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Analytical Chemistry

More on Screening For Coronavirus Therapies

Time for a word about screening for new coronavirus drugs. Things have gone on long enough for quite a few groups to produce supplies of the various viral proteins and set up small-molecule screens against them. That’s no bad thing in itself, although it is a slow thing, a very slow thing by the standards of what people are looking for in the epidemic. Screening a new protein against a collection of small molecules is one of the first steps along a pretty lengthy road – you’re looking at several years if everything works perfectly.

That’s a big reason why that the small-molecule antiviral drugs that we have (which is not a large set compared to many other therapeutic areas) are very much skewed towards long-running viral diseases like HIV and hepatitis C. Those have had a time scale that matches with drug discovery, especially when you consider that really effective small-molecule antiviral therapies tend to be cocktails of several drugs hitting several targets simultaneously. Coming up with a whole new suite of drugs is no small order.

Contrast those diseases with things like SARS and MERS, which (fortunately) vanished by the time anything in the small-molecule line could be developed specifically against them. Even Ebola, which has clearly been a longer-lasting problem, has still messed around with clinical development efforts. Remdesivir, famous now because of its possible utility against the coronavirus, was originally identified during the 2013-2016 Ebola outbreak, but then faced a shortage of human patients for efficacy trials. Unfortunately, the re-emergence in 2018 provided more opportunities, which actually led to the discovery that the drug was not as effective as the monoclonal antibodies that had also been developed. That’s why I’ve been highlighting the drug-repurposing efforts when it comes to the small molecule therapies, because those are ready to go into humans right now. Fresh screens are not uninteresting, but their impact is just not as great and cannot be as great, especially for the current outbreak.

Most such efforts have focused (very reasonably) on the “main protease”, often known as Mpro. Many viruses have such a thing, in a bootstrapping sort of mechanism – a virus will force cells to crank out one or two viral protease enzymes along with some long protein chains, whereupon the proteases start cleaving the long stuff down into other functional viral proteins. It’s a neat process if you could just watch it from afar, in the cells of some other species. The SARS coronaviral main protease, for example, cuts at 11 different sites in a complex sequence of events that’s like watching a robot assemble itself by unfolding from a small shipping crate. In the case of a virus, though, that robot proceeds to take over the rest of the equipment in the house to make more shipping crates, leaving the place totally destroyed and blowing the new supply of crates all over the neighborhood.

Here’s a paper from a large team in China who came together with commendable speed to obtain the X-ray crystal structure of the new coronavirus Mpro enzyme. Note that although this was published in Nature on April 1, it was received on February 9 – as I say, these folks got moving quickly. Here’s another structure from a joint German-Chinese collaboration, published on March 20. Earlier in March another group at the Diamond synchrotron facility in the UK also obtained the protease structure in collaboration with the Chinese research teams and ran a fragment screen against it, which they have expanded to a crowdsourced effort to find new inhibitors.

I should be more into this work than I am, when I consider how much I like structural biology, fragment screening, etc. But as you can tell from the above paragraphs, I find myself so loaded with immediate concerns that the beginnings of longer-term work that might bear fruit in a few years just keep moving down the list for me. My longer-term hopes for therapies against this virus lie in vaccines (especially) and perhaps monoclonal antibodies, and both of those will read out, multiple times, before the first molecules that eventually come from these screening efforts will make it into human patients. That actually makes these small-molecule efforts more important in a way, though, because if they eventually become useful, it will be because those other attempts at treatment have failed, and then they will be very important indeed. I very much hope that we don’t get to that point. It’s a psychological problem for me: initially I react to these screens with doubts about their utility, and then if I picture the situation where they are indeed useful I react with horror.

Now to some practical considerations for the folks doing this work and those reading about it. These viral enzymes tend to be cysteine proteases with a busy, nucleophilic SH group in their active sites. And that leads to some problems when you screen against them. As anyone who’s done small-molecule screening knows from experience, There Are Some Compounds (and some compound classes) that just tend to hit more often than others. Call them PAINS, call them any nasty name you want – you’ll have plenty of opportunities to see them, because they will be back around again. With cysteine proteases, you will be seeing electrophiles that can react with the SH group, and plenty of them. Such things will indeed shut down the enzyme, but they are likely to shut down a lot of other stuff, too.

You can see that in the structures that are shown in Figure 3 of the Nature paper. That’s quite a crew of known drug compounds: you have ebselen (which I wrote about here) and which hits so many things that we’re still trying to figure them all out, disulfiram (mentioned in this post as “a shotgun” of a compound), tideglusib, a covalent inhibitor of glycogen synthase kinase 3 that has failed a clinical trial in Alzheimer’s (no great distinction, everything else has too), carmofur, an investigational oncology drug that also binds covalently and was pulled from clinical trials due to adverse events, shikonin (that link is to its enantiomer, alkannin, but they’re both hideous deep-red napthoquinones that will react covalently and do all sorts of redox chemistry to boot), and PX-12, a thioredoxin inhibitor that has failed in the clinic and is another reactive disulfide. These are just the sort of things I would expect to see in a cysteine protease screen, and to be honest, they are pretty much the wretched refuse of the teeming shore.

