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Trana Develops Assay That ID’s Protein That Helps HIV Replicate

Trana Discovery announced this week that its HIV high-throughput screening assay, designed to identify compounds that inhibit the use of tRNA, which is required for HIV replication, can select compounds with anti-HIV bioactivity.
According to the company, disrupting the virus’s ability to use tRNA may represent a novel target for antiretroviral therapy. Trana plans to license the assay to pharma companies that will use it to screen “several hundred thousand, maybe even millions, of compounds.”
The company claims that while lower-throughput methods can take around a week to screen a group of compounds, Trana’s assay, called HIV 201, “takes just a few hours.”
“An ultra-conserved region of the tRNA protein called the anticodon stem loop is actually the communicative end of the tRNA,” Trana CEO Steve Peterson told CBA News this week.
He said this loop must join up in a very particular way with the viral RNA because the HIV virus cleaves the cross-linkages in this tRNA protein and unwinds it, and then flips it into a shape that is completely unique to HIV. The restructured form of the tRNA stabilizes binding to viral genomic RNA.
“One part of the [anticodon stem loop] is kept the same, however,” Peterson said. “Trana has created a mimic of that very critical part of the loop.”
The biomolecular interaction from Trana’s assay uses two synthetic RNA mimics, Peterson said: one RNA oligomer comprising 12 bases mimics the human tRNA lysine sequence and the other oligomer mimics the HIV genomic sequence.
He said the assay screens for compounds that inhibit the binding of the fluorescently labeled human tRNA with the biotin-labeled HIV genome in the presence of PerkinElmer AlphaScreen beads.
Peterson said that at the High-Throughput Screening Center at the Southern Research Institute, several compounds were identified using the Trana HIV 201 assay that inhibited the assay. The compounds screened came from SRI’s molecular library.
In a subsequent cell-based screening study, a subset of those compounds were examined for inhibitory qualities in the replication of the HIV-1 Ba-L virus using live peripheral blood mononucleocytes, said Peterson. The compounds were found to have anti-HIV activity.
Peterson said that further testing revealed that the antiviral activity was not due to the inhibition of reverse transcriptase, which is the mechanism of action of many currently available antiretroviral drugs. These preliminary data suggest that the assay can identify HIV inhibitors with a novel mechanism of action, tRNA inhibition.
“The next step is for us to go to mostly big pharma companies that have large compound libraries and work out a licensing agreement for them to take our assay into their shop and basically come up with a screen of several hundred thousand, maybe even millions of compounds,” Peterson said.

“One part of the ASL is kept the same, however…Trana has created a mimic of that very critical part of the ASL loop.”

According to Peterson, the speed of the HIV 201 assay can be an attractive feature to potential drug makers. “We can screen at least 50,000 compounds per day, and depending on how big a library we are looking at, it can be geared up to have multiple robots run it if necessary,” he said.
Peterson said that conversely, if a pharmaceutical company has compounds with bioactivity against HIV, or inhibitory qualities, but it does not know the mechanism of action, it can use the assay to determine if the compounds inhibit tRNA.
“Right now [Trana is] looking for multiple pharma partners, although we are open to an exclusivity arrangement,” Peterson said. He said that the company is currently in talks with several undisclosed pharmaceutical companies, and would like to start screening compounds with them as early as next month.
Peterson said that the HIV 201 assay is Trana’s first, and that it is targeted at HIV because certain viruses, mostly retroviruses, will use the tRNA that they harvest from the human cell in their replicative process.       
“What [Trana is] hoping to come up with is another class of drugs that would be a component of [highly active anti-retroviral therapy], and if the virus ever became resistant to it, it would still not be able to replicate.”                
He said the company plans to take this same technology into every pathogen that it can, including all bacteria, all fungi, and even all protozoans responsible for human infectious diseases because tRNA is essential for building proteins, he said.
Without building new proteins, bacteria cannot replicate and thrive, so the infectious process is halted through the use of tRNA inhibitors, said Peterson. He also said that this represents a new mechanism of action against things such as hospital-acquired methicillin-resistant Staphylococcus aureus or community-acquired MRSA, and against malaria and Escherichia coli.
Peterson said the company is currently working on an MRSA assay. He mentioned that Trana hopes to start negotiating with pharmaceutical companies to have them screen compounds with Trana’s MRSA assay later this year, probably in the third or fourth quarter.
“The mechanism of action that we will have is unaffected by the mechanisms through which S. aureus has become resistant to methicillin or … other penicillins,” he said.

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