24 February 2022 Episode 244 : Update on treatment and varia

Thu, 02/24/2022 - 12:34

Dear colleagues,

Again, this episode is built from suggestions and hints by several amongst you (thanks!).

I will first update on the polymerase inhibitor Remdesivir (GS-441524 or Veklury-Gilead co.) and the main protease (3CL pro) inhibitor Nirmatrelvir (PF-07321332 or Paxlovid-Pfizer co.).  Next I will present a new promising protease inhibitor S-217622  (Shionogo co.).

I will also briefly discuss 2 metanalysis studies on antiviral treatment and provide some outlook on NSP3 inhibitors . 

The remainder papers complement several topics from the latest episodes.


Established drugs Remdesivir and Paxlovid

Ep 244-1: NIH Guidelines in the 21 Feb issue of “The Medical Letter”:

Remdesivir IV, already approved for hospitalized patients, now also approves the drug for treatment of mild to moderate COVID-19 in outpatients ≥12years old who weigh ≥40 kg and are at high risk for progression to severe disease  during 3 days (based on Ep 244-2).

Paxlovid per os, in combination with Ritonavir, is approved for a similar indication during 5 days (based on Ep 244-3).  

Alternatives are a single IV injection of the monoclonal Sotrovimab or 5-days oral course of the  polymerase inhibitor Molnupiravir (the latter only in adults).  

Note: In this letter paxlovid and sotrovimab are said to be the treatment of choice in the omicron era.  However, while the monoclonal cocktails  casirivimab plus imdevimab (Regeneron) as well as bamlanivimab plus etesevimab (Eli Lilly) are not recommended, because of loss of activity against omicron, we know that even Sotrovimab, which was still active against the original BA.1 omicron,  is presumably inactive against Omicron sublineage BA.2 (Ep 242-2). 


Ep 244-2: Gottlieb NEJM 27 Jan 2022: Early Remdesivir to Prevent Progression to Severe Covid-19

in Outpatients.

  • Covid-19–related hospitalization or death in 2 patients (0.7%) in the remdesivir group and in 15 (5.3%) in the placebo group (hazard ratio, 0.13 p = 0.008).
  • A total of 4 of 246 patients (1.6%) in the remdesivir group and 21 of 252 (8.3%) in the placebo group had a Covid-19–related medically attended visit by day 28 (hazard ratio, 0.19).
  • No patients had died by day 28.


Ep 244-3: Hammond NEJM 16 Feb 2022: Oral Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19.


  • Incidence of Covid-19–related hospitalization or death by day 28 was 0.77% (3 of 389 patients) in the nirmatrelvir group, with 0 deaths, as compared with 7.01% (27 of 385 patients) in the placebo group, with 7 deaths.
  • The viral load was lower with nirmaltrelvir plus ritonavir than with placebo at day 5 of treatment, with an adjusted mean difference of −0.868 log10 copies per milliliter when treatment was initiated within 3 days after the onset of symptoms.
  • Dysgeusia (5.6% vs. 0.3%) and diarrhea (3.1% vs. 1.6%) occurred more frequently with nirmatrelvir plus ritonavir than with placebo.


S-217622, a 3CL protease inhibitor

Introduction: SARS-CoV-2 has 2 proteases NSP3 papain-like protease PLpro and NSP5 3CL pro (also referred to as Mpro), with complementary cleavage target sites in the Open Reading Frames 1a and 1b, encoding the “non-structural proteins” (amongst which the polymerase complex, the proteases as well as various other NSP with immune-modulatory activities).

The structural proteins are translated from individual (subgenomic) mRNAs, that are transcribed from antigenomic RNA.   (see Ep 244 Cycle and drug targets)

The papain-like protease (PLpro) domain of NSP3 is responsible for the proteolytic cleavage of nsp 1-4. The protein NSP5, or 3C-like protease (3CLpro), is responsible for the processing of other cleavage sites that results in nsp 5-16. NSP4 is uniquely cleaved by NSP3 on the N-terminus and NSP5 on the C-terminus.


Ep 244-4:  Unoh bioRxiv 26 Jan 2022: Preclinical development of S-217622


  • S-217622 exhibited antiviral activity in vitro against all SARS-CoV-2 variants and showed favorable pharmacokinetic profiles in vivo for once-daily oral dosing.
  • Furthermore, S-217622 inhibited intrapulmonary replication of SARS-CoV-2 in mice.


Ep 244-5: Sasaki bioRxiv 15 Feb 2022: extensive studies in hamsters showing clear-cut antiviral effect of S-217622, but also mitigation of body weight loss and lung pathology of infected animals, treated from the day of infection or from the next day. (MPV = Molnupiravir 200 mg/kg)

Reducing transmission: only the contact hamsters were prophylactically treated with S-217622 or MPV (b.i.d.) n, o, Viral RNA levels (n) and virus titers (o) in lungs from the contact hamsters after 6 days of co-housing with the infected hamster


Ep 244-6: Press release on phase 1 and phase 2/3 human trials:


・ A rapid virus reduction effect was confirmed in the S-217622 group compared to placebo.

・ A rapid decrease in proportion of patients with viral titer positively in the S-217622 group compared to placebo.

・ No high-grade or serious adverse events were observed and tolerability wasobserved in this trial.


No preprint or peer-reviewed papers found….




