Coronavirus Spike Protein Binder Design • Hacker News Board

Re: Coronavirus Spike Protein Binder Design

#21

Post by hditorkeif » Tue, Mar 03, 2020, 12:52 PM UTC

This is what antibodies do, right?

How exactly does the body figure out how to configure the variable part of the antibody so that it binds? Does it just try countless variations until it finds a match?

Can we take an antibody from a healed person and reverse engineer the binding protein?

Re: Coronavirus Spike Protein Binder Design

#22

Post by candiodari » Tue, Mar 03, 2020, 1:06 PM UTC

hditorkeif wrote: post #21

This is what antibodies do, right? How exactly does the body figure out how to configure the variable part of the antibody so that it binds? Does it just try countless variations until it finds a match? Can we take an antibody from a healed person and reverse engineer the binding protein?

Yes and no. Antibodies bind against essentially anything on the virus surface, and (depending on the exact type of antibody) do that to multiple virus particles. This is often enough to prevent the membrane from successfully merging with a cell and therefore prevents or seriously reduces the infection rate (you don't have to get infection rate to zero, just low enough). Additionally these antibodies are collected and expelled by other parts of the immune system.

But afaik the immune system does nothing to target active sites. This makes sense: specificity matters. For example disabling HIV is easy: just prevent CD4 binding. That will prevent the virus from attacking any human cell. Unfortunately, it has the same effect as AIDS, over time it cripples the immune system. You want to bind, not to the active sites, but to whatever is on the virus and isn't on anything else.

Re: Coronavirus Spike Protein Binder Design

#23

Post by ppf » Tue, Mar 03, 2020, 1:25 PM UTC

moomin wrote: post #18

Aissen wrote: post #2

I know it's fun, and I think participative science is such a huge shift in paradigm … But considering the global impact of coronavirus, I'm wondering if there shouldn't be a better way to fund this type of endeavor. Any cloud provider willing to donate compute to researchers?

So close, and yet so far... What you're looking for is a well-funded public health system. And to vote out politicians that defund healthcare.

Public health systems, well-funded or not, are not a cure-all. I'd be curious to hear if you have any examples - if anything, they are reliant on research funded by the huge amount of money sloshing around the US healthcare system. Given a fixed annual budget, a public health system essentially has to decide what "healthy" or "cured" means, and set some quality of life to cost of treatment ratio. Some examples: my dad, an incredibly fit ultra-runner, suddenly found himself unable to run more than a few miles, and was gasping for air. He was initially told he was fine for his age, and had to fight for further diagnosis. A close friend of my wife's died of bowel cancer - this is a known "loophole" in the diagnosis pathways of our public health care system. Essentially, it was decided that the cost of early diagnosis is too high for the relatively tiny amount of people who have it, which is why most cases are found when they are terminal.

Re: Coronavirus Spike Protein Binder Design

#24

Post by gruez » Tue, Mar 03, 2020, 1:31 PM UTC

sschueller wrote: post #3

Aissen wrote: post #2

I know it's fun, and I think participative science is such a huge shift in paradigm … But considering the global impact of coronavirus, I'm wondering if there shouldn't be a better way to fund this type of endeavor. Any cloud provider willing to donate compute to researchers?

How about the government giving access to its huge computing power or commandeering free resources at large providers for the common good?

>commandeering free resources at large providers for the common good?

Sounds like a good way to get every cloud provider to pull out of your country.

Re: Coronavirus Spike Protein Binder Design

#25

Post by seibelj » Tue, Mar 03, 2020, 1:32 PM UTC

moomin wrote: post #18

Aissen wrote: post #2

I know it's fun, and I think participative science is such a huge shift in paradigm … But considering the global impact of coronavirus, I'm wondering if there shouldn't be a better way to fund this type of endeavor. Any cloud provider willing to donate compute to researchers?

So close, and yet so far... What you're looking for is a well-funded public health system. And to vote out politicians that defund healthcare.

It seems that the virus has spread in every country regardless of their healthcare system. Not trying to demean your desire for such a system, just in regard to this virus it is an equal-opportunity pandemic that all countries are suffering from. Universal healthcare has not prevented it.

