Solution structure of peptides from HIV-1 Vpr protein that cause membrane permeabilization and growth arrest

An insight into the binding mechanism of Viprinin and its morpholine and piperidine derivatives with HIV-1 Vpr: molecular dynamics simulation, principal component analysis and binding free energy calculation study

HIV-1 Vpr is an accessory protein responsible for a plethora of functions inside the host cell to promote viral pathogenesis. One of the major functions of Vpr is the G₂ cell cycle arrest. Among several small molecule inhibitors, Viprinin, a coumarin derivative, has been shown to specifically inhibit the G₂ cell cycle arrest activity of Vpr thus making it an excellent choice for a lead molecule to design antiretroviral drug. But the exact mechanism of binding of the Viprinin and its two potent derivatives with Vpr is still not understood. In this study with combined molecular docking, molecular dynamics simulation, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method, Principal component analysis and Umbrella sampling simulation, we have explored the binding mechanism of Viprinin and its two derivatives with Vpr. MM-PBSA and Umbrella sampling calculations suggest that Viprinin and ViprininD1 have higher binding energy than ViprininD2. Molecular dynamics simulation shows that the ligands are not very stable inside the initial binding pocket and various hydrophobic interactions are responsible to hold the ligands with Vpr. Vpr backbone Principle Component Analysis (PCA) shows various unique essential motions of Vpr bound with Viprinin and its two derivatives. This study may give detailed insight of the mode of binding of the specified compounds at atomic scale and provide valuable information about the possibility of using these compounds as a potent Vpr inhibitor. Communicated by Ramaswamy H. Sarma.

The HIV-derived protein Vpr52-96 has anti-glioma activity in vitro and in vivo

Patients with actively replicating human immunodeficiency virus (HIV) exhibit adverse reactions even to low irradiation doses. High levels of the virus-encoded viral protein R (Vpr) are believed to be one of the major underlying causes for increased radiosensitivity. As Vpr efficiently crosses the blood-brain barrier and accumulates in astrocytes, we examined its efficacy as a drug for treatment of glioblastoma multiforme (GBM).

In vitro, four glioblastoma-derived cell lines with and without methylguanine-DNA methyltransferase (MGMT) overexpression (U251, U87, U251-MGMT, U87-MGMT) were exposed to Vpr, temozolomide (TMZ), conventional photon irradiation (2 to 6 Gy) or to combinations thereof. Vpr showed high rates of acute toxicities with median effective doses of 4.0±1.1 μM and 15.7±7.5 μM for U251 and U87 cells, respectively. Caspase assays revealed Vpr-induced apoptosis in U251, but not in U87 cells. Vpr also efficiently inhibited clonogenic survival in both U251 and U87 cells and acted additively with irradiation. In contrast to TMZ, Vpr acted independently of MGMT expression.

Dose escalation in mice (n=12) was feasible and resulted in no evident renal or liver toxicity. Both, irradiation with 3×5 Gy (n=8) and treatment with Vpr (n=5) delayed intracerebral tumor growth and prolonged overall survival compared to untreated animals (n=5; p_{3×5 Gy}<0.001 and p_Vpr=0.04; log-rank test).

Our data show that the HIV-encoded peptide Vpr exhibits all properties of an effective chemotherapeutic drug and may be a useful agent in the treatment of GBM.

Expression and purification of soluble HIV-2 viral protein R (Vpr) using a sandwich-fusion protein strategy

Viral accessory proteins of the human immunodeficiency virus (HIV), including virus protein R (Vpr), are crucial for the efficient replication of the virus in the host organism. While functional data are available for HIV-1 Vpr, there is a paucity of data describing the function and structure of HIV-2 Vpr. In this report, the construction of a His6-MBP-intein1-Vpr-intein2-Cyt b5-His6 fusion protein is presented. Unlike previous research efforts where only microgram quantities of HIV-1 Vpr could be produced, this construct enabled soluble milligram yields via an Escherichia coli over-expression system. Straightforward protein purification of HIV-2 Vpr was achieved by standard chromatography routines and autocatalytic intein cleavage. Preliminary structural studies by circular dichroism (CD) and NMR spectroscopy revealed that the protein is stable in the presence of micellar concentrations of the detergent DPC and adopts an α-helix secondary structure.

Anti-cancer activity of the HIV accessory molecule viral protein R (Vpr): Delivery as a DNA expression plasmid or biologically active peptides

By virtue of its ability to induce cell cycle arrest and apoptosis, the HIV accessory protein Vpr (viral protein R) has been evaluated by us and others as an anti-proliferative/anti-cancer agent. We have demonstrated that Vpr, when delivered to established experimental B16.F10 melanoma tumors in mice as a DNA expression plasmid through in vivo electroporation, can result in complete regression of the established tumors. We have also demonstrated that Vpr peptides from the carboxy region of the protein can inhibit in vitro growth of both B16.F10 melanoma as well as human HeLa cervical carcinoma tumor cells. These findings, summarized in this report, underscore the potential of Vpr as an anti-cancer agent and warrants, we believe, further experimental as well as clinical evaluation.

