Novel inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives

The global emergence of SARS-CoV-2 has triggered numerous efforts to develop therapeutic options for COVID-19 pandemic. The main protease of SARS-CoV-2 (Mpro), which is a critical enzyme for transcription and replication of SARS-CoV-2, is a key target for therapeutic development against COVID-19. An organoselenium drug called ebselen has recently been demonstrated to have strong inhibition against Mpro and antiviral activity but its molecular mode of action is unknown preventing further development. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of ebselen derivatives. A free selenium atom bound with cysteine 145 of Mpro catalytic dyad has been revealed by crystallographic studies of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct, formation of a phenolic by-product is confirmed by mass spectrometry. The target engagement of these compounds with an unprecedented mechanism of SARS-CoV-2 Mpro inhibition suggests wider therapeutic applications of organo-selenium compounds in SARS-CoV-2 and other zoonotic beta-corona viruses.


Introduction
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic of corona virus disease 2019 (COVID- 19) with confirmed infection cases of over 70 million and 1.5 million fatalities within a year. SARS-CoV-2 is the most devastating zoonotic coronavirus to infect humans following SARS-CoV-1 and MERS-CoV (Middle East respiratory syndrome) which emerged in 2002 and 2012, respectively 1 . Similar to the other coronaviruses, SARS-CoV-2 primarily infects the respiratory system and develops critical pneumonia that highly necessitates ventilatory support and intensive care, particularly in elderly and immunocompromised individuals 2 . Whilst there have been tremendous strides forward in the development of vaccines, the current roll-out is supply and time limited. Several vaccine candidates have been developed in advance stage and recently approved for mass immunity first in the UK 3 . However, some effective vaccines need to be stored at deep freeze temperatures that may not be deployable in developing areas of the world. Moreover, some mutations in SARS-CoV-2 genome may impact the effectiveness of developing vaccines to control the virus 4,5 . These underline the requirement for the parallel development of therapeutic options for SARS-CoV-2 treatment.
SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA virus with a large genome of about 30,000 nucleotides. The whole genome of SARS-CoV-2 is 96% identical to a bat coronavirus and closely related to SARS-CoV-1 with 80% sequence identity 6 . Two overlapping polyproteins, pp1a and pp1ab, are encoded by the replicase gene (ORF 1a/1b) that constitutes two-thirds of the genome. The remainder of the genome encodes for accessory and structural proteins such as the spike glycoprotein, envelope protein, matrix protein and the nucleocapsid phosphoprotein 7 . pp1a and pp1ab are proteolytically digested into 15 non-structural proteins (NSPs) by the two viral proteases. The 33.8kDa main protease (M pro ) or NSP5 is responsible for cleaving polyproteins at 11 cleavage sites giving NSP4-9 and NSP12-15. The released NSPs form the viral RNA polymerase complex are involved in replication and transcription of fresh virus in the host. Due to vital function of in SARS-CoV-2 life cycle and absence of homologous proteins in human, M pro has been extensively explored by high-throughput screening of re-purposed druggable compounds 8 and fragments 9 to devise effective inhibitors aimed at arresting the growth of SARS-CoV-2 in host's cell.
SARS-CoV-2 M pro is a homodimeric enzyme consisting of three domains 8 . The substrate-binding site with a catalytic dyad of His41 and Cys145 is located between chymotrypsin-like domains I and picornavirus 3C protease-like domain II. Domain III plays an important role in M pro dimerization through a salt-bridge interaction between protomers. Several inhibitors and fragments have been co-crystallised and identified to block catalytic cavity [8][9][10] .
Ebselen is an organo-selenium molecule that can function as a glutathione peroxidase and peroxiredoxin mimic 11 . It has been shown to form a selenosulphide bond with thiol groups of cysteine (Cys) on a number of proteins which results in anti-inflammatory, anti-microbial and neuroprotective effects [12][13][14] . Moreover, ebselen is being investigated in clinical trials as a potential therapy for stroke, hearing loss and bipolar disorder with good safety profiles with no adverse effects [15][16][17] . Recently, ebselen was identified in high-throughput screen as a potential hit of SARS-CoV-2 M pro inhibitor. Molecular dynamics simulations suggested that ebselen is able to bind at two probable sites 18 . One is at Cys145 within the catalytic cavity through a selenosulphide bond, and another is at the dimerization region. However, no experimental data for the site of its binding in SARS-CoV-2 M pro has become available.
In our previous work, we have designed CNS penetrant ebselen-based derivatives and demonstrated their good neuroprotective effects and low cytotoxicity in cell-based and mouse models of motor neuron disease 19 .
Here, ebselen and five derivatives were assessed for their inhibition of SARS-CoV-2 M pro and anti-coronaviral activity. Two of these ebselen-based selenium compounds exhibit greater inhibitory effectiveness than ebselen against M pro enzyme and SARS-CoV-2 replication. We show from co-crystallographic studies of M pro enzyme with ebselen and another potent compound (MR6-31-2) that these compounds solely bind at the M pro catalytic site by donating a selenium atom, forming a covalent bond and blocking the histidine-cysteine catalytic dyad. We propose that the ebselen-enzyme drug protein adduct is hydrolysed by the conserved water in the catalytic pocket.
The release of phenol by-product has been confirmed by mass spectrometry studies of M pro incubated with compounds. This novel unpreceded mechanism of inhibition and direct observation of covalent binding of the selenium atom together with sub-micromolar antiviral activity provides a rational for utilising ebselen as potential therapy and improving selenium-based compounds using the ebselen scaffold for greater anti-coronaviral activity.

