In a recent study posted to the bioRxiv* pre-print server, a team of researchers discovered S-217622, a non-covalent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3C-like protease (3CLpro) inhibitor clinical candidate, for the treatment of coronavirus disease 2019 (COVID-19).
To date, over 364 million confirmed COVID-19 cases have been reported globally including 5.6 million deaths. Lack of therapy options for treating COVID-19 infections and related hospitalizations necessitates the development of oral COVID-19 treatment options, especially for non-hospitalized patients to minimize the severity of the disease.
Potential drug candidates for COVID-19 treatment include non-covalent, non-peptidic, small molecule inhibitors which need further optimization to achieve appropriate pharmacokinetic (PK) profile and potency against SARS-CoV-2.
About the study
The present study described the discovery of the first non-peptidic, non-covalent SARS-CoV-2 3Clpro inhibitor, S-217622, as a clinical candidate for COVID-19 treatment, along with its preclinical characterization.
The study utilized a structure-based drug design (SBDD) strategy that included a virtual screening based on molecular docking and a biological screening conducted with an in-house
compound library. Interactions between known inhibitors were used as a basis to investigate pharmacophores in the binding site of 3Clpro. The in-house library compounds were docked followed by the application of the pharmacophore filter on each docking pose.
The assessment of 300 top-scoring compounds was conducted by mass spectrometry using enzymatic assays. One of these compounds, compound 1, was of notable significance due to its favorable PK profile. Multiple parameters in compound 1 were optimized to develop the clinical candidate, S-217622. Cytopathic effects of S-217622 on VeroE6/transmembrane serine protease 2 (TMPRSS2) cells evaluated the antiviral ability of the clinical candidate.
The antiviral efficacy of S-217622 was measured in vivo in SARS-CoV-2 Gamma strain-infected mice. The interactions between the receptor-binding domain (RBD) of the spike protein in the Gamma strain and the angiotensin-converting enzyme 2 (ACE2) were promoted by the mutations in the RBD.
The study results showed that compound 1 had in vitro metabolic stabilities of 97% and 71%, respectively, when measured after 30 minutes of incubation in human and rat microsomes. A clearance of 7.3 mL/min/mg and 111% oral bioavailability (F) was observed in the in vivo PK study conducted in rats. On resolving the X-ray complex structure of compound 1 with 3CLpro, the binding mode of compound 1 was found to be similar to that of the protease.
As compared to compound 1, S-217622 exhibited a 90-fold increase in enzymatic inhibitory activity while conserving its drug metabolism and pharmacokinetics (DMPK) profile. S-217622 also displayed biochemical activity with an IC50 value of 0.013 μM and antiviral activity with an EC50 value of 0.37 μM. Furthermore, oral dose-related DMPK profiles like high metabolic stability of 96% and 88% in human and rat microsomes, respectively, high oral absorption of 97%, and a low clearance rate of 1.70 mL/min/mg in rats were observed.
S-217622 also had notable DMPK values in dogs and monkeys as compared to rats, with long half-lives (t1/2) of around 30 hours and 10 hours in dogs and monkeys, respectively, along with low clearance. The drug candidate also exhibited high oral bioavailability in all animals that were tested, indicating significant potential as a once-daily treatment option for COVID-19, without requiring a PK booster like ritonavir. It also exhibited a wide range of usability against all tested SARS-CoV-2 variants.
The antiviral activity of S-217622 against SARS-CoV and SARS-CoV-2 was similar especially at the site where homology of 3CLpro was well conserved. S-217622 also exhibited potent antiviral ability against the Middle East respiratory syndrome (MERS), human coronavirus OC43 (HCoV-OC43), and human coronavirus 229E (HCoV-229E). S-217622 exhibited no inhibitory effect against host-cell proteases, such as cathepsin B/D/G/L, caspase-2, chymotrypsin, and thrombin at up to 100 μM, indicating its high specificity for coronavirus proteases.
The current study findings showed how the SBDD strategy for a de novo search of non-peptidic 3CLpro inhibitors to find an oral therapy for COVID-19 led to the clinical candidate S-217622. The optimization of the structure based on the SBDD strategy enabled 600 times better clinical activity with a good DMPK profile yielded in S-217622. This drug candidate had a favorable preclinical profile as an oral therapeutic drug for the treatment of COVID-19.
The significant antiviral activities of S-217622, in vivo long t1/2 in dogs and monkeys, excellent oral bioavailability, and remarkable efficacy in an in vivo SARS-CoV-2-infected mouse model, have prompted clinical trials on S-217622. This therapeutic candidate also exhibited significant antiviral activity against a wide range of coronavirus variants, indicating its potential as a therapeutic agent in future coronavirus-induced pandemics.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.