Archive for December, 2010

HIV: catching it from all sides

10 December, 2010

Back when I started teaching virology – 1981 it was, so I’ve been doing it for 30 years come January! – there were precious few agents that did anything to viruses, apart from antibodies and that wonderful new and precious stuff called interferon.  Oh, and nucleoside analogues like adenine arabinoside (araA), ribavirin, and the legendary amantadine and rimantidine – which pretty much only covered herpes- and influenza viruses, according to Fenner and White’s Medical Virology of 1986.

And then along came HIV….and everything changed.

All of a sudden, we have an embarrassment of riches – against retroviruses, anyway.  Consider the following:

  • Nucleoside and nucleotide reverse transcriptase inhibitors (NRTI) inhibit reverse transcription
  • Non-nucleoside reverse transcriptase inhibitors (NNRTI)
  • Protease inhibitors (PIs) target viral assembly
  • Integrase inhibitors inhibit integration of viral DNA into the DNA of the infected cell
  • Entry inhibitors (or fusion inhibitors) interfere with binding, fusion and entry of HIV-1 to the host cell by blocking one of several targets.
  • Maturation inhibitors inhibit the last step in gag processing in which the viral capsid polyprotein is cleaved

Of course the above serve to vindicate most thoroughly my “Entrance, Entertainment and Exit” mantra / mnemonic for virus replication, in that they block entrance, interfere with entertainment (replication), and mess with exit too.

But wait, there’s more: a brand-new paper in PLoS Pathogens describes the wide-spectrum anti HIV-1 and -2 activity of a new class of small molecule antiretroviral compounds.  These directly target HIV-1 capsid (CA; p24 protein) via binding into a “pocket” in the N-terminus, and thereby interfere with both assembly and uncoating of virions.

HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention.
Blair WS, Pickford C, Irving SL, Brown DG, Anderson M, et al. (2010)
PLoS Pathog 6(12): e1001220. doi:10.1371/journal.ppat.1001220   Published December 9, 2010

Despite a high current standard of care in antiretroviral therapy for HIV, multidrug-resistant strains continue to emerge, underscoring the need for additional novel mechanism inhibitors that will offer expanded therapeutic options in the clinic. We report a new class of small molecule antiretroviral compounds that directly target HIV-1 capsid (CA) via a novel mechanism of action. The compounds exhibit potent antiviral activity against HIV-1 laboratory strains, clinical isolates, and HIV-2, and inhibit both early and late events in the viral replication cycle. We present mechanistic studies indicating that these early and late activities result from the compound affecting viral uncoating and assembly, respectively. We show that amino acid substitutions in the N-terminal domain of HIV-1 CA are sufficient to confer resistance to this class of compounds, identifying CA as the target in infected cells. A high-resolution co-crystal structure of the compound bound to HIV-1 CA reveals a novel binding pocket in the N-terminal domain of the protein. Our data demonstrate that broad-spectrum antiviral activity can be achieved by targeting this new binding site and reveal HIV CA as a tractable drug target for HIV therapy.

So, yet another target in HIV for chemotherapeutic agents – but what, exactly, are these new magic bullets?

And in Figure 5 of the original paper, you can see what it is that they do:

Figure 5: Structure of the novel inhibitor binding site and context in the NTD

a) Overlays of capsid structures with PF-3450074 in blue and CAP-1 in pink bound to capsid N-terminal domain; b) Close up view of PF-3450074 site (binding site residues labelled in black, R1-3 sub-pockets labelled in purple)…. c) Location of resistant mutations (purple) in relation to PF-3450074 capsid binding site.

The authors conclude their article with this:

The broad spectrum activity of this series [of drugs] is particularly exciting and highlights this novel mechanism [binding the CA protein] as a significant therapeutic opportunity.

Definitely not an over-stated conclusion!  And nicely rounding out a recent series of HIV-combatting articles and developments covered here recently.  And let me also refer you here to AJ Cann’s most recent post, on HIV entry – which, surprisingly, is still not a nailed-down and simple model.  And which I discovered literally while writing this, so seriously hot off the press.