M pro enzymatic and antiviral activities of ebselen and derivatives
In our previous study, ebselen and some selenium-based derivatives have were developed as neuroprotective agents in relation to motor neuron disease 19 . The co-crystalised structures of those compounds with superoxide dismutase 1 (SOD1) were proven to form a selenylsulphide bond with Cys111 at dimer interface.
Thus, ebselen and derivatives were considered for their reactivity with Cys145 and their potential for impairing proteolytic activity of M pro in an attempt to arrest the growth of SARS-CoV-2. A fluorescence resonance energy transfer assay was conducted to evaluate the inhibition level against M pro enzyme of ebselen and five other selenium-based derivatives. Fig. 1 shows chemical structures, inhibitory curves against M pro and the half-maximal inhibitory concentrations (IC50s) for each of the compounds. The data clearly demonstrates that these compounds including ebselen are potent M pro inhibitor with sub-micromolar levels of IC50. Some compounds are twice as effective for M pro inhibition than the parent ebselen, especially MR6-7-2 and MR6-18-2. All of these compounds were also assessed for in vitro antiviral activity against SARS-CoV-2 infected human Vero cells. All of the compounds tested were somewhat superior to ebselen with MR6-31-2 being nearly three times more effective with an EC50 of 1.8 M (Fig. 1g). These results indicate clear on-target interaction of these compounds with M pro with significant inhibitory power for SARS-CoV-2 and as such potential for development as treatments for COVID-19 patients.

Structures M pro with ebselen and MR6-31-2 reveal selenium atom bound in catalytic site.
The interaction of ebselen and its derivative with M pro was directly visualised by co-crystallisation of organoselenium compounds with M pro . The structures of ligand-free and M pro complexes with ebselen and MR6-31-2 have been solved at the resolution of 1.6-2.0Å. The statistics of data collection and structure refinement is summarised in Table 1 for ligand-free M pro , M pro -ebselen and M pro -MR6-31-2. There is only one M pro protomer found in asymmetric unit where the global structures are almost identical (Fig. 2a). The M pro catalytic site including cysteine-histidine dyad of individual structures are given in Fig. 2b-c. Electron density is clearly visible and allowing amino acid residues and water molecules to be defined accurately. Interestingly, a clear patch of electron density is observed between Cys145 and His41 in co-crystallised crystals of M pro -ebselen and M pro -MR6-31-2. This density is too strong to be a water, but the size is too small for the corresponding complete inhibitors.
To identify the origin of this clear density, anomalous electron density map of selenium was calculated from diffraction data using X-ray at the wavelength near selenium absorption edge (0.97Å). No selenium anomalous density is observed in ligand-free enzyme (Fig. 2b), but a strong density is present only at the cysteine-histidine catalytic dyad in ligand-treated M pro structures ( Fig. 2c and 2d). Thus, selenium atom was modelled into the density with the distances of 2.2 Å away from Cys145 and His41. Calculated B-factor suggest that the occupancy of selenium in M pro -ebselen and M pro -MR6-31-2 crystals are 60% and 80%, respectively. These data are consistent with ebselen and MR6-31-2 primarily binding at M pro catalytic pocket and form a selenyl-sulphide bond with Cys145. There was no density associated with the organic backbone of either ebselen or MR6-31-2 in the cocrystallographic structures. As only selenium atom is observed in the enzyme's active site, it is the inactivation of cysteine by selenium that results in the inhibition of M pro activity and viral replication. Interestingly, selenium binding does not affect the conformation of surrounding amino acid residues within the active site. According to crystallographic evidence, we noted that ebselen and selenium-based derivatives have unusual mode of action by selenation of M pro catalytic dyad.

LC-MS characterization of salicylanilide generated by hydrolysis of ebselen.
Co-crystalised structures of M pro with ebselen and MR6-31 -2 demonstrated that the compounds would inhibit by selenation at Cys145 of catalytic dyad. This evidence suggests that the compounds may be hydrolysed within M pro active site that releases its phenolic by-product (salicyanilide for ebselen, Fig. 3a). In order to identify the hydrolysis product derived from M pro -ebselen adduct, LC/MRM-MS method was optimized using standard salicyanilide. A representative chromatogram from standard salicyanilide (85.2 ng/mL) is shown in Fig. 3a.
Samples obtained from the incubation of ebselen showed strong peaks at 6.37 minutes corresponding to salicylanilide (Fig. 3b). The MS/MS spectrum of molecular ion at m/z 214 showed product ions at m/z 121 and m/z 94, which are attributed to the ions derived from the cleavage of the amide bond (Fig. 3c). To measure the levels of salicyanilide formed in the incubation, an 8-point calibration line was generated for salicylanilide in BSA (r 2 = 0.99, data not shown). The measured concentration of salicylanilide in these samples after 240 minutes was 1.28 ng/ml. The formation of salicyanilide in the incubation of M pro with ebselen is time dependent (Fig. 3d).

