Analysis of the efficacy of HIV protease inhibitors against SARS-CoV-2′s main protease

Abstract

Background The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of infections worldwide. While the search for an effective antiviral is still ongoing, experimental therapies based on repurposing of available antivirals is being attempted, of which HIV protease inhibitors (PIs) have gained considerable interest. Inhibition profiling of the PIs directly against the viral protease has never been attempted in vitro, and while few studies reported an efficacy of lopinavir and ritonavir in SARS-CoV-2 context, the mechanism of action of the drugs remains to be validated. Methods We carried out an in-depth analysis of the efficacy of HIV PIs against the main protease of SARS-CoV-2 (Mpro) in cell culture and in vitro enzymatic assays, using a methodology that enabled us to focus solely on any potential inhibitory effects of the inhibitors against the viral protease. For cell culture experiments a dark-to-bright GFP reporter substrate system was designed. Results Lopinavir, ritonavir, darunavir, saquinavir, and atazanavir were able to inhibit the viral protease in cell culture, albeit in concentrations much higher than their achievable plasma levels, given their current drug formulations. While inhibition by lopinavir was attributed to its cytotoxicity, ritonavir was the most effective of the panel, with IC50 of 13.7 µM. None of the inhibitors showed significant inhibition of SARS-CoV-2 Mpro in our in vitro enzymatic assays up to 100 µM concentration. Conclusion Targeting of SARS-CoV-2 Mpro by some of the HIV PIs might be of limited clinical potential, given the high concentration of the drugs required to achieve significant inhibition. Therefore, given their weak inhibition of the viral protease, any potential beneficial effect of the PIs in COVID-19 context might perhaps be attributed to acting on other molecular target(s), rather than SARS-CoV-2 Mpro.

SARS-CoV-2 Mpro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors

“…Furthermore, from a computational point of view, docking studies have shown that ritonavir possesses a low affinity score (−6.4 kcal/mol) in comparison to other HIV protease inhibitors docked on M pro . While the IC 50 value of lopinavir proved to be rather unfavorable, ritonavir was the most effective among the panel of tested compounds by Mahdi M. and co-workers, with IC 50 of 13.7 µM [ 53 , 54 ]. Therefore, lopinavir was progressively replaced with other commercially available antiviral drugs in the protease inhibitor combinations.…”

Drug repurposing for COVID-19: Approaches, challenges and promising candidates

“…Following viral RNA replication comes the translation and proteolytic processing of viral proteins. Here, HIV protease inhibitors such as atazanavir, saquinavir and ritonavir were considered as repurposing candidates against SARS-CoV-2's 3C-like protease alongside danoprevir, a hepatitis C protease inhibitor ( Chen et al, 2020 ; Mahdi et al, 2020 ). Disulfiram and famotidine were also proposed as repurposing candidates against SARS-CoV-2's papain-like protease ( Lin et al, 2018 ; Samimagham et al, 2020 ).…”

Repurposed Therapeutic Strategies towards COVID-19 Potential Targets Based on Genomics and Protein Structure Remodeling

“…Saquinavir [DB01232] inhibiting HIV1/2 protease-mediated lysis of HIV gag and pol polyproteins was found cytotoxically active at conc. Above 50 μM [56]. Rupintrivir (DB05102) a broad-spectrum antiviral agent is a potent 3C-Like protease inhibitor against norovirus, picornavirus, and coronavirus proteases in development against human rhinoviral (HRV) infections that has been recently co-crystallized with its target [57].…”