Will general antiviral protocols always be science fiction?

December 17th, 2032:

Following an exhausting red-eye flight across the country to visit with family over the winter holiday, you get off the plane and amble over to the terminal’s rideshare pickup area. A couple days later, you’re coughing mildly. You go to the drugstore. They swab you and sequence whatever bug you got. It turns out to be this year’s strain of influenza-A virus — the flu. Your viral load was subsequently quantified from the same swab overnight; The results come back the next day: Just 10⁴ (ten thousand) viral RNA copies per mL, nothing so strong (yet). The pharmacist asks if you’d like take-home treatment. Eager to avoid a week being laid up alone instead of time with the family, you gladly accept.

The pharmacist looks up which among the several hundred pre-cleared flavonoids (commonly-encountered compounds from plants) were most recently verified for effective antiviral activity against this year’s rhinovirus strain. This thanks to a newly expedited approval process ratified by the FDA’s board, where supplements with a long-familiar and highly tolerant human safety profile are verified for efficacy in animals and clinical trial volunteers who caught the same bug just months before you did.

She swabs you once more before handing you a bottle full of capsules of the relevant flavonoid, a pack of disposable vials of sample buffer, long cotton swabs, and a QR code for an app to download that will beep a reminder every four hours to take your next dose. Per the pharmacist’s instructions, you begin your flavonoid therapy while producing a fresh swab sample every day. By day 3, your symptoms no longer persist. You drop the samples off at the pharmacist who emails you a report the next day.

‘Your 2nd sample before starting the therapy was 10⁶ (one million) viral RNA copies per mL — a growing viral load. Your subsequent 3 home samples after commencing therapy clocked in at 10⁴ (ten thousand), 10³ (one thousand), and 10² (one hundred) copies per mL, consecutively. Your viral load is successfully receding to undetectable levels. Please continue your therapy to completion.’

To avoid experiencing the oft-reported viral rebound, you continue taking your flavonoid therapy for the rest of the week. Afterward you go on to enjoy a rejuvenating Christmas dinner with family.

Of course this scenario remains a distant fantasy; Even as antibiotics are easily administered today against infections from a wide range of bacterial species, we still live in a world sorely lacking effective protocols against common virus species. Rare exceptions to this reality are rightfully celebrated as well-known feats of enormously hard-won scientific investment: Paxlovid for COVID-19, inhibitors for HIV and hepatitis-C spanning years of R&D, trials, and agency approvals. Could the fictional account describing an off-the-shelf general antiviral protocol ever become a reality? To answer that, we’ll need some context:

XKCD under CC BY-NC 2.5

Flavonoids (nothing to do with flavor)

Before the pandemic, several research papers reported flavonoid inhibition of the SARS (from 2003) virus component called the main protease. In 2021, appreciating the structural similarity of the SARS protease to the pandemic’s SARS-CoV-2 protease, several stakeholders and I had set out to initiate a covid clinical trial leveraging a commonly consumed flavonoid derived from plants.

A sticky situation

Polyphenols have a reputation among medicinal chemists for being “sticky”. One med chemist even uses a more colorful metaphor to describe their interaction with proteins: “dog poop sticks to a blanket — any blanket”. My own longitudinal analysis of researchers’ bioassay contributions to the open public chemicals database PubChem (see the Appendix below) demonstrates that polyphenols’ reputation for promiscuous binding is indeed well-earned. Polyphenols are easily found to bind to between 5%-30% of all targets they are screened against — that’s a whole lot of distinct protein & enzyme species. That reputation however is then cited as a reason that polyphenols should be ignored from consideration as therapeutic leads for clinical investigation for any particular condition. Noted opinion-leader for industry med chemists, Derek Lowe, writes of the most frequently studied flavonoid, quercetin:

A phenol molecule. Multiple phenols form polyphenols. [image by NEUROtiker]
Several flavonoids from left to right: hesperetin, diosmetin, and quercetin, respectively; Note the several OH’s (hydroxyls) on each molecule. (Discussion of oxygens serving as hydrogen acceptors omitted for clarity).
Enzymes (red symbols) sticking to the surface of accumulated aggregating compounds (ignore the yellow symbols which are irrelevant to the discussion); From Auld et al.

Promiscuous, but selectively so

A toolbox of promiscuous compounds leaves us in a precarious position regarding polyphenols as antiviral candidates. Are they sticky and bind to everything indiscriminately? Or could they be sufficiently selective to avoid causing excessive trouble elsewhere in the body while hitting our intended targets of interest?

Left: Luteolin; Right: Luteolin-7-O-glucuronide — note the glucuronic acid “tag” highlighted in green. (Credits: LHS: public domain; Yikrazuul, RHS NotWith under CC BY-SA 3.0)
From Sheridan, R. Spelman, K. (2022)
Shimoi’s mechanism (This example uses the frequently-researched flavonoid quercetin as the example). From Sheridan, R. Spelman, K. (2022)
From Sheridan, R. Spelman, K. (2022)

So perhaps there’s a mechanism — what can we do with it that we don’t know about already?