Discussion
From a chemical mechanism of action perspective, we fully expected to see the SARS-CoV-2 M pro drugadduct 2 from ebselen 1, through nucleophilic attack of the Cys145 thiolate on the electrophilic selenium centre as shown in Fig. 4. Unlike other M pro covalent inhibitors 8,20,21 , the organic framework of ebselen was not present in the co-crystallographic structures with evidence of extrusion of selenium from the ebselen core in an unprecedented reaction at a cysteine protease active site. We propose that His41 can assist a water mediated attack on intermediate adduct 2 in an SNAr type hydrolysis reaction with intermediate 3 possibly stabilised in a manner akin to peptide hydrolysis tetrahedral intermediates within the oxyanion hole of the active site. With increased activity in the drug-design field in the covalent modification of catalytic and non-catalytic thiols, there have been several reports of aromatic warheads tuned with leaving groups (halides for example) to enable nucleophilic aromatic substitution, so the SNAr aspect of the proposed mechanism is with precedent [22][23][24] . Based on this mechanism, we would expect to see the generation of the hydrolysis product 4. Using LCMS analysis of the SARS-CoV-2 M pro and comparison with a commercial of 4, we were able to show that 4 is generated from ebselen by the enzyme in a time-dependent manner. This provides strong support for our proposed mechanism for selenation of the SARS-CoV-2 M pro active site.
We have succeeded in obtaining co-crystallographic structure of M pro grown with ebselen and its derivative MR6-31-2, showing selenium coordinates directly to Cys145 upon hydrolysis of the organoselenium compounds. The clear target engagement paves the way for further development for more effective delivery to the catalytic cysteine and greater inhibition whilst having an acceptable safety profile. Though our study is of clear immediate interest for SARS-CoV-2, it has wider therapeutic applications of organo-selenium compounds by novel chemical mechanism of the selenation of cysteines of proteases in other current zoonotic beta coronaviruses and those that may emerge in the future.

Synthesis of compounds
Ebselen was obtained from a commercial supplier (Sigma Aldrich). Other lead compounds were produced and purified at Department of Chemistry, University of Liverpool. Details of the synthesis of ebselenbased derivatives have been described in our previous report 19 .

M pro inhibition activity assay
The inhibition activity assays were performed using 0. EnVision multimode plate reader (Perkin Elmer). Initial rate was obtained using the data from the first 10 min by linear regression. To exclude inhibitors possibly acting as aggregators, a detergent-based control was performed by adding 0.01% freshly made-up Triton X-100 to the reaction at the same time. The IC50 was calculated by plotting the inhibition rate against various concentrations of testing inhibitor by using a four parameters dose−response curve in GraphPad Prism software. All experiments were performed in triplicate.

Antiviral activity assay
A clinical isolate of SARS-CoV-2 (nCoV-2019BetaCoV/Wuhan/WIV04/2019) was propagated in Vero E6 cells, and viral titer was determined as described previously 25 . For the antiviral assay, pre-seeded Vero E6 cells wavelength at 3.0Å resolution. The data was integrated by using DIALS 26 and scaled by using Aimless 27 . Phase problem was solved by molecular replacement with MOLREP 28 using a SARS-CoV-2 M pro structure (PDB: 6Y2E) as an initial model. Structure models were edited manually in COOT 29 and refined by using Refmac5 30 .
Geometry and quality of final models were validated by using MolProbity 31 .

Liquid chromatography-mass spectrometry (LC-MS).
10mg/mL M pro in 25mM ammonium bicarbonate pH 7.5 (20 µL) was incubated with 1mM ebselen at 37 o C for 0, 2, and 4 h. At the end of incubation, 2.5mM acetaminophen (10 µL) was added as an internal standard to normalize extraction. Then, loading and compounds of interest were extracted by adding ice-cold acetone (250 µL). Standard curve was constructed by spiking salicylanilide (concentration range: 0.1-0.8 µM) into 10mg/mL bovine serum albumin (BSA) solution. After centrifugation at 14000 rpm for 20 min, the extracts were transferred to clean tubes and evaporated in a Speed Vac and reconstituted in 50 µL 30% ACN/0.1% formic acid. 10 µL samples and standards were analysed immediately by a QTRAP 5500 mass spectrometer (AB Sciex,) coupled with an Ultimate 3000 HPLC system (Dionex, ThermoScientific) and a Kinetex C18 column (2.6uM, C18, 50mm x 2.1mm, Phenomenex, Maclesfield, Cheshire, UK). The MS experiments were conducted using electrospray ionization with positive ion detection. A gradient program of acetonitrile (5% for 1 min; 5% to 95% over 5 min; 95% for 2 min; 95% to 5% over 0.1 min; 5% for 4 min) in 0.1% formic acid (v/v) was applied at a flow rate of 300 µL/min. The multiple reaction monitoring transitions for each analyte were as following: salicylanilide