That description goes for a lot of the compounds that have been suggested so far through physical or virtual screening. The comments here have been filling up with people from outside the field talking about quercetin, for example, and the reason that I know that they’re from outside the biomedical field is that they’re talking about quercetin. That’s a classic little polyphenol flavonoid found in all sorts of plants. It has wonky pharmacokinetics (but little or no toxicity) and it has been through all sorts of small trials, hits in all sorts of assays all the time, and has rarely been found to be particularly useful for anything. Honestly, if you come up with quercetin, ebselen, disulfiram and the like as your screening hits it just means that you have to keep looking. This is no secret – the various groups doing these screens know this as well as anyone, and they are indeed looking further. But under the current conditions, when these things show up in the literature, people who have not been around these particular blocks so many times can have a tendency to jump on them as The Latest Hope – it’s understandable, for sure, but it’s not doing anyone any good.

66 comments on “More on Screening For Coronavirus Therapies”

  1. JB says:

    Agree with most of those being garbage, but disulfiram despite having a promiscuous mechanism has been used in thousands of people for long courses of treatment.

    1. Derek Lowe says:

      That it has! I doubt if many people would be pleased with its main effects, though. . .

      1. Simon Auclair the Great and Terrible says:

        Yeah! You get a huge headache if you drink with Disulfuram!

        The Horror, the Horror…

      2. kriggy says:

        I mean if it works why not?

  2. Thank you for writing this perspective Derek. This is a message that more people need to hear. The sad part about this, is that most people *within* pharma (big and small) do not understand this. From the bench chemist to the CSO, all they understand is that there are *Hits*! And once you have a Hit, a drug must be just one step away! In fact, if you are so fortunate to have *multiple* Hits, you must be even closer and are therefore in a great position to cut the timelines in half!

  3. Peter Kenny says:

    Covalent inhibition of cysteine proteases does not present special challenges when covalent bind formation in reversible. However, reversible, covalent, inhibitors typically need to be designed and you’re unlikely to discover novel inhibitors of this type by HTS. Irreversible, covalent inhibitors can be taken forward but you do need to be fully aware of what you’re getting yourself into by going down this path. I have prepared a short document on reversibility of cysteine protease inhibition in the context of drug design and linked it as the URL for this post.

  4. TroyBoy says:

    Yes, I don’t like any of those hits from the Nature paper. Ugly, ugly, ugly.

    On the other hand, Pfizer says that they have a drug candidate against a protease. I don’t know if it’s against MPro (nsp5) or one of the other proteases (PL1pro or PL2pro).

    https://www.wsj.com/articles/pfizer-identifies-lead-coronavirus-drug-candidate-11586427303

    I don’t know if the drug candidate is covalent or not. Anybody know more about what Pfizer is doing?

  5. Jim Hartley says:

    Active cysteines, natural or engineered, are the starting point for Jim Wells’ tethering approach. PubMed PMID: 15139811. Which led to the first small molecules targeting KRAS.

    1. Peter Kenny says:

      The tethering approach is based on reversible disulfide bond formation and I wouldn’t describe the cysteines as ‘active’ (which could be taken to mean ‘catalytic’). The cysteines used in tethering approaches are typically near active sites and leads discovered in this manner would usually not be bound covalently.

  6. Adonis says:

    “Honestly, if you come up with quercetin, ebselen, disulfiram and the like as your screening hits it just means that you have to keep looking. ”

    This is something that funding agencies need to hear. Quercetin and its friends have been perhaps the most profitable cash generating machines for academic researchers for many years now and are unlikely to go away anytime soon. The only way for this to stop would be some kind of decree because scientific arguments will never win.

  7. Giannis says:

    Derek please do a report on the option of creating attenuated vaccines. Some young people want to be infected so they can get back to work. Maybe an attenuated vaccine would be a better option than then getting the WT virus.

  8. Brian Shoichet says:

    In defence of the authors, and perhaps the Reviewers :-), they did note, “In general, such molecules are expected to be promiscuous binders and therefore, as they stand, may have limited potential as drug leads.”

    1. Derek Lowe says:

      Absolutely, Brian – that’s why I mentioned that the people screening these know this as well as anyone. Got to start somewhere, but such compounds are only a very qualified “start”.

      And you know, in an alternate reality, I would be coming back from UCSF today after having spoken to you folks there yesterday! Showed up on my calendar today as a reminder. . .