A shortlist of polyphenolic antiviral candidates

First and foremost, verification of the Shimoi selectivity mechanism reinforces the value of mining the extensive polyphenolic antiviral in vitro literature base to provide candidates for effective, well-tolerated antivirals. Researchers in polyphenolic antivirals are most likely correct in studying the aglycone in vitro as an antiviral rather than its glucuronide, so long as the virus under study induces the inflammatory response in vivo.

IC50 values. DENV = Dengue Virus, FMDV = Foot and Mouth Disease Virus, JEV = Japanese Encephalitis, CHIKV = Chikungunya Fever, ZKV = Zika virus. Generally any IC50 value less than 10µM is considered a decent starting point for an antiviral) Source: Sheridan, R. Spelman, K. (2022)

Therapeutic window

There’s another encouraging implication of Shimoi’s mechanism. While researchers produce IC50 values from laboratory antiviral screens, a critical step they also inevitably undertake is to determine the CC50 (the cytotoxic concentration, or cell-toxic dose that will kill 50% of healthy cells so administered) value. The higher that CC50 is a multiple of IC50, the better. 10X is a good starting point, and we would of course love to see 50X+ and beyond. That way, we can safely target trialing higher doses toward the IC90 or IC99 end of things (90% and 99% viral replication inhibition, respectively) without running headlong into the CC50.

Diosmetin PK profile (isolated from glucuronides in circulation); The annotations are a simplification — peaks will actually compound on each other with subsequent doses. Image adapted under CC by 4.0 license from Russo et al. (2018)

Evolutionary basis

We can only speculate on why the Shimoi mechanism exists. And to be sure, accepting its very existence should require further end-to-end verification in multiple animal species, humans included. Perhaps it is simply incidental that mammalian metabolism relates otherwise independent phenomena together.

What next?

Now focus turns toward building awareness for studies investigating therapies that exploit the putative Shimoi selectivity mechanism.

In a nutshell:

There may be a class of compounds readily accessible from the plant kingdom that can inhibit viral replication (much as paxlovid does for SARS-CoV-2), with very generous safety profiles owing to a selectivity mechanism characterized over the past two decades. Verification of several polyphenols exploiting the mechanism to show safe antiviral effect in infections from several different virus species would provide a strategic bank to draw from for future pandemics. During a future pandemic of an uncharacterized virus, so long as it induces an inflammatory response in human hosts, then the strategic bank of polyphenols of known safety profiles could be quickly assayed and trialed in in vivo studies to determine which among them is most effective for reducing that particular virus’ viral load in infected patients. Reduction of severe outcomes and faster recovery from infections could be reasonably anticipated.

Disclaimer

This piece advocates for supporting a particular line of clinical research and nothing more. Emphatically, no one should read this and consider self-administering discussed compounds for the purposes described. More than just boilerplate, there are relevant compounds and corner cases I’ve not covered here that my conscience would really, sincerely prefer readers not do trial-and-error on.

Acknowledgments

The author would like to thank everyone acknowledged in the manuscript, stakeholders & supporters of last year’s proposed clinical trial, M. Hu PhD for technical consultation, and D. Stein, S. Molnar PhD, Dr. Angela Reiersen MD-PhD, S. Ferguson PhD, Yu Wai Chen PhD, and K. Spelman PhD for reviewing article drafts & encouraging feedback.

About the Author

Rick Sheridan cheerleads for researchers & clinicians laboring in underrecognized lines of research. He has served as an instructor on in silico modeling & baselining techniques for a plant research institute, and led drafting of the FLAVOCOV clinical trial protocol. By day he runs a venture in the agricultural industry.

Appendix for mol bio folks

  • Here are more examples of flavonoid glucuronides from the pharmacology literature studied. You can note their similarities to the luteolin figure above — can you spot the glucuronic acid structure(s) in each?:
A) diosmetin-3’-glucuronide B) diosmetin-7–3’-glucuronide C) hesperetin-3’-glucuronide’ D) hesperetin-7-glucuronide E) quercetin-3-O-glucuronide
  • As alluded to earlier, we also collected data from the literature and did original analysis on it to verify the med chemists’ premise. Yet, since the data collection was only secondary to the article’s central thesis (and anyways was in happy agreement with the preliminary aspect of the med chemists’ reasoning), we decided to remove that section and maintain as a pure review.
    Of course, because this is a Medium post and not a paper for peer-review, I can provide all the original work I want☺ Here is that data:
  • By sifting through several hundred thousand in vitro screens submitted to Pubchem (specifically the Pubchem bioassays database, as very helpfully pre-sorted by University of Bonn medicinal chemistry researchers), this data shows that polyphenols do indeed bind to targets promiscuously — much more so than natural product molecules that lack phenolic groups. (Interestingly, even single phenol molecules were as or more promiscuous on average as polyphenols). So the med chemists’ suspicions about promiscuity are actually well borne out here.
  • Additional Phase II metabolic pathways for polyphenols have been documented like sulfation & methylation. Glucuronidation remains the dominant metabolic process however.
  • Per the license terms, edits to the XKCD image are described: “cancer cells” struckthrough and changed to “infected”.

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EMSKE Phytochem

EMSKE Phytochem

Coming from a multidisciplinary technical background in Silicon Valley, SE Asia, & East Africa, the author builds awareness of plant medicines. Tw: @EMSKEPhyto