Inhibition of the activities of reverse transcriptase and integrase of human immunodeficiency virus type-1 by peptides derived from the homologous viral protein R (Vpr)

Shortly after infection by human immunodeficiency virus (HIV), two complexes are formed in a stepwise manner in the cytoplasm of infected cells: the reverse transcription complex that later becomes the preintegration complex. Both complexes include, in addition to cellular proteins, viral RNA or DNA and several proteins, such as reverse transcriptase (RT), integrase (IN), and viral protein R (Vpr). These proteins are positioned in close spatial proximity within these complexes, enabling mutual interactions between the proteins. Physical in vitro interactions between RT and IN that affect their enzymatic activities were already reported. Moreover, we found recently that HIV-1 RT-derived peptides bind and inhibit HIV-1 IN and that an IN-derived peptide binds and inhibits HIV-1 RT. Additionally, HIV-1 Vpr and its C-terminal domain affected in vitro the integration activity of HIV-1 IN. Here, we describe the associations of Vpr-derived peptides with RT and IN. Of a peptide library that spans the 96-residue-long Vpr protein, three partially overlapping peptides, derived from the C-terminal domain, bind both enzymes. Two of these peptides inhibit both RT and IN. Another peptide, derived from the Vpr N-terminal domain, binds IN and inhibits its activities, without binding and affecting RT. Interestingly, two sequential C-terminal peptides (derived from residues 57-71 and 61-75 of full-length Vpr) are the most effective inhibitors of both enzymes. The data and the molecular modeling presented suggest that RT and IN are inhibited as a result of steric hindrance or conformational changes of their active sites, whereas a second mechanism of blocking its dimerization state could be also attributed to the inhibition of IN.

Development and characterization of ten monoclonal anti-Vpr antibodies

HIV-1 Vpr is a 96-amino acid auxiliary protein that performs numerous activities during viral infection. In the present study, 10 antibodies were generated after mice immunization with either the N- or the C-terminus domain of Vpr, respectively, Vpr(1-51) and Vpr(52-96). ELISA and immunoblot experiments using pure synthetic overlapping Vpr peptides suggested that these anti-Vpr antibodies could be classified into five groups and that they recognized conformational or linear Vpr epitopes. Further analysis revealed the effect of C-terminal arginine mutations on the antibody binding. Two of the antibodies precipitated Vpr expressed after transfection of a Vpr-encoding vector in human cells. More importantly, one of them was able to detect Vpr in HIV-1-infected U1 cells and in HIV-1-infected human PBMC. Surface plasmon resonance experiments demonstrated that some of these antibodies prevented the interaction between Vpr and one of its cellular partners, the adenine nucleotide translocator. Thus, these anti-Vpr monoclonal antibodies may be useful to any laboratory working on the molecular mechanism of HIV-1 infection.

UBA domains mediate protein-protein interactions between two DNA damage-inducible proteins

The Saccharomyces cerevisiae genes RAD23 and DDI1 were identified in a screen for multicopy suppressors of the temperature-sensitivity of a mutant allele of S. cerevisiae PDS1. Pds1 is a regulator of anaphase that needs to accumulate and then be degraded by the ubiquitin-proteasome pathway at the metaphase-anaphase transition for cells to progress normally through mitosis. Both the Rad23 and Ddi1 pds1 suppression phenotypes depend on a shared motif known as a UBA domain found in a variety of proteins associated with ubiquitin metabolism. UBA domains were found to be essential for homodimerization of Rad23 and heterodimerization between Rad23 and Ddi1, but not for homodimerization of Ddi1. This observation, coupled with the findings that Rad23 and Ddi1 UBA domains bind ubiquitin and that dimerization of Rad23 blocks ubiquitin binding, suggests a possible mechanism for regulating Rad23 and Ddi1 function.

Residues within the HFRIGC sequence of HIV-1 vpr involved in growth arrest activities

HIV-1 Vpr is a virion-associated protein that can cause growth arrest when produced inside the cell but when added externally it can cause cell death. Employing the yeast model system, the C-terminal domain, in particular the sequence HFRIGCRHSRIG (Vpr(71-82)), is essential for both the growth arrest and cytocidal activities. Conservation of this sequence in HIV-2 and SIV suggests that these residues may be functionally important. Using site-directed mutagenesis we show that the most highly conserved aa residues, His71 and Gly75, were important for the cell cycle inhibitory effects. In contrast, we show that the wild-type Vpr(71-82) peptide and three variants of this peptide with Gly75 changed to Ser, Ala, and Ile all exhibited the same cytocidal activity suggesting that the intracellular and extracellular effects are unrelated.