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

Abstract

BackgroundThe 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. MethodsWe 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.ResultsLopinavir, 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. ConclusionTargeting 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.

Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields

“…However, 11r was not identified as a strong binder with c36. From the experimental data 25,62 , the binding free energies of 11r, 13a, 13b, darunavir ligands were -9.23, -7.70, -8.45, and -6.14 kcal/mol, respectively. In terms of consistency with experimental data, MM-PBSA with ffSB99 correctly identified 11r as the strongest binder.…”

A detailed review of the outbreak of COVID-19

“…The drug proved effective in reducing the fever [81] and the duration of the hospital stay [82] but could not obtain desired outcome in open-label randomised clinical trials [83]. Moreover, questions have been raised for the drug's effectiveness against 3CLpro as its structure is very different from the HIV proteases [84]. Thus, WHO has put off Lopinavir-ritonavir from the solidarity trails for COVID-19 [85].…”

Spiking dependence of SARS‐CoV‐2 pathogenicity on TMPRSS2

“…These social distancing measures can slow down but cannot stop the spread of SARS‐CoV‐2 unless a significant population of the world has contracted the virus 19 . In addition to the destruction caused by SARS‐CoV‐2, the nonavailability of viable drugs like antivirals against this new disease makes the condition challenging to deal with 20 . In the review, we have evaluated the role of TMPRSS2 protease in SARS‐CoV‐2 infection and how differences in respiratory expression of this protease can explain the associated discrepancy in SARS‐CoV‐2 infection and COVID‐19 outcomes.…”