  9. KN says:

    I wonder if finding inhibitor of PPI between virus’ spike protein and its cellular targets would be better (more straightforward at least) approach.

    1. GM says:

      That’s how “neutralizing” antibodies are likely to work. Small molecule PPI modulators are not straightforward to design or screen for.

        1. Ron Magnusson says:

          As a molecular biologist not involved in drug design, I was impressed by the very tight binding found by quercitin in this study. But from your article, I assume you think this is BS or not useful. Can you explain.

          1. drsnowboard says:

            Dog poop sticks to a blanket, any blanket, very tightly. Polyphenol structures like quercetin, warfarin usually come out of any screen, in fact if you don’t see these promiscuous binders (and the other PAINS) then you forgot to add a reagent. Selectivity then becomes an issue for use as drugs as opposed to ‘pharmacological probes’ AKA publication generators

  10. JNS says:

    Speaking of the Mpro of the novel Coronavirus, what do you think about this inhibitor that was discovered recently by a group from Germany?
    https://science.sciencemag.org/content/early/2020/03/20/science.abb3405
    They’ve been in the business of CoV-proteases since several years and thus have some experience dealing with these kinds of enzymes (as may have numerous others).
    As it was published in Science, you might already have stumbled over this one. I find it especially interesting, because they were even considering the route of administration for these peptidic inhibitors. How do you like the approach of delivering it via inhalation, knowing there’s much fluid and probably all kinds of other proteases in the lungs of the badly ill patients? I cannot recall a peptide delivered by the inhalative route…

    1. Derek Lowe says:

      That paper is one of the ones linked in the post. Their compound is also covalent (presumably reversible), and is at least at first more attractive than the others mentioned. . .

    2. Peter Kenny says:

      The people coordinating the COVID moonshot are considering IV infusion for critical care. This makes a a lot of sense since lungs are particularly well infused (good for getting drug to where it is needed quickly) and plasma concentration is well-controlled (makes tox more manageable). I’ve never worked on an inhalation project but I’d guess that IV infusion will get the drug to where it is needed more efficiently than inhalation if there is fluid in the lungs. Martin Stoermer and I whipped up some notes on design implications of the crystal structures and I’ve linked these as the URL for this post.

      1. Anonymous says:

        I have colleagues who worked on IPF and inhalant mode of delivery is something they come up to time and time again, and the argument is that the effectiveness of that delivery is dependent on ability to inhale, unsurprisingly, which is troublesome for a patient in respiratory distress. That’s a good way out of my wheelhouse, so I defer to the scientists who seem to agree that what you just said re: vasculature in the lungs as an opportune route for drug delivery.

  11. George Stanchev says:

    I really appreciate this blog and your viewpoint. Perhaps, because I am not a scientist I don’t understand why someone like Michel Chrétien would go after quercetin and attempt to trial it in China as news reports from a month and a half ago indicated. Is it the academia cash cow as some of your readers have suggested. His credentials are not of someone with a “quack doctor” label. As a layman I found the number of publications of Q as a broad antiviral, cancer, COPD intriguing. Obviously, there are things working against it (poor solubility, bio availability) but I don’t understand why it can’t have even prophylactic effect when taken in large doses.

    Admitting I am not one of “you”, but in this crisis we’re all together and I appreciate a comment why such hostility against it? People making up stuff? Natural supplements industry sponsoring such studies (just like the imposingly “Big Pharma” is skewing things for own good). Genuinely interested to hear comments on this…

    1. Derek Lowe says:

      It’s just that it shows up as a hit in so many assays, and has been linked to so many diseases and conditions. There are quite a few compounds in that category, and people have been burned by them in the past trying to get something to work. Just in the 2019-2020 papers in Pubmed in a search for “quercetin trial” you see human data on breast cancer, fatty liver, COPD, acne, thalassemia, blood pressure, glycemic control, and exercise-induced muscle damage. Is one compound good for all of those? The odds are very much against it, and when you see so many varied results, you start to wonder if it’s really much good for anything in particular. . .

  12. Alan Goldhammer says:

    It also strikes me that a lot of the in silico molecular docking studies are not particularly useful. A lot of the antivirals with known activity against RNA polymerases tend to show very high binding energies to the Mpro enzyme. Obviously these types of studies can be suggestive of what to try in vitro but should not be overly relied upon. I saw a preprint today showing darunivir to have very little in vitro activity. The big problem is how to translate in vitro activity to the decision point of a clinical trial. I’ve been appalled that the powers to be still have not designed a clinical trial process capable of rapidly aggregating data and getting information out to clinicians. We have far too many hydroxychloroquine trials going on all over the world at the sacrifice of finding a drug that works. There is no creative thinking going on about how to do this. The academics in charge of this would do well to learn from the big pharma companies who routinely do this type of clinical research.