Re: Coronavirus Spike Protein Binder Design

#26

Post by nolongerlowres » Tue, Mar 03, 2020, 1:32 PM UTC

ppf wrote: post #23

moomin wrote: post #18

Earlier quoted context omitted.

So close, and yet so far... What you're looking for is a well-funded public health system. And to vote out politicians that defund healthcare.

Public health systems, well-funded or not, are not a cure-all. I'd be curious to hear if you have any examples - if anything, they are reliant on research funded by the huge amount of money sloshing around the US healthcare system. Given a fixed annual budget, a public health system essentially has to decide what "healthy" or "cured" means, and set some quality of life to cost of treatment ratio. Some examples: my da…

I’m sorry to hear about your wife’s friend. But both examples you gave (people having to fight for further diagnoses of outside-case health problems) are really common with private healthcare in the United States too - we’ve just shifted the burden of cost of treatment/quality of life decisions to private entities who typically are only interested in furthering shareholder value. To give a personal anecdote as well: A close friend of my wife’s had to fight and fight to get insurance to cover appointments in order to get her breast cancer diagnosed.

I would like to understand if the world really does rely on US private-healthcare funded research - I’ve heard this argument mentioned before and have always been curious about it.

Re: Coronavirus Spike Protein Binder Design

#27

Post by gmm1990 » Tue, Mar 03, 2020, 1:42 PM UTC

hditorkeif wrote: post #21

This is what antibodies do, right? How exactly does the body figure out how to configure the variable part of the antibody so that it binds? Does it just try countless variations until it finds a match? Can we take an antibody from a healed person and reverse engineer the binding protein?

Yeah probably an oversimplification but it just creates different combinations and the ones that attach to the pathogen (and don't attach to non-pathogenic things in the body) are reproduced. But the immune system is wild I would say comes close to the neurological system from a how does this exist perspective. https://en.wikipedia.org/wiki/Antibody#Immunoglobulin_divers...

Re: Coronavirus Spike Protein Binder Design

#28

Post by DrAwdeOccarim » Tue, Mar 03, 2020, 1:49 PM UTC

There is already stuff like this out there: https://www.biorxiv.org/content/10.1101/2020.02.01.929976v2....

Also, it appears as though convalescence therapy is working (i.e., treating people with the plasma from recovered patients) https://www.straitstimes.com/asia/east-asia/china-seeks-plas... https://news.yahoo.com/chinese-doctors-using-plasma-therapy-...

Re: Coronavirus Spike Protein Binder Design

#29

Post by tucosan » Tue, Mar 03, 2020, 1:55 PM UTC

seibelj wrote: post #25

moomin wrote: post #18

Earlier quoted context omitted.

So close, and yet so far... What you're looking for is a well-funded public health system. And to vote out politicians that defund healthcare.

It seems that the virus has spread in every country regardless of their healthcare system. Not trying to demean your desire for such a system, just in regard to this virus it is an equal-opportunity pandemic that all countries are suffering from. Universal healthcare has not prevented it.

The virus will have a stronger impact in Africa than in Europe. The US healthcare system will probably be less resilient than that of Korea. There is great variation in how well countries are prepared to such a pandemic.

Re: Coronavirus Spike Protein Binder Design

#30

Post by ppf » Tue, Mar 03, 2020, 2:00 PM UTC

nolongerlowres wrote: post #26

ppf wrote: post #23

Earlier quoted context omitted.

Public health systems, well-funded or not, are not a cure-all. I'd be curious to hear if you have any examples - if anything, they are reliant on research funded by the huge amount of money sloshing around the US healthcare system. Given a fixed annual budget, a public health system essentially has to decide what "healthy" or "cured" means, and set some quality of life to cost of treatment ratio. Some examples: my da…

I’m sorry to hear about your wife’s friend. But both examples you gave (people having to fight for further diagnoses of outside-case health problems) are really common with private healthcare in the United States too - we’ve just shifted the burden of cost of treatment/quality of life decisions to private entities who typically are only interested in furthering shareholder value. To give a personal anecdote as well:…

Agreed, the US system is flawed. I suppose with public-funded healthcare, everyone is on the same level - the survival rates of breast cancer and bowel cancer is the same for all (unless you can afford to fly to the US and pay for care there).