Virus sequestration and tropism shaping - an evolutionary solution to viral pathogenicity and drug resistance
An idea co-developed by Joseph P. Keogh and Michael P. Carlton

(C) Copyright, 2001, and free for use under the terms of the GNU general public license. This file and those associated with it constitutes a list of instructions, executable in a biochemical, cellular, human or programmable machine platform, and constitute free software, for sequestration of viruses. See the included gpl.txt for details.

You can modify and/or redistribute it under the terms of version 2 of the GNU General Public license as published by the Free Software Foundation.

These instructions are distributed in the hope that they will be useful but WITHOUT ANY WARRANTY, without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU general public license for more details here

Background

In the summer of 2001 Mr Keogh asked me a question as we repaired the roof of a house in the south of Sydney.

He said "HIV attacks white cells, does it not?"

I answered, "Yeah, CD4+ T-lymphocytes."

He asked me "What would happen if they attacked red cells?"

I thought about it for a moment, and replied with an enthusiastic expletive not generally printed in journals of scientific repute. It was in theory a great idea, obvious straight away. The virus, if it could be coaxed to diffuse into an erythrocyte, would find its coat proteins embedded in the cell membrane of the erythrocyte, and its capsid stuck inside with no cell machinery available for takeover for the purpose of retroviral encoding into the host cell DNA. This is because mature red cells have no DNA inside them, nor organelles, or even a nucleus. Such a viral sequestering agent wasn't on the market anywhere, and I'd never heard of such a trick other than in immunology - but of course, with HIV, the virus exploits the very same cell as is supposed to play a significant role in the virus' immunological recognition and destruction.

So I spent some time looking into how to pull it off.

The Literature

There was lots of stuff being done using liposomes, which were being used to deliver therapeutic drugs to specific tissues. I found nothing in the liposome literature suggesting liposomes themselves were being used as the agent by which a virus was to be brought into an environment which was, by itself, a therapeutic agent - in other words, nowhere did I read anything about liposomes being used to exploit the virus' propensity to invade something with an appropriate suite of proteins on it, looked to the virus like just another potential host. Dressing up a liposome so it looked like a CD4+ T cell (with other co-receptors, of course) and letting the virus deliver itself into the inner environment of the liposome didn't appear to be mentioned anywhere.

The development of the idea

We considered our opponent, a remarkably resilient sexually transmitted retrovirus, already responsible for millions of deaths and untold suffering. It has evolved resistance to AZT, ddI and related chain terminators, also strains of it have evolved which are no longer amenable to interference by protease inhibitors. There will doubtless also be strains which appear in the future, exhibiting resistance reverse-transcriptase inhibitors and also to error-catastrophe agents, since when one is trying to eradicate a virus, one is trying simultaneously to eradicate multiple variants of it in the one host and a few of these will exhibit avoidance for the error-catastrophe agents. We need to exploit the virus' ability to evolve into something else.

There were obvious potential problems with the process of covering an erythrocyte with CD4+ proteins. Apart from the fact that the erythrocytes didn't go everywhere the virus tended to be (that is, in the lymphatic system) we'd need to engineer human stem cells to make such erythrocytes in the first place, and that was a tricky process, not necessarily under long-term control as you'd like it to be if allografted back into a HIV sufferer since altering the DNA of stem cells is an error-prone business with sometimes unexpected results. Besides this, during the process of maturation, late stage BFU-E cells might still have had enough cytosolic machinery in them to provide the virus with a possible way to reproduce before the committed erythrocyte cells ennucleated themselves.

In addition, in about 1991-1992 some researchers had already electroinserted recombinant CD4 into erythrocyte ghost cell membranes and shown that HIV was absorbed into such cells - prior art for erythrocytes. Anything you could possibly do with stem cells was already tightly bound with patents, too.

We thought about taking normal CD4+ T-lymphocytes, stopping their metabolism, sticking them in an infected person and seeing if they functioned as virus traps, but this was really only for proof-of-concept purposes. What good was a dead CD4+ T-Lymphocyte other than macrophage fodder or yet more garbage destined for reasonably rapid removal by the spleen?

So the final state of the development of the idea culminated as a variation on liposomes coated in the appropriate receptors - we also arrange to fill the liposomes with materials hostile to HIV RNA prior to administering them to a patient, though this is not, in my opinion, probably necessary.

We went as far as fabricating a provisional patent on the sequestration process, and did an international patent search, which was inconclusive concerning the use of antigenically-coated liposomes as a means of viral entrapment.

Giving it to humanity

Eventually, due to lack of interest from a large Aust biotech firm, and our accelerating impoverishment due to steep price scales in the legal system, we decided to stop work on the idea. However, we also felt that it should be made free for anyone to play with, since in our experience we consider the patent process is in fact an impediment to getting these things investigated and for public benefit to be derived from them, and, well, people are dying of this disease. This is probably because research is mired in legal impediment and, also, the development of a vaccine would erode the customer base for the large pharma corporations who profit by selling the current treatments (not cures) over a long period.

The main advantage of the approach, I consider, is that over prolonged regimes of treatment with liposomes immunologically dressed up to look like cells the virus wants to invade, one places the virus on an evolutionary topology where the only way it can avoid being drawn into and trapped by the "liposome masquerading as a CD4+ TL" is to evolve in such a way as to lose its tropism for the receptors which attract it to CD4+ T-lymphocytes. It doesn't matter extremely if this means that the virus acquires glycoprotein/receptor-mediated tropism for some other tissue, since there would hopefully be enough functioning CD4+ immune system cells left to deal with whatever else the virus had learned to infect.

What we don't know, and need to find out, is the pharmacokinetics, and at what dosage vs shedding rate one destroys more viruses than are produced by the successful destruction of one infected CD4+ T-lymphocyte by a retroviral shedding event. We can assume that the invaded liposomes themselves will provide some cells with the opportunity to phagocytose HIV components without having to phagocytose a functioning competant HIV virion, which might prove immunologically beneficial. Of course this all has to be investigated. Ultimately, of course, it would also be nice if someone finds that it prevented people from dying a messy, painful and protracted death as a sequel to virus-mediated immunological collapse.

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Click here to read The Patent Which Never Was (Word)
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Click here to read The GPL, under which the liposomes for viral sequestration idea (which is, really, a thought process defining a method space for creating a molecularly-executable, information-enriched structure , and therefore programmatical in nature) is released. Yes, we want to enable it to be free for all the scientific community to work on in perpetuity.