  13. Dr. Nemo says:

    A naive question (I am not a medicinal chemist, so please bear with me): would it be worth testing Tecfidera or Vumerity for cysteine protease inhibition? They metabolize to monomethyl ester of fumaric acid, which could react with cysteine residues at blood plasma pH. There is also Fumaderm (dimethyl fumarate / monoethyl fumarate salt composition).
    Along the same lines, would it be worth checking whether there is any protective effect (lower incidence of COVID-19) in multiple sclerosis or psoriasis patients that are taking these drugs at this time?

    1. HU says:

      dimethyl fumarate is one mighty shotgun, but I would also like to hear Derek’s opinion about it

    2. Cb says:

      Indeed, thank you ,nice suggestion: hopefully it has been tested in some lab already.

      On Jan 29th I posted: “What about non-specific covalent inhibition of the Coronavirus cysteine protease (3C-like protease) for only a couple of days (when the viral load increases). E.g. the cysteine may be covalently inactivated with dimethyl-fumarate (DMF) : up to ~500mg/day oral dose seems to be allowed hitting all sorts of cysteines”

      On march 6th I posted: “Why do these nice algorithms for machine learning do not suggest dimethyl-fumarate (Tecfidera) as possible repurposed drug. On the one hand this drug (and its metabolite: mono-methyl ester) is a well-known thiophilic Michael acceptor which should inhibit the papain-like protease and on the other hand this drug would reduce IL-6 induced lung inflammation.”

      On Feb 7th I posted “Interestingly, the reactive metabolite of the analgesic acetaminophen (paracetamol): NAPQI is also a non-specific cys protease inhibitor.”

      I may add that Omeprazole (its active rearranged sulfenamide) is also a non-specific irreversible Cys protease inhibitor.

      During my career I saw many screening campaigns on Cys proteases and indeed all the compounds described in the Nature paper-and many more frequent hitters- were found as they covalently bind with Cys in the catalytic domain.

      I worked for a big Pharma where covalent-inhibitors were forbidden, even (relatively) selective ones (they did not believe such a thing exist); fortunately a very nice inhibitor from my lab was developed by another company and is now on the market 😊.

      Most likely the inhibitors of Pfizer are peptidomimetics with a reactive warhead similar to dimethyl-fumarate and as described e.g. in WO2004093860

      Of course if the selective i.v. drugs of Pfizer can be on the market next year: GREAT!, but why are we so afraid to give non selective irreversible Cys protease binders for 1 or 2 weeks p.o. in the mid of the pandemic if we use them as existing drugs already and are apparently safe enough (acetaminophen/paracetamol, omeprazole, dimethyl-fumarate, disulfiram)…why have these compounds/ active metabolites not tested on cellular systems yet: because these are non-selective covalent inhibitors….very dangerous………yeh, yeh…..or are they not active enough, that would be all in the game and discontinued.

      1. milkshake says:

        Was it in South San Francisco, by chance? Maybe I worked one floor below you, on the Factor VIIa project.

  14. particleman says:

    The IKEA interpretation of virology… I love it!

  15. particleman says:

    More seriously… how aggressive is the work looking as hrsACE2 as a “decoy”?

    If effective, it would probably allow more aggressive treatment with dexamethasone along with hrsACE2 in cases of severe pulmonary inflammation to first reduce lung damage (and at the same time reducing viral load). A taper of the dex followed by a taper of hrsACE2 could allow the immune system to mount a more durable antibody defense.

  16. particleman says:

    …and for the thought left wanting…

    …dex is the big hammer. No so much need to worry about IL-6 or IL-1 for selective downregulation if the virus load can be reduced by hrsACE2….

  17. milkshake says:

    My former colleagues from a virtual company are now trying to re-purpose their thiol-loving cancer chemotherapy drug for COVID19.

    (Our virtual company) “does not currently have the expertise or resources to pursue this project in a relevant timeframe and is urgently seeking a development partner and/or institutional investors interested in this unique solution.”

    This all based just on a single spike protein sequence homology modelling paper (based on MERS X-ray data) from Egyptian-Saudi group, a paper that suggests that SARS_CoV2 might be using additional receptor for entry point.

    The company clams that their drug targets this receptor, even though the biology is totally shaky. Normally i would say it is a house of cards built on house of cards, but the scientific rationale is in my opinion secondary – now they are out to bilk some investors and hurt some patients in the process. They have manipulated the animal and patient data before, and they kept the really problematic stuff from FDA. They still have faked data prominently on their company website.