Comparison with PF-07321332 (Paxlovid) in the hamster model


Ep 244-7: Abdelnabi Nat Comm Feb 2022


Fig 2 In vivo efficacy of PF-332 against Beta SARS-CoV-2 (B.1.351)              Fig 3 The effect of treatment with PF-332 on the transmission of the Delta variant to untreated sentinel hamsters


It is difficult to compare two different lab settings but in Fig 2 the same set-up is used (treatment starts at day + 1): the viral load is more suppressed and the body weight better preserved at the highest conc used.

The transmission experiments cannot directly be compared as for S-217622, the contact animal is prophylactically treated, whereas for PF332, the source animal is treated.   


Meta-analysis on drug repurposing


Ep 244-8: Vegivinti provides a very extensive review in BMC Infect Dis Jan 2022 (including publications up to Sept  2021).  The conclusion is sobering:

Clearly, Lopinavir/Ritonavir, hydroxychloroquine, arbidol etc arz considered not really active

No antiviral treatment demonstrated efficacy at reducing COVID-19 mortality.


Remdesivir (in hospitalized patients) exhibited efficacy in reducing need for mechanical ventilation (OR = 0.48) and more rapid discharge from hospital time to recovery (OR = 1.48) , but results were inconsistent across trials.

Sofosbuvir/daclatasvir (originally developed as hepatitis C polymerase inhibitors) results suggested clinical improvement, although statistical power was low.


Ep 244-9: Hsu Int J Antimicrobial Agents Jan 22 selected 8 small studies on Sofosbuvir-based regimens (of which 7 from Iran) and shows moderate benefit.


Combination therapy

Ep 244-10: Wang Communications Biology Feb 2022 Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease

Based on in vitro data, the authors claim that hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir act as exonuclease inhibitors and have a synergistic effect on the polymerase inhibitors Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527.  However, looking at the actual inhibition curves, I’m not very convinced.


What about NSP3 as a drug target?


Ep 244-11: Overview of potential inhibitors of NSP3 and NSP5.

As explained, the protease inhibitors in clinical development today targer NSP5 (3CLpro).  In this paper also potential inhibitors of NSP3 are discussed.  In fact this ORF has two functional domains:

  1. The papain-like protease, which releases NSP1 to 4 from the original polyprotein.
  2. The ADP-ribose phosphatase (ADRP) domain, also known as macrodomain (Mac1) or Macro X domain, which has a crucial role in the viral replication.

The structure of the 2 NSP3 domains

Large screening efforts have been done and some interesting lead inhibitors have been found against PLpro and ADRP. 


So far, no preclinical or clinical development of these inhibitors….  



  1. Remdesivir and Paxlovid now have an established role as early outpatient treatment for subjects at risk for severe complications. Unfortunately, the development of oral Remdesivir has been stopped. See Ep 236: despite encouraging data on outpatient IV treatment and favorable oral treatment in animal models, the development of an oral treatment for humans has been halted.  It is not clear on which oral alternative Gilead will work
  2. S-217622 is a good candidate as a second oral NSP5- 3CL protease inhibitor.  The activity in hamsters might be less than Paxlovid, but clinical studies provide encouraging results, according to the company
  3. The role of Molnupiravir, Sofosbuvir, Sotrovimab remains to be determined.
  4. There is no news on the polymerase inhibitor AT-527.  See Ep 236: AT-527:  interesting compound with good potency in vitro and a double mechanism of action, which may reduce chances on resistance.  After “failed” phase 2, Roche has withdrawn, but ATEA continues development  
  5. NSP3 could be an interesting additional drug target, since it has two druggable domains: a papain-like protease and a ADP-ribosyl phosphatase, for which lead inhibitors have been identified.   

It is very crucial that antiviral treatment is started early (before hospitalization) in subjects at risk for severe disease.  

Results of trials with a logical combination of a polymerase and protease inhibitor are awaited….




Ep 244-12:  Denise Goh in Res Square reports on persistent replicative virus in tissues from 2 patients with long COVID.  In one patient with peritonitis, the appendix tissue was positive and the second patient with ductal breast carcinoma, the surrounding breast tissue was positive. 

Clearly, these are isolated case reports, but there is quite some literature on prolonged shedding from the gastro-intestinal tractus, with also positive biopsies months after the acute phase.


Ep 244-13: Stegger medRxiv 22 Feb 2022 Reinfection with BA.2 after BA.1

Within 1.8 million infections between Nov 22 and Feb 11 in Denmark, there were 187 reinfections (> 20 days and <60 after first infection.

Clearly, reinfection over short time frame is rare (187/1,800,000). 

  • 47 cases of reinfection with the same variant (17 BA.A + 30 delta)
  • 47 cases of BA.2 after BA.1: these were usually mild infections in young (mean 16 years) unvaccinated (68%) subjects.


Ep 244-14: Callaway BA.2 in Nature16 Feb. Largely summarizing what we described in Ep 242.


Ep 244-15: A very nice review by Su Min Pack and Peter J. Peters  providing insight on how “structural vaccinology” has already shaped the present generation of vaccines (e.g. by mutations that enhance the stability and accessibility of neutralization-inducing antigenic sites) and a perspective on how the field will evolve.  Don’t be afraid to start reading: it is didactically explained….


Best wishes,