Prophylactically yours….

7 December, 2010

It’s not often we have something to report on locally – I rely on Alan Cann to do that…B-) – but I am very pleased to be able to do so now.

Hot on the heels of another South African success in the fight against HIV and AIDS comes the news (from the UCT Monday Paper) that:

Prophylactic antiretrovirals could check HIV infection

Assoc Prof Linda-Gail BekkerBeing there: UCT’s Assoc Prof Linda-Gail Bekker led the South African component of the six-country study on the prophylactic use of an antiretroviral tablet.

It’s a long way from being the final word in HIV prevention, but a major study involving UCT researchers and published in the New England Journal of Medicine reveals that the daily use of an antiretroviral tablet as a prophylactic could curb infection among those at high risk by nearly 44%.

The findings are based on an HIV-prevention trial conducted at 11 international sites in six countries (including the Desmond Tutu HIV Foundation [DTHF], associated with UCT’s Faculty of Health Sciences), from June 2007 to May 2010. The study, named the Pre-Exposure Prophylaxis Initiative (iPrEx), looked at the prophylactic use – in other words, for people not infected with HIV – of a tablet that contains two widely-used HIV medications, emtricitabine and tenofovir (FTC/TDF).

Results showed that high-risk individuals – men and transgender women who have sex with men – who took the tablet experienced an average of 43.8% fewer HIV infections than those who received a placebo. In all, 64 HIV infections were recorded among the 1 248 study participants who received a placebo pill, while 36 HIV infections were recorded among the 1 251 participants who received the study drug.

The iPrEx study found that this pre-exposure prophylaxis (PrEP) was more effective among those who reported taking the pill more regularly. Among participants who used the tablet on 50% or more of days, as measured by pill counts, bottle counts and self-reports, risk of HIV infection fell by 50.2%; while among those who used the pill on 90% or more of days, as determined by the same measures, the PrEP pill reduced infection risk by 72.8%.

“I think this is a very significant study in that what we have here is the first proof of concept that taking an antiretroviral prophylactically – in other words, taking it before exposure to HIV – would actually prevent HIV infection,” says UCT’s Associate Professor Linda-Gail Bekker, deputy director of the Desmond Tutu HIV Centre.

tablets (brand-named Truvada)As the tablets (brand-named Truvada) are readily available, anyone can buy and use these. But Bekker is quick to point out that a lot of work still has to be done on the treatment, especially on its use outside of trial conditions. (For example, the tablet can affect renal and liver function, so participants’ kidneys and livers were monitored closely.)

Also, those recently infected and still developing antibodies to the HIV (ie seroconverting) are cautioned not to take the tablet, as it exposes the virus to two agents, upping the risk of building resistance to the treatment. “You may inadvertently affect or impact your chances of good treatment down the line,” says Bekker.

Naturally, high-incidence countries like South Africa will take plenty of interest in the study. But at around R400 for 30 tablets, this may not be the treatment to turn things around for the country.

“It is unlikely that we will be able to treat our way out of this epidemic,” said the DTHF in a statement. “We are going to have to find innovative, affordable and practical ways to stop the ongoing transmission of HIV.”

Fortunately, the study found that participants did not relax their use of safer-sex practices. On the contrary, self-reported HIV-risk behaviour decreased among participants, while condom use increased.

Professor Anna-Lise Williamson, of UCT’s Institute for Infectious Disease and Molecular Medicine and a member of the South African AIDS Vaccine Initiative, welcomes the treatment as another valuable advance in curbing the spread of the disease, but remains cautious of the human-behaviour element. For one, she says, people have to recognise that they are at risk before they’ll commit to the tablet.

“But it gives people options, and the more options they have, perhaps they’ll find a prevention strategy that suits their lifestyles,” she says. “But in the long term, I still believe we need a vaccine to prevent HIV infection.”

Concerns about risk compensation – increases in risky behaviour prompted by decreases in perceived risk – will remain, says Bekker. For this, education will be essential.

Also, the tablet’s use as a prophylactic will have to be but one tool in an arsenal of measures.