    1. Miles says:

      Are they being too Bold…

      1. milkshake says:

        Lets not speculate about the company name but everything I know about these nice people points out that they are a public menace, and serial cheats – and they want to do it again. The idea is buy out the majority investor out of a soured investment while the pandemics is still going strong. There is an old company that had shuttered in house research four years ago and gone virtual from then on, operating on skeleton crew. That company is being let to die quietly because there is no clinical evidence that the technology really works and moreover every clinical/preclinical project is tainted by research misconduct. It turns out, what was hailed as a “deal of the year” was a blunder – the fund that bought itself into this shell of a company did not do due diligence, did not lean about all the criminal activity and research misconduct until too late. Now to get their money back, they figured they could sell the only project that looks like an asset, to themselves – by selling it to a “new” virtual company, which they launched themselves, with the same CEO, the same people on the Board, and with some of the scientists from the old company. And now the brilliant COVID switch – I think they will get more attention that than can handle.

  18. Jim Thibodeau says:

    Any news on whether hydrochloroquine works?

    1. David Young MD says:

      Still don’t know. I suppose that if it helps, it helps just a little. It might not help at all. Consider this. It is highly likely that for the past 3 to 4 weeks that every patient who is hospitalized is put on HydroxyChloroquine. The drug has been readily available to hospitals. So…… if HydroxyC is as good as “they” say (meaning Dr. Raoult and everyone who believes him) then there should be a drastic decrease in deaths and a meaningful shortening of ICU time and hospitalization. But I have not noticed that. Yes, people are still dying of Covid19 and these people were all given Hydroxychloroquine. This does not mean that it might be somewhat valuable or that it might work better in combination. But I don’t see it being a wonder drug at this time.

      1. Jim Thibodeau says:

        Yeah it doesn’t look like it’s going to be effective, but I think I read a few days ago the WHO was doing a study with it and a few other drugs, and I was just wondering if we’re going to have better data soon or if it’ll be a few weeks.

  19. Tudor Oprea says:

    I sent the link to that paper to my group yesterday with the following text:

    >>> begin quote <<>> end quote <<<

    I totally agree that we need to keep looking.

    These aren't the droids you're looking for.

  20. Tudor Oprea says:

    My comment got processed between quotations, here’s what was missing:

    …and the usual suspects are…

    drum roll, please

    ebselen, disulfiram, PX-12 and shikonin

    drug leads for SARS-CoV-2 Mpro (main protease), paper accepted in Nature.

    what is wrong with peer reviewers?!

  21. Anders Bach says:

    It would have been worth a Nature paper if these compounds were NOT hits.

  22. Jon Schultz says:

    What about BHT, which reportedly dissolves the coating of lipid-coated viruses?

    http://projectwellbeing.com/wp-content/uploads/2020/03/BHTbook-StevenWmFowkes-200302.pdf

    I’m taking it, to hopefully lessen the severity of an infection, along with complementary supplements. Interesting protocol at:

    https://www.lifeextension.com/protocols/infections/2019-novel-coronavirus-sars-cov2-covid-19

    1. Jon Schultz says:

      No one willing to look at The BHT Book and comment? With BHT being an inexpensive, obtainable compound which might help ward off a serious infection if taken in appropriate doses prophylactically, I think it’s important that intelligent scientists evaluate the available data and opine. No one should be told that if they take BHT they will be protected, of course, only – perhaps – that it might help. Do you think the data presented in The BHT Book at least warrants some experimentation? You could have two comparable groups in an area where the outbreak is just taking root, with one taking BHT (and perhaps some complementary supplements like Vitamins C and D, NAC and EGCG) and the other not, comparing outcomes within a few weeks. And perhaps people should be made aware of the possibility of assistance NOW.

      http://projectwellbeing.com/wp-content/uploads/2020/03/BHTbook-StevenWmFowkes-200302.pdf

  23. AI says:

    Dutch researchers found a possible method by which COVID-19 causes damage.

    If I understand correctly, the virus reduces available ACE2 in the lungs, and one of the functions of ACE2 is inactivate bradykinin. When bradykinin builds up, it causes the lungs to start leaking.

    https://www.preprints.org/manuscript/202004.0023/v1

  24. Gabriel Navarrete-Vazquez says:

    Invalid Metabolic Panaceas (IMPS) are present in natural sources in relatively high abundance and represent the “PAINS” from the natural products world…

  25. JP Leonard says:

    https://blogs.sciencemag.org/pipeline/archives/2020/04/10/more-on-screening-for-coronavirus-therapies#comment-315887
    I am going to try Quercetin along with zinc supplements because it is an OTC zinc ionophore (It makes zinc more bio-available. Zinc is what Dr. Cardillo says needs to be given together with hydroxychloroquine, if you want it to work against the virus.)
    Drawback with quercetin, it has bio-availability issues of its own.
    One source suggests combining it in zinc tablets.
    https://nutritionalpharmacology.wordpress.com/2020/03/21/combating-covid-19-with-zinc-and-quercetin/

    Quercetin as an Antiviral Agent Inhibits Influenza A Virus (IAV) Entry
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728566/

