Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease

Abstract

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic. The main protease (Mpro, 3CLpro) of SARS-CoV-2 is a key enzyme that processes polyproteins translated from the viral RNA. Mpro is therefore an attractive target for the design of inhibitors that block viral replication. We report the diastereomeric resolution of the previously designed SARS-CoV-2 Mpro α-ketoamide inhibitor 13b. The pure (S,S,S)-diastereomer, 13b-K, displays an IC50 of 120 nM against the Mpro and EC50 values of 0.8–3.4 μM for antiviral activity in different cell types. Crystal structures have been elucidated for the Mpro complexes with each of the major diastereomers, the active (S,S,S)-13b (13b-K), and the nearly inactive (R,S,S)-13b (13b-H); results for the latter reveal a novel binding mode. Pharmacokinetic studies show good levels of 13b-K after inhalative as well as after peroral administration. The active inhibitor (13b-K) is a promising candidate for further development as an antiviral treatment for COVID-19.

Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)

“…It was also anticipated that oxidation of the thioether to generate a new stereocenter would allow optimal stereochemical control and furnish a new locus for H-bonding interactions. The warhead (Z) was chosen to be an aldehyde or latent aldehyde bisulfite adduct, however, for comparative purposes, we also interrogated the effect on potency of an α-ketoamide [ 15 , 31 , 32 ] or masked α-ketoamide [ 33 ], and nitrile [ 24 , 34 ] warheads, as well as the effect of deuteration, on potency [ 35 ].…”

Therapeutic strategies for COVID-19: progress and lessons learned

“…Each subunit of the M pro homodimer possesses a catalytic dyad that is formed by a nucleophilic cysteine at position 145 (Cys145) and a nearby histidine residue at position 41 (His41) 73 , 74 . The M pro catalytic dyad catalyses the formation of a covalent carbon–sulfur bond between the Cys145 thiolate and the main-chain carbonyl of the substrate’s P1 glutamine 75 (Fig.…”

Advanced crystallisation methods for small organic molecules

“…Work by Marsh, Maple, Hilgenfeld and co-workers examined a series α-ketoamides inhibitors of M pro . 117 To support this work, the ENaCt methodology was applied to aid in the determination of their relative and absolute stereochemistry. Single crystals of an example α-ketoamide inhibitor were grown and the absolute stereochemistry determined to be C10( S ), C12( S ) and C17