“We’re going to have to layer different kinds of preventative strategies together to come up with foolproof prevention,” Bekker warns, “but it’s probably not going to be dependent on only one strategy.”

Amen.  So we have – in order of increasing efficacy – an HIV candidate vaccine regime, a vaginal gel, and now pre-exposure prophylaxis.  And if you combine them…??  Basically, an additive effect – except that the vaccine is not available….  Time to fast-track, people!!

Viruses as nanomachines! Or: what you can believe from YouTube

6 December, 2010

I have for some years now been teaching my undergrad students that virus particles are nanomachines: that is, they are highly sophisticated nanoscale (read: ultramicroscopic) devices whose function is to specifically deliver genetic material into an environment where it can be expressed and replicated, so as to make more virus particles.

Nanoscale von Neumann machines, then – and if you want to see what a macroscale vN machine could do, just watch “2010: Odyssey Two“.

Ah, but what’s a von Neumann machine, you ask?  Well, I note Wikipedia has the following:

  • Self-replicating machines, a class of machines that can replicate themselves
  • Universal Constructors, self-replicating cellular automata
  • Von Neumann probes, hypothetical space probes capable of self-replication
  • Nanorobots capable of self-replication

I especially like the last two – because, as I showed in a previous blog post, I like the idea of virus particles or virions as “inner space craft”.  That this neatly marries my recreational and professional reading is no coincidence – because they cross-pollinate one another, in that I get ideas about the nature of viruses from SF, and my virology training informs scenarios I would like to write about.  Someday.  Soon, possibly.  Really.  Instead of writing about parallel universes contactable via the internet….

However, there is more to viruses and nanotechnology than phages with contractile tails, whether or not they have been around for billions of years: mimiviruses too have both nanoscale DNA loading and rapid-delivery systems, as previously discussed here.

Although I have a passing fondness for possibly my most successful animation – made from actual EMs, done by Linda Stannard.

T4 phage infecting a cell

So it was with some pleasure I saw recently on YouTube a video labelled “Viruses are nanotechnology (how a virus works)“.  I was a little less pleased when a voice confidently announced that “…a virus isn’t alive, people – it’s non-metabolising…”, as if that was the sole and necessary criterion for life.  I am at one with another Polish-named person – one Bernard Korzeniewski – in thinking  that life is (from MicrobiologyBytes)

The phenomenon associated with the replication of self-coding informational systems” © E.P. Rybicki, 1996. Incidentally, I find another person with a Polish name has said something very similar, in 2001 – which means it must be true. Bernard Korzeniewski describes life as: “A network of inferior negative feedbacks subordinated to a superior positive feedback.”

See, no mention of metabolism – or even of cells!  But what got the hairs on the back of my neck standing up, however, was some of the rest of it – delivered in a smooth, folksy manner, with stunning video footage.  Absolute cr@p, most of it: viruses are too complicated to have evolved, so they have to be alien nanotech???

Obviously some weird kind of conspiracy theory cross technobabble – but very seductive, to the uninformed.  Some of the comments are also just out of this world – literally!

Fortunately, there are some real science videos out there too – some of which I have also used in lecturing, if only to illustrate just how cool structural biology can be when used to study viruses.  Prime among these is one of T4 virus (Enterobacteria phage T4) infecting E coli; another magical one  from the same source is a depiction of the molecular motor which winds DNA into T4 heads.  A longer video has Michael Rossman, whose lab did the structural work behind the videos, explaining how the phenomenon could be useful in understanding viruses like herpesviruses in humans, which also appear to have molecular motors for DNA delivery – and, of course, how we can mess with them.

Self-assembly of viruses is also a good topic for video – and the full-length  Seyet T4 video is stunning in this regard.  So too is this one, showing a PhiX174 microvirus particle assembling.  One of my favourites, though, is the simplest: this is the depiction of how simple shapes can be induced to self-assemble into a virus-like particle – just by shaking.

I suppose, like everything, you get what you pay for with YouTube: which is nothing, most of the time.

But every now and then, a gem – which is what makes it fun to look.  I’m off to hunt down a Rolling Stones video virus replication videos!