Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Abstract

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for Mpro-ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to Mpro. Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease

“…One strategy for designing novel, drug-like, noncovalent compounds is the optimization of low-affinity hits that are existing drugs with known pharmacokinetic properties. We have previously reported the optimization of the antiepileptic drug perampanel, initially identified in a virtual screen, from a weak inhibitor of M pro (half-maximal inhibitory concentration [IC 50 ] 100–250 μM), to several lead compounds with activities in the low-nanomolar range by means of an iterative approach complementing free-energy perturbation calculations and compound synthesis with structural characterization ( Ghahremanpour et al., 2020 ; Zhang et al., 2021 ). Moreover, this lead optimization approach yielded compound 26 , which showed promising antiviral activity (half-maximal effective concentration [EC 50 ] 2.0 ± 0.7 μM) and cytotoxicity (half-maximal cytotoxic concentration [CC 50 ] >100 μM) ( Zhang et al., 2021 ).…”

“…We have previously reported the optimization of the antiepileptic drug perampanel, initially identified in a virtual screen, from a weak inhibitor of M pro (half-maximal inhibitory concentration [IC 50 ] 100–250 μM), to several lead compounds with activities in the low-nanomolar range by means of an iterative approach complementing free-energy perturbation calculations and compound synthesis with structural characterization ( Ghahremanpour et al., 2020 ; Zhang et al., 2021 ). Moreover, this lead optimization approach yielded compound 26 , which showed promising antiviral activity (half-maximal effective concentration [EC 50 ] 2.0 ± 0.7 μM) and cytotoxicity (half-maximal cytotoxic concentration [CC 50 ] >100 μM) ( Zhang et al., 2021 ). This effort provides the most extensive description to date of several noncovalent inhibitors of M pro derived from an FDA-approved chemical scaffold with in vitro activities that improve upon activities of recently described covalent inhibitors ( Dai et al., 2020 ; Zhang et al., 2020 , 2021 ).…”

Interaction of selected terpenoids with two SARS-CoV-2 key therapeutic targets: An in silico study through molecular docking and dynamics simulations

“…Hydrophobic patches are found at the Mpro binding site, in particular at S1, S2 and S4 subsites, and hydrophobic interactions have been extensively targeted in several studies to improve binding affinities of inhibitors towards Mpro [ [46] , [47] , [48] , [49] ].…”

“…The mechanism of action of a covalent inhibitor, such as N3, containing carbonyl groups [ 54 ] or Michael acceptors [ 55 ], consists in blocking the activity of the cysteine protease covalently, modifying the catalytic Cys145 residue in the S1’ region [ 48 ]. Several publications reported covalent inhibitors that target the catalytic cysteine, while other studies identified non-peptide and non-covalent inhibitors, such as compound 1 [ 47 ] ( Fig. 3 ), that claim the active site region hampering the proteolytic activity of the enzyme.…”

Prioritisation of Compounds for 3CLpro Inhibitor Development on SARS-CoV-2 Variants

“…Glutamine at the P1 position is crucial for proteolysis to occur. As there are no known native human enzymes with such cleavage sites, M pro looks to be an ideal drug target, since there is a low risk for toxic effects on host cells [ 31 , 32 , 33 ]. Structural data on the enzyme is available and reporter assays developed making this target suitable for novel antiviral design [ 34 , 35 ].…”