    Zinc ionophore activity of quercetin and epigallocatechin-gallate: from Hepa 1-6 cells to a liposome model.
    https://www.ncbi.nlm.nih.gov/pubmed/25050823

    “quercetin may serve as an effective oral immunomodulator for improving cell-mediated immune defense”
    https://www.ncbi.nlm.nih.gov/pubmed/32184034

    It might have other good properties but for Covid19 it’s most interesting as a zinc transporter

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  27. Jacob says:

    Do you expect the work on the SARS-CoV-1 Mpro (3CL) biology to map to SARS-Cov-2? Specifically its polypeptide targets, autocleaving, etc? I believe the proteases have much sequence identity, but have not looked at its targets as mentioned in that 2016 paper you cite.

  28. JM says:

    Perhaps another effort to keep an eye on is the screening of this deck:

    https://www.scripps.edu/news-and-events/press-room/2020/20200318-reframe-drug-repurposing-covid19.html

    This deck contains many compounds with at least some human clinical safety data, so if any of these hit there may be a shot to get into patients fairly quickly (with the usual caveats around in vitro potency, PK/PD, margin, CMC, etc.). Fingers crossed as always…..

  29. Jim Palmer says:

    The promiscuous hits mentioned should be discounted, however, directed (ie structurally-informed) cysteine protease inhibitors make sense. Rupintrivir (from Agouron) is quite structurally similar to one compound co-crystallized with the main protease.

    It makes perfect sense to use chemically irreversible inhibitors in this context because of the acute nature of the unmet medical need. This is not a chronic indication. Pathogens, whether they be viral, fungal, or bacterial, can quite easily be knocked over by irreversible enzyme inhibitors, because resynthesis of their key enzymes is often on a time scale not requiring 24 hour IC50 coverage — in other words, PD of irreversible inhibitors is Cmax dependent rather than AUC-dependant. So you can often get away with a bolus dose. Penicillin, arguably one of the greatest drugs ever invented, if not the greatest, is an irreversible protease inhibitor. Yes, some are allergic, but if we spend years trying to find the perfectly safe reversible inhibitor suitable for rest-of-life administration, we would be barking up the wrong tree.

    But…a concern that has been addressed in this field about 5 years ago — would cysteine protease inhibitors effective against SARS main protease in vitro work in vivo — the answer is perhaps not. Yes, you can knock over the target, but you also have to work with the host response. This is why a study comparing the use of cysteine protease inhibitors (yes, irreversible ones!) and the serine protease inhibitor camostat, which is marketed in Japan, both as monotherapy and in combination in an in vivo study where mice were inoculated with a lethal infection of SARS virus, showed that only the group given camostat, which modulates the host response, was successful (60% of mice survived) — no improvement by adding the cysteine protease inhibitors — vinyl sulfones with excellent in vitro activity and adequate PK — and the group receiving the CPI alone was not helped at all. Look up Antiviral Research 2015 and camostat on PDB to find this study.

    1. Cb says:

      Rupintrivir and -probably related- candidate drug (see e.g. WO2004093860) from Pfizer is a 3C-like-protease (3CLPro) irreversible inhibitor of the virus https://www.pfizer.com/news/press-release/press-release-detail/pfizer_advances_battle_against_covid_19_on_multiple_fronts, whereas the compound you refer to as described in the article from 2015: K11777 is a (human) lysosomal CatB/L inhibitor (different P1 group, different warhead) . So we must not confuse one thing with another, or do I miss some other argument why irreversible 3CLPro inhibitors would not expected to be efficacious (giving early in the infection)

  30. Researcher says:

    If Quercetin wasn’t useful then why did DARPA and the Defense Dept study it after the last SARS/MERS outbreaks and then develop Q-force chews especially for the military and first responders?

    Maybe they know something you don’t.

    1. Derek Lowe says:

      I would be very happy if you could point me to any statement that DARPA has made about the efficacy of those. Not what the company says – what DARPA says. Thanks!

        1. TP Finlay says:

          Link doesn’t work.

          1. Marko says:

            https://www.darpa.mil/attachments/TestimonyArchived(March%2013%202008).pdf

            “DARPA researchers have identified a very safe, natural antioxidant – called Quercetin – and
            developed it into a new form that is now available to the military and the general public. Among Quercetin’s many potential benefits is illness prevention. In a randomized, placebo-controlled study, Quercetin helped prevent viral illnesses, like colds and flu, after physical exertion. Following a strenuous three day exercise routine, 50 percent of the control group became ill with colds and flu, whereas only five percent of the Quercetin supplemented group did. This important immune protective effect will help keep our warfighters healthy during training and deployment. Quercetin has been commercialized as RealFX Q-Plus soft chews, which are now available through several commercial vendors, as well as to all military personnel at a 50 percent discount.”

