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Discovery of a druggable pocket in the SARS-CoV-2 spike protein
- jxcl 6y ago> In rhinovirus, a virus causing the common cold, a similar pocket was exploited to develop potent small molecules that bound tightly to the pocket distorting the structure of the rhinovirus, stopping its infectivity. These small molecules were successfully used as anti-viral drugs in human trials, defeating rhinovirus in the clinic. So why isn't there a cure for the common cold? If there still isn't a cure for the common cold, why should we expect this drug target to be different? Surely whoever wrote this article should have anticipated these questions? (Edited to be less flippant)
- gostsamo 6y agoOn the other hand, Oracle is mentioned twice, in case we didn't spot it the first time.
- yobert 6y agoThe Oracle plugs are hilarious. "Enabled by Oracle high-performance cloud computing, a 3-D structure of SARS CoV-2 Spike protein was generated allowing the researchers to peer deep inside the Spike identifying its molecular composition." As if the cloud provider had anything to do with anything there.
- function_seven 6y agoI only trust IBM® Watson™️ Brand clinical research.
- craftinator 6y agoI heard Watson cured all of cancer!
- goldcd 6y agoNow it's quite clearly a plug - but serious amounts of compute power are required for protein analysis, and chucking cloud at it is a pretty good way of doing that. Look at Folding@Home
- HappySweeney 6y agoSure, but they intimate that only Oracle could get the job done.
- Quarrelsome 6y agoOracle cloud must be absolute garbage given how hard its being marketed. Didn't part of the US deal with Tiktok _force_ the application into using Oracle cloud as part of the deal? I have a lot of sympathies for the TikTok devs if its not very good as its now mandatory. Its like instead of building something good or getting techie buy in they've instead tried to lobby governments to make it mandatory for some enslaved customers.
- mdifrgechd 6y ago> Its like instead of building something good or getting techie buy in they've instead tried to lobby governments to make it mandatory for some enslaved customers Haha, yes, you are literally describing the business model of SAP, Oracle, IBM, and most sales-led enterprise software or services companies. You can replace "lobby governments" with "lobby c-level of large corporations" as well
- rossdavidh 6y agoI do recall Microsoft using a similar tactic to try to get Windows Mobile more widely used.
- stateofnounion 6y agoDon't tug too hard at that thread, the entire narrative might unravel.
- IgorPartola 6y agoWhat does that mean?
- inscionent 6y agoFeels like an AD. No real author. Most of the paragraphs are long quotes with no follow up or analysis. Suspicious product placement.
- skim_milk 6y agoThe common cold isn't any specific virus, it's a huge range of viruses that cause "cold" symptoms. Some coronaviruses cause "colds" as well. Common cold viruses are research targets to discover knowledge that can be weaponized to prevent pandemics.
- mquirion 6y agoI almost never comment, but the answer here is simple: markets. The common cold doesn't kill. There's almost no economic impetus for a cure. Note, I said "almost." There may be some, but there's still not enough to drive R&D in a corporate lab, and certainly not enough to drive policy in a government lab. There are 100 other questions that would follow from science to logistic once you answer: Can we create a drug that kills infection in clinical tests?
- newsbinator 6y agoSurely there's a Nobel Prize in it though?
- throwmeaway_pls 6y agoNyQuil’s and Alka Seltzer’s sales figures beg to differ.
- karlshea 6y agoThose aren’t cures.
- lm28469 6y agoYou'll make much more money selling symptoms relievers every years than fixing the issue once and for all.
- grahamburger 6y agoYou'd make a lot more money selling a yearly treatment that prevented the symptoms entirely. I probably spend $50/year on cold-symptom medications. I'd easily spend $100/year to just not get a cold in the first place.
- mquirion 6y agoNyQuil and Alka Seltzer would beg you not to kill the cash cows. Plus NyQuil and AS can be produced and sold in such a way as to net a profit. We don't know that's the case for a cold cure.
- eximius 6y agohttps://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000281 https://journals.plos.org/plosbiology/article?id=10.1371/jou... It might be from 2019 so there may simply have not been enough time.
- whymauri 6y agoDefinitely not enough time for traditional pharma to have actionable, public insights.
