses also associate with K
α as a prerequisite step for nuclear entry. Specific molecular interactions for a number of viruses have been identified and may serve as templates for drug discovery programs. ITI plans to expand the Company's research and development programs into these other pathogens after human clinical trials begin on the HIV-1 drug candidate.

Figure 1: HIV-1 Binding to Target Cell

Figure 2: Capsid Maturation and Release of Pre-Integration Complex

Figure 3: Nuclear Entry of the HIV-1 PIC

Figure 4 Nuclear Protein Transport

Figure 5 Molecular Target: Association of Karyopherin
α with NLS in PIC


Bukrinsky, M. I., N. Shanova, M. P. Dempsey, T. L. Stanwick, A.G. Bukrinskaya, S. Haggerty, and M. Stevenson. (1992). Active nuclear import of human immunodeficiency virus type 1 preintegration complexes. Proc. Natl. Acad. Sci. USA 89, 6580-6584.

Dobrovsky, L., P. Ulrich, G. J. Nvovo, K. R Manogue, A. Cerami, and M. Bukrinsky. (1995). Nuclear localization signal of HIV-1 as a novel target for therapeutic intervention. Mol. Med. 1, 217-230.

Popov S., L. Dubrovsky, M-A. Lee, S. Pennathur, O. K. Haffar, Y. Al-Abed, P. Tonge, P. Ulrich, M. Rexach, G. Blobel, A. Cerami, and M. Bukrinsky. (1996). Critical role of reverse transcriptase in the inhibitory mechanism of CNI-H0294 on HIV-1 nuclear translocation. Proc. Natl. Acad. Sci. USA 93, 11859-11864.

Bukrinsky, M.I., and O.K. Haffar. (1997). HIV-1 nuclear import. Frontiers in Biosciences 2, 578-587

Haffar O.K., M. D. Smithgall, S. Popov, P. Ulrich, A.G. Bruce, S.G. Nadler, A. Cerami, and M. I. Bukrinsky (1998). CNI-H0294 a nuclear entry inhibitor of the human immunodeficiency virus type-1 genome abrogates virus replication in infected activated peripheral blood mononuclear cells. Anti-Microb. Agents Chemotherapy. 42, 1133-1138.

Bukrinsky, M. I., and O. K. Haffar. (1998). HIV-1 nuclear import: matrix protein is back on central stage, this time together with Vpr. Molec. Med. 4, 138-142.

Haffar, O.K., S. Popov, L. Dubrovsky, L Agostini, H. Tang, T. Pushkarsky, S.G. Nadler, and M. Bukrinsky. (2000). Two nuclear localization signals in the HIV-1 matrix protein regulate nuclear import of the HIV-1 pre-integration complex. J. Mol. Biol. 299:359-368.

Glushakova, S., L. Dubrovsky, J. Grivel, O. Haffar, and M. Bukrinsky. (2000). Small molecule inhibitor of HIV-1 nuclear import suppresses HIV-1 replication in human lymphoid tissue ex vivo: a potential addition to current anti-HIV drug repertoire. Antiviral. Res. 47:89-95.

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