  31. Marko says:

    You need to copy/paste the above link. Not clickable because it gives this site indigestion.

  32. John Cookson says:

    The link works when copied and pasted into the browser URL field.
    Marko is correct in the statements he has made.
    Also I should mention that a previous poster JP Leonard is correct to bring up the potential usefulness of Quercetin acting as a Zinc Ionophore (Allowing Zinc To enter human cells).
    This is the same mechanism that Hydroxychloroquine (Also a Zinc Ionophore) uses to get Zinc into the cell whereby it stops SARS-Cov-2 viral replication replication.
    I would also like to mention that both Hydroxychloroquine and Quercetin efficacy is likely to be reduced considerably if not accompanied by Zinc supplementation.

    Hydroxychloroquine is likely to be more effective in this role compared to Quercetin which carries a much shorter half life. Owing to a lack of studies on Quercetin, it is also difficult to ascertain dosing requirements for efficacy in human subjects.

    Finally I would like to mention that both of these antivirals should ideally be used in the outpatient stage of Covid19, ideally within 5 days of symptom onset. The hospital and ICU setting is often not reached by patients until the viral replication stage has already progressed to a life threatening level.

    It exasperates me why study designs seem unable to grasp that timing (Early intervention) is everything, and Zinc should always be used.

  33. Ryan says:

    Hi Derek –

    I appreciate your insightful blog posts, and have learned a lot from them. I would really appreciate any additional information you can provide about quercetin (specifically bio-available forms, such as quercetin phytosome). I’m not a researcher, however I’ve found a number of (to my eye) credible reports that indicate quercetin can be an effective antiviral in vitro and in vivo tests. I understand that quercetin is a frequent hitter, but the reports look to be going beyond an initial screen. If I’m missing something, then I’d very much appreciate being set straight. Here are a couple of links. Thanks in advance.

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997876/
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360794/

    1. Hi Ryan,

      My sympathies – You’re making the error of bringing rationality to a groupthink gunfight.

      Also, this is an old enough thread that you’re unlikely to get a response from DL or the other med chemists that haunt the comments section. (As non-med chemists ourselves, we keep tabs on this thread because it’s salient to understanding incumbents’ perceptions to phytochemicals research).

      To your query, it’s worth keeping in mind that quercetin is one of a couple thousand (at least) flavonoids depending on the definition of flavonoid one subscribes to. And flavonoids as a class are just one of the many classes of phenolic compounds (some tens of thousands of primarily nature-derived compounds that drive med chemists’ assays batty as DL outlines in his post).

      When anything in a scientific space is difficult to measure, yet has a lot of money & status riding on the outcome, then the thinking among the professionals benefiting from incumbency in that space inevitably coalesces around ‘schools of thought’. (Think economics schools, or the different flavors of string theory in theoretical physics). Looking from far enough away, especially from the point of view of outsiders to the space, these schools accrete around a central groupthink. This behavior ensures that in the absence of hard evidence, their actions will at least be socially acceptable to peers (who can influence things like corporate budget allocations or grant funding).

      By interfering in many assays’ readouts, compounds like polyphenolics effectively serve as a blindspot to med chemists’ work, which is why they don’t like them. Rather than be creative and think up & verify new assays that can accurately assess these compounds’ capabilities (or cut straight to animal model research in the face of a high-priority pandemic), it’s much easier to slap a label like PAINS on them and catcall them all at once in order to focus on other compounds.

      So the PAINS concept and whatever characteristics du jour earn any particular compound a PAIN appellation and therefore not worth further investigating becomes a school of thought in its own right. The school’s acolytes will say anything and everything disparaging about pan-assay interfering compounds *except* come out stating explicitly, free of any career-sheathing online pseudonyms, that none of these compounds can ever demonstrate safe, inhibitory activity on any particular virus’ action in the human body.

      One frequent and longtime commenter on this blog, Peter Kenny, writes a great ‘J’accuse…’ post picking apart the PAINS groupthink: http://fbdd-lit.blogspot.com/2015/10/a-painful-convolution-of-fact-with.html . I highly recommend giving it a read as it directly challenges practitioners’ reflexive adherence to the PAINS school.

      Will close with this quote from this 16th century individual who once committed the same epistemological error as you did:

      “What do you have to say about the principal philosophers of this academy who are filled with the stubbornness of an asp and do not want to look at either the planets, the moon or the telescope, even though I have freely and deliberately offered them the opportunity a thousand times? Truly, just as the asp stops its ears, so do these philosophers shut their eyes to the light of truth” -Galileo Galilei

      Best,
      Rick

      1. Derek Lowe says:

        I’ll take the other side of some of Rick’s arguments (starting with the one that the question is unlikely to get a reply from me!) It’s true that these polyphenol compounds hit a lot in assays. But rather than being a blind spot, they’re a bit more like a flashlight in the eyes, keeping us from seeing more useful stuff. Polyphenols have indeed been into many animal assays over the years, but their pharmacokinetics (blood levels, half life) are often very poor. So you have things that hit in the in vitro assays – but hit in a lot of them, suggesting a lot of different activities/side effects – and don’t tend to have in vivo effects because they get cleared so easily. Is it any wonder that we are leery of working on them? This is a rational prejudice more than an irrational one, to my mind. Peter Kenny’s thoughts on PAINS are indeed well worth reading. But somehow I don’t think he’d sign up for a lot of polyphenol development, either.