- deleted 6y ago[deleted]
- wittyreference 6y ago>> So why isn't there a cure for the common cold? The "common cold" refers to a benign, self-limited upper respiratory viral infection by over 200 viral subtypes, including many strains of coronavirus (causing collectively 10-15% of colds), adenovirus, enteroviruses (echovirus, coxsackievirus) rhinovirus (over 100 serotypes, collectively causing 30-50% of colds), metapneumovirus, bocavirus, influenza and parainfluenza viruses (~5% of colds each), and respiratory syncytial virus (another 5%). I think this is general lay knowledge. Certainly, any article that uses the words "glycoprotein" is aiming at the sort of audience that knows "common cold is a syndrome caused by a buncha different viruses."
- nashequilibrium 6y agoWhen I go for the usual flu vaccine in November, how would I know which strains its protecting me against?
- liability 6y agoThere is no "usual flu vaccine", they make a new one twice a year, meant to address whatever strain is in circulation.
- wittyreference 6y agoI think they meant when they go for their regularly scheduled -"usual" flu vaccine, and their question was meant to address what strains would be targeted in a given year.
- wittyreference 6y agoThere's cross-reactivity, and they target both Influenza A and Influenza B strains (usually), so you'll get broader protection than strictly the strains most targeted by the vaccine. That said, you can ask the pharmacist for a copy of the FDA package insert, or google it yourself for the specific vaccine they're giving you. The package insert, under "DESCRIPTION" (Section 11), should tell you the precise strains that the antigens were developed from. For example, google "FLUVIRIN fda package insert",and the one for the 2017/2018 flu season on page 8 you'll find "A/Singapore/GP1908/2015,IVR-180 (an A/Michigan/45/2015 (H1N1)pdm09- like virus; A/Hong Kong/4801/2014, NYMC X-263B (H3N2) (an A/Hong Kong/4801/2014- like virus); and B/Brisbane/60/2008, wild type (a B/Brisbane/60/2008-like virus)". Google the same document for Fluzone quadrivalent, and you should find, for the 2020/2021 flu season, the strains "A/Guangdong-Maonan/SWL1536/2019 CNIC-1909 (H1N1), A/Hong Kong/2671/2019 IVR-208 (H3N2), B/Phuket/3073/2013 (B Yamagata lineage), and B/Washington/02/2019 (B Victoria lineage)" on pg 21.
- leptons 6y ago>These small molecules were successfully used as anti-viral drugs in human trials, defeating rhinovirus in the clinic. Because it's still in trials, and not widely available, due to the long process of approving such medicines. It still seems possible that there will be a drug that can be used to combat rhinovirus, as well as coronavirus someday, possibly sooner rather than later.
- DoofusOfDeath 6y ago"Enabled by Oracle high-performance cloud computing, ..." Anyone know why that phrase is in there? It sounds very much like product marketing, but I can't see why the researchers or this story's author would be motivated to promote Oracle.
- peeters 6y ago> Funding: ... This work received generous support from the Oracle Higher Education and Research program to enable cryo-EM data processing using Oracle’s high-performance public cloud infrastructure (https://cloud.oracle.com/en_US/cloud-infrastructure https://cloud.oracle.com/en_US/cloud-infrastructure) ... https://science.sciencemag.org/content/early/2020/09/18/science.abd3255 https://science.sciencemag.org/content/early/2020/09/18/scie... Why this summary of the work includes it prominantly, rather than in the footnotes like in the original paper, I'm not sure. Perhaps it was a condition the authors had for contributing to the article. Or perhaps it was Oracle's PR that got them the article in the first place. There is a comment from Oracle later in the article.
- DoofusOfDeath 6y agoThanks. I didn't think to look in the original sciencemag.org article.
- leptons 6y agoAlso possible Oracle donated the resources with the stipulation that they get mentioned in any articles about the research.
- deleted 6y ago[deleted]
- tyingq 6y ago"Should I acknowledge Oracle support for my research project work, for example, in publications or on websites? Please acknowledge the “Oracle for Research” program in any publications or on websites." https://www.oracle.com/oracle-for-research/faq.html https://www.oracle.com/oracle-for-research/faq.html Apparently pushed as a requirement for the "free" Oracle cloud resources researchers can apply for.
