My Old Neglected Vaccine Could Nail COVID-19

Humanity versus the coronavirus. Who’s winning? So far, advantage COVID-19. But things could change rapidly for the better if a scientific procedure I published 39 years ago is dusted off and brought to bear on this new nemesis. What we lack right now is a vaccine that can stimulate antibodies in our bloodstreams like the one at left, shown grabbing onto a surface molecule of the SARS virus. Remember that bug? In 2003 Severe Acute Respiratory Syndrome killed quite a few people, though its pandemic was smalltime compared to what we’re facing now. After ten years or so, scientists got a look at this anti-SARS antibody (the white and blue strands) clutching the viral protein (red strands) that gives coronaviruses their spiky appearance. It was a tour-de-force of science to get that image, but of course it came a decade too late to help anyone. So, is there anything we can do to hasten the process this time around?

There is.

Ever heard of the “Hopp and Woods Hydrophilicity Analysis Method?” No. I suppose not, unless you’re a scientist—and then only if you’re a vaccine researcher. But this is a widely used molecular biology method I invented, that has great potential to solve our need for a COVID-19 vaccine. Yesterday, I decided to rev up my old computer program “HYDRO” and have a look at COVID-19 to see what I could see. Wow! Was I surprised!

This Hopp and Woods profile for the spike protein of  COVID-19 may not look like much, but great potential lies within it. I’ll get to that in a moment, but first consider this: the genetic sequence of this virus was published just two weeks ago. Since then scientists have been racing to find ways to make a vaccine, but their best estimates are it may take months or even years to come up with a useful product.

But things could be different this time. It turns out my old method easily spotted a key target on COVID-19’s spiky surface where it can be “neutralized.” The image at right shows the amino acid sequence of the spike protein with the short segment my technique zeroed in on shown in red (Peak 1 in the data plot above). According to Hopp and Woods, this is a prime target for making a synthetic peptide vaccine. A what? It’s a type of vaccine that can be made virtually overnight—well, okay, in three days of hard work and late nights in the lab. Can you imagine the tingling up and down my spine as I stared at the computer screen? Here in this humble plot is the blueprint for a vaccine that could save many lives if only I had the lab facilities and chemicals for the task. I’m still getting chills as I write this.

Though I’m retired, there are many labs around the world fully equipped for this sort of vaccine work. I’ve begun making some inquiries, but the wall of corporate secrecy and people unwilling to discuss ongoing projects makes it hard to know if anyone has adopted the idea. Furthermore, there are defective imitations of my computer methods out there, so some labs might end up with sub-par products. Therefore, I’ve decided to lay this out for all to see and let the chips fall where they may. Maybe somewhere someone will pick up this idea and run with it—and wisely so.

I imagined just the sort of pandemic we now face, when I was a grad student at Cornell Medical College in New York City in 1976. I got the idea to use a computer to quickly scan virus sequences and identify the precise spots where antibodies grab on and block the virus’s ability to spread infection. I worked hard and published the method several years later. The Hopp and Woods algorithm is now used by immunochemists around the world to identify “antigenic determinants” that can serve as vaccines. There are now thousands of reports in the literature of immunizations of this type. However, no one ever developed a human vaccine. Admittedly, there’s a reason for that. You see, the immunity to a Hopp and Woods vaccine does not last all that long, only a few months. So the scientific establishment turned up its nose at my method. But tell me folks—right now, would you settle for a few months of immunity to COVID-19? Duh!

I see the dawn of a new day for the technique I pioneered so long ago, precisely because we need a COVID-19 vaccine YESTERDAY. With CDC, NIH, and WHO promising vaccines next fall or next year, how about one we could start testing in just a few days, folks? As the thrill of seeing how well my technique could work wears off, I’m beginning to get a little frustrated. So, let me appeal for help. If you know someone who knows someone who knows someone else who has a vaccine lab, send them my way, all right? Once the necessary chemicals are in hand, we’ll make a vaccine for COVID-19 in three days, or my name ain’t Hopp… of Hopp and Woods. Here’s a link to the original article.

Now, if you’ll bear with me, I’ll explain in more detail just how my method draws a bullseye on the coronavirus. This image zooms in on the molecular interface between the antibody chains (blue for the antibody’s heavy chain, white for its light chain) and again the viral spike protein in red. The interaction has two parts. On the left, the blue heavy chain entangles one part of the viral protein. On the right the light chain surrounds another part. Notice how that right-hand side of the red chain has several Y-shaped things standing up almost like hairs in an electric field? Those are two of the amino acids in the sequence I highlighted in red above. It is precisely this sort of electrostatic interaction that the Hopp and Woods method seeks out. And it seems to have done its job exceedingly well in this case. It has led us directly to the most important target on the whole coronavirus.

In my years of retirement, I haven’t been completely idle. As an exercise in imagination, I wrote a novel that dramatizes an outbreak of a deadly virus and follows scientists as they come up with—you guessed it—a Hopp and Woods vaccine to try and neutralize the threat. The Smallpox Incident was a forum for me to work out the details of just how such a feat might be accomplished. Maybe it should be required reading for vaccinologists responding to the COVID-19 threat, because it breaks the mold of the old vaccine culture that is currently telling us to wait so long.

Given the gravity of the matter at hand—namely life or death by COVID-19—I think it’s time my old method got a second look. So, again, if you know someone with the ways and means to make synthetic peptide vaccines (there are thousands of labs around the world capable of doing this), then send them my way. I’ll help them make it, and then I’ll take the first injection.

This is Part One of a three-part posting about the vaccine. Here are convenient links to:

About Tom Hopp

Thomas P Hopp is a scientist and author living in Seattle. He writes medical thrillers, natural disaster novels, and the Dinosaur Wars science fiction series.
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2 Responses to My Old Neglected Vaccine Could Nail COVID-19

  1. Dev DuRuz says:

    Thanks Tom – brilliant
    The monolith of Big Government; FDA,NIH,CDC seems to be uninterested in any immediate therapies or potential solutions if they can’t drive industrial pharma patents and profits.


    • Tom Hopp says:

      Thanks Dev. So true. And thanks for reminding me that my real, unstated mission here is to try my best to bring out a vaccine that will save human lives, and bring it out as quickly as possible. Governments and corporate profits be damned. This one is for the people!

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