Ebselen as a highly active inhibitor of PL^ProCoV2

Abstract

Since December 2019 a novel a coronavirus identified as SARS-CoV-2 or COV2 has been spreading around the world. On the 16th of May around 4.5 million people got infected and over 300,000 died due to the infection of COV2. The effective treatment remains a challenge. Targeted therapeutics are still under investigation. The papain-like protease (PL Pro ) from the human SARS-CoV-2 coronavirus is a cysteine protease that plays a critical role in virus replication. Its activity is required to process the viral polyprotein into functional, mature subunits. Moreover, COV2 uses this enzyme to modulate the host's immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. In this work, we discovered that ebselen, a synthetic organoselenium drug molecule with anti-inflammatory, anti-oxidant and cytoprotective activity in mammalian cells and cytotoxicity in lower organisms, is a highly active inhibitor of PL Pro CoV2. We proved that ebselen is a covalent, fast-binding inhibitor of PL Pro CoV2 exhibiting a low micromolar potency. Furthermore, we identified a difference between PL Pro from SARS-CoV-1 (the corona virus which caused the 2002-2004 outbreak, SARS) and SARS-CoV-2 that allows to explain the difference in dynamics of the replication, and, thus, the disease progression. Namely, we present that they show differences in the binding affinity of substrates that we observed through kinetics and molecular docking studies. Using a novel Approximate Bayesian Computation method we were able to find kinetic constants for both enzymes. Molecular modeling study on the structure of the active site and binding mode of the ebselen with SARS and COV2 showed also significant differences that could explain our observation that ebselen is less active and slower bounding with SARS than COV2. In conclusion, we show that ebselen inhibits the activity of the essential viral enzyme papain-like protease (PLpro) from SARS-COV-2 in low micromolar range.

Discovery of potent inhibitors of PLproCoV2 by screening a library of selenium-containing compounds

“…Organoselenium compounds were found to be irresistible inhibitors toward both enzymes. Similar to recently published ebselen [12] they show irreversibility of the mode of action. All of phenylbenzisoselenazol-3(2 H )-ones inactivated completely PL pro Cov2 in concentration equal 20μM (see Table 1).…”

“…However, 1d , 1e , 2d and 2e inhibited PL pro CoV2 at this concentration. The investigation of IC 50 revealed that 1d , 1e , 2d and 2e obtained approximately 250 nM that is one magnitude better than in the case of ebselen (around 2 μ M as reported in [12]).…”

“…Previously, these derivatives were proven to be highly effective towards human methionine aminopeptidase 2 [19] and antiviral and antimicrobial agents [20]. We show that some of them indeed possess higher activity than ebselen, that has been recently reported as PL pro CoV2 inhibitor [12], and, thus, could be considered as novel potential drugs against COVID-19. Organoselenium compounds were found to be irresistible inhibitors toward both enzymes.…”

“…The most significant results obtained in this study were further illustrated with molecular modeling (Figure 1 and 2). The modeled interactions do not show significant changes in the overall binding mode architecture compared with the ebselen-PL pro CoV2 [12]. Similar to ebselen complexes with enzyme, hydroxyl derivative occupies the same intersection between catalytic Cys111-His272-Asp286 triad and Trp106 and it is wrapped by other Tyr268, Ala289 and Leu298 making with 6 them face-to-edge stacking and π-alkyl interactions, respectively (Figure 1).…”

“…The identification of SARS-CoV-2 PL pro as an essential viral enzyme [10] offers a great possibility for drug discovery. In recent studies, peptide analogues [11] and ebselen [12] have been identified as highly active inhibitors for PL pro . Ebselen is a seleno-organic drug with well-known anti-inflammatory, anti-atherosclerotic, cytoprotective properties and low toxicity in humans [13].…”