- est31 6y agoThere are plenty of covid-19 vaccine trackers, but I can't find trackers for antivirals, especially novel, non-repurposed ones. E.g. what happened to compound 11a from this paper? https://science.sciencemag.org/content/368/6497/1331 https://science.sciencemag.org/content/368/6497/1331 The best I could find was an overview in this survey paper: https://www.sciencedirect.com/science/article/pii/S0960894X20304881 https://www.sciencedirect.com/science/article/pii/S0960894X2...
- whymauri 6y agoThe best I have a Lancet review for repurposed drugs found via computational methods (published last week). Ignore the "AI;" most of these are just graph algorithms or vanilla neural networks. I haven't seen anything this comprehensive for novel therapeutics. https://www.thelancet.com/action/showPdf?pii=S2589-7500%2820%2930192-8 https://www.thelancet.com/action/showPdf?pii=S2589-7500%2820...
- stevespang 6y agofiendish Larry Ellison made it a requirement himself, any use of Oracle's network require lavish praise upon the providers . . .
- ourmandave 6y agoLike drag and drop isn't complicated enough, they have to add a Druggable event? Oracle's cloud API really is expanding.
- rossdavidh 6y agoSo, it's great that they're investigating, but this reads a bit too breathless to be taken entirely seriously: "stop virus in its tracks" "a potential game changer" "ground-breaking study" ...but further down: "The question now is how to turn this new knowledge against the virus itself and defeat the pandemic." Yes, that would be the question, which is much closer to the beginning of the process of developing and producing and rolling out a new treatment, than it is to the end. In other words, while it's great that this kind of thing is being investigated, it is extraordinarily unlikely to impact _this_ pandemic. No doubt Covid-19 will come back again, several years after this pandemic has run its course, and it's great to investigate how to be better prepared for that. But this is not going to result in a treatment fast enough that this pandemic will not already have spread to its (historically normal, typical, well-nigh-inevitable) conclusion.
- nradov 6y agoCOVID-19 (SARS-CoV-2) won't "come back again" because it will never go away in the first place. It has already spread so widely that it is now endemic in the worldwide human population (plus some other mammal species). Just like at least 4 other coronaviruses.
- FuckButtons 6y agoBut we made no attempt to eliminate those corona viruses and we have, the last I checked, something like 20 vaccines in development for this one, if anything is a candidate for going the way of smallpox it’s sars cov 2, there’s too much inertia behind our efforts to stamp it out, it might just take a while.
- nradov 6y agoWe were able to eradicate smallpox because it had no significant animal host reservoir. That isn't the case with SARS-CoV-2. Are you going to vaccinate all the bats?
- rossdavidh 6y agoTechnically, you're correct, but the 1957 flu "came back" in 1968, and again in 2009 if I recall correctly. Yes, I'm sure they were never completely gone, but at some point there are enough non-resistant people and it flares up again, and we would want to have better options for that "next time". But yes, technically, you're correct, it will never quite go away.
- booleandilemma 6y agoI'm left wondering, can AWS generate 3-D structures of SARS CoV-2 Spike proteins?
- jmpman 6y agoI’m wondering if a long strip of tape, the ability to move left or right, and the ability to write a symbol to the tape could generate 3-D structures of SARS CoV-2 Spike proteins.
- 0n34n7 6y agoDoes this mean a diet rich in linoleic acid could lessen the symptoms?
- lioeters 6y agoMy impression is that they've only just begun to study the correlation. Following my curiosity, I found a list of dietary sources of linoleic acid: https://en.wikipedia.org/wiki/Linoleic_acid#Dietary_sources https://en.wikipedia.org/wiki/Linoleic_acid#Dietary_sources --- Here are the relavant passages from the article: > Unexpectedly, the research team's analysis revealed the presence of a small molecule, linoleic acid (LA), buried in a tailor-made pocket within the Spike protein. > LA is a free fatty acid, which is indispensable for many cellular functions. The human body cannot produce LA. Instead, the body absorbs this essential molecule through diet. > Intriguingly, LA plays a vital role in inflammation and immune modulation, which are both key elements of COVID-19 disease progression. LA is also needed to maintain cell membranes in the lungs so that we can breathe properly. > From other diseases we know that tinkering with LA metabolic pathways can trigger systemic inflammation, acute respiratory distress syndrome and pneumonia. These pathologies are all observed in patients suffering from severe COVID-19. > A recent study of COVID-19 patients showed markedly reduced LA levels in their sera.