A short hairpin loop-structured oligodeoxynucleotide targeting the virion-associated RNase H of HIV inhibits HIV production in cell culture and in huPBL-SCID mice

Abolishing HIV-1 infectivity using a polypurine tract-specific G-quadruplex-forming oligonucleotide

Background

HIV is primarily transmitted by sexual intercourse and predominantly infects people in Third World countries. Here an important medical need is self-protection for women, particularly in societies where condoms are not widely accepted. Therefore, availability of antiviral microbicides may significantly reduce sexual HIV transmission in such environments.

Methods

Here, we investigated structural characteristics and the antiviral activity of the polypurine tract (PPT)-specific ODN A, a 54-mer oligodeoxynucleotide (ODN) that has been previously shown to trigger the destruction of viral RNA genomes by prematurely activating the retroviral RNase H. The stability of ODN A and mutants thereof was tested at various storage conditions. Furthermore, antiviral effects of ODN A were analyzed in various tissue culture HIV-1 infection models. Finally, circular dichroism spectroscopy was employed to gain insight into the structure of ODN A.

Results

We show here that ODN A is a powerful tool to abolish HIV-1 particle infectivity, as required for a candidate compound in vaginal microbicide applications. We demonstrate that ODN A is not only capable to prematurely activate the retroviral RNase H, but also prevents HIV-1 from entering host cells. ODN A also exhibited extraordinary stability lasting several weeks. Notably, ODN A is biologically active under various storage conditions, as well as in the presence of carboxymethylcellulose CMC (K-Y Jelly), a potential carrier for application as a vaginal microbicide. ODN A’s remarkable thermostability is apparently due to its specific, guanosine-rich sequence. Interestingly, these residues can form G-quadruplexes and may lead to G-based DNA hyperstructures. Importantly, the pronounced antiviral activity of ODN A is maintained in the presence of human semen or semen-derived enhancer of virus infection (SEVI; i.e. amyloid fibrils), both known to enhance HIV infectivity and reduce the efficacy of some antiviral microbicides.

Conclusions

Since ODN A efficiently inactivates HIV-1 and also displays high stability and resistance against semen, it combines unique and promising features for its further development as a vaginal microbicide against HIV.

The reverse transcriptase-RNase H: from viruses to antiviral defense

Ubiquitous, reverse transcriptase may have contributed to the transition from the RNA to the DNA world, a transition that also involved RNase H-like activities. Both enzymes shaped various genomes and antiviral defense systems as endogenous retroviruses (ERVs) and transposable elements (TEs). A close relationship between a dozen components of retroviruses and the small interfering RNA (siRNA) antiviral-defense machinery has been characterized. Most antiviral-defense systems involve RNase H-like enzymes destroying invading nucleic acids, RNA, or DNA. Such enzymes include RNases H, Argonaute, Dicer, Cas9, transposases, integrases, and enzymes for immunoglobulin rearrangement and splicing. Even in mammalian cells, where protein-based defense dominates, the siRNA machinery remains active, demonstrated by increased virus production and apoptosis after Dicer knockdown. We have noticed a surprising homology between the siRNA silencing system and the interferon response, as well as to siDNA and the CRISPR system. Further, ERVs serve in defense, in addition to having roles in gene regulation and cancer.

RNase H: specificity, mechanisms of action, and antiviral target

The Ribonuclease (RNase) H is one of the four enzymes encoded by all retroviruses, including HIV. Its main activity is the hydrolysis of the RNA moiety in RNA-DNA hybrids. The RNase H ribonuclease is essential in the retroviral life cycle, since it generates and removes primers needed by the Reverse Transcriptase (RT) for initiation of DNA synthesis. Retroviruses lacking RNase H activity are noninfectious. Despite its importance, RNase H is the only enzyme of HIV not yet targeted by antiretroviral therapy. Here, we describe functions and mechanisms of RNase H during the HIV life cycle and describe a cleavage assay, which is suitable to determine RNase H activity in samples of various kinds. In this assay, an artificial, fluorescence-labeled RNA-DNA hybrid is cleaved in vitro by an RT/RNase H enzyme. Cleavage products are analyzed by denaturing polyacrylamide gel electrophoresis (PAGE). This assay may be used to detect the RNase H, assess the effect of inhibitors, or even activators, of the RNase H, as we have described, as candidates for novel antiretroviral agents.

Premature activation of the HIV RNase H drives the virus into suicide: a novel microbicide?

Sexual transmission of HIV is the major cause of spread of HIV in Africa and the Third World and is an unmet medical need. Recently, microbicides have attracted attention because they allow females to protect themselves and their offspring. We are exploiting one of the four retroviral enzymes, the ribonuclease H, RNase H, as a novel approach for a microbicide. It is the only enzyme of HIV not yet targeted by antiretroviral therapy. The enzyme is linked to the reverse transcriptase (RT) and hydrolyzes the RNA moiety of RNA-DNA hybrids. The RNase H is located inside virus particles and normally functions during viral replication inside cells. Here we show that activating the RNase H prematurely inside the virus particles destroys the viral genome and abrogates viral infectivity. The antiviral compound consists of a synthetic oligodeoxynucleotide (ODN), which creates an artificial RNA-DNA hybrid substrate for the RNase H inside the particle. The compound was analyzed in mouse models including humanized SCID mice and the vagina of mice. Infection was reduced up to 1000-fold or could be completely prevented. The compound is suitable as microbicide or to prevent mother-to-child transmission.

Targeting the retroviral ribonuclease H by rational drug design

Ribonucleases H or RNases H are conserved and exist in almost every organism. They generate and remove RNA primers, which are required for DNA replication. RNases H hydrolyze RNA in RNA-DNA hybrids. RNases H and related enzymes contribute to reduction of gene expression in antisense and small-interfering RNA mechanisms for gene silencing. Retroviruses code for RNases H, which are required for DNA provirus synthesis. Their RNase H is fused to the reverse transcriptase and essential for virus replication inside the cell. Retroviruses code for four enzymes, three of which have been targeted by antiretroviral therapies. A drug against the fourth one, the retroviral RNase H, does not yet exist. The viral but not cellular RNases H should be targeted by drug design. Some details will be discussed here. Furthermore, a compound is described, which enables the RNase H to kill cell-free HIV particles by driving the virus into suicide - with potential use as a microbicide.

Short hairpin-looped oligodeoxynucleotides reduce hepatitis C virus replication

Background

Persistent infection with hepatitis C virus (HCV) is a leading cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Standard therapy consists of a combination of interferon-alpha and ribavirin, but many patients respond poorly, especially those infected with HCV genotypes 1 and 4. Furthermore, standard therapy is associated with severe side-effects. Thus, alternative therapeutic approaches against HCV are needed.

Findings

Here, we studied the effect of a new class of antiviral agents against HCV, short, partially double-stranded oligodeoxynucleotides (ODNs), on viral replication. We targeted the 5’ nontranslated region (5’ NTR) of the HCV genome that has previously been shown as effective target for small interfering RNAs (siRNAs) in vitro. One of the investigated ODNs, ODN 320, significantly and efficiently reduced replication of HCV replicons in a sequence-, time- and dose-dependent manner. ODN 320 targets a genomic region highly conserved among different HCV genotypes and might thus be able to inhibit a broad range of genotypes and subtypes.

Conclusions

ODNs provide an additional approach for inhibition of HCV, might be superior to siRNAs in terms of stability and cellular delivery, and suitable against HCV resistant to standard therapy. This study underlines the potential of partially double-stranded ODNs as antiviral agents.