        Quercitin, for its part, has been in so many assays and so many animal models that I couldn’t count them all. It has, to the best of my knowledge, never delivered any useful activity against any particular disease or condition. On the other hand, it appears to be extremely safe, so if you want to take some it’s probably not going to do any harm. But i wouldn’t bet on it doing any good. I think that the people who are still pushing its benefits are the ones with the stubbornness of an asp, to borrow that Galileo quote. The use of which in 2020, amateur astronomer thought I am, is usually a warning sign. . .

        1. Marko says:

          ” ( Quercitin ) has, to the best of my knowledge, never delivered any useful activity against any particular disease or condition. ”

          What about the study referenced in the darpa.mil document linked above , which you specifically asked for , and then when the link was provided , you clammed up ?

          Do you think it’s bogus ? If so , why ? If it’s not bogus , doesn’t it provide evidence for the “useful activity” that supposedly doesn’t exist ?

        2. “but hit in a lot of them, suggesting a lot of different activities/side effects” (and to this would have to be added the April zinger, “when you see so many varied results, you start to wonder if it’s really much good for anything in particular. . .” )

          

In fact I’ve long wondered about the April stance. If the stakes were just about creating some new anti-inflammatory candidate on a limited corporate budget then I get the concept of placing bets on a softer contextual basis like this. But different stakes are at hand, and for my part I see a more rigorous epistemological standard needing to be applied. 


          “and don’t tend to have in vivo effects because they get cleared so easily”.


          One well-known nat product (albeit not a polyphenolic one), artemisinin, gets cleared in just 2-5 hrs time. At any given time pre-clearance, just thousandths of the oral dose are extant in the bloodstream. And yet that’s plenty for it to do the work of inhibiting malaria’s P. falciparum over a five-day course.

          By my back-of-the-envelope calcs on OurWorldinData’s malaria stats, there are up to 5 million sub-Saharan Africans still with us today who would be glad that any concerns about rapid in vivo clearance did not arrest artemisinin’s development.

          – –

          I’m not a standard-bearer for quercetin, (even though it serves as a good stalking horse for eliciting the trade’s opinion on our own polyphenol candidates). But when earnest non-practitioners come citing academic papers and government reports on a compound, and rather than seeing the usual caliber of ITP critical analysis a la mAb’s and vaccines, they get ‘FUD’ (or even just static) instead, it paints a picture.

          – –

          [Artemisinin PK source: https://pubmed.ncbi.nlm.nih.gov/8957153/#:~:text=Artemisinin%20is%20available%20only%20for,can%20be%20considered%20as%20prodrugs. ]

          [OurWorldinData malaria: https://ourworldindata.org/malaria ]

  34. “. . .but hit in a lot of them, suggesting a lot of different activities/side effects” (and to this would have to be added the April zinger, “when you see so many varied results, you start to wonder if it’s really much good for anything in particular. . .” )

    
In fact I’ve long wondered about the April stance. If the stakes were just about creating some new anti-inflammatory candidate on a limited corporate budget then I get the concept of placing bets on a softer contextual basis like this. But different stakes are at hand, and for my part I see a more rigorous epistemological standard needing to be applied. 


    “. . . and don’t tend to have in vivo effects because they get cleared so easily”.

    One well-known nat product (albeit not a polyphenolic one), artemisinin, gets cleared in just 2-5 hrs time. At any given time pre-clearance, just thousandths of the oral dose are extant in the bloodstream. And yet that’s plenty for it to do the work of inhibiting malaria’s P. falciparum over a five-day course.

    By my back-of-the-envelope calcs on OurWorldInData’s malaria stats, there are up to 5 million sub-Saharan Africans still with us today who would be glad that any concerns about rapid in vivo clearance did not arrest artemisinin’s development.

    – –

    I’m not a standard-bearer for quercetin, (even though it serves as a good stalking horse for eliciting the trade’s opinion on our own polyphenol candidates). But when earnest non-practitioners come citing academic papers and government reports on a compound, and rather than seeing the usual caliber of ITP critical analysis a la mAb’s and vaccines, they get ‘FUD’ (or even just static) instead, it paints a picture.

    – –
    [citation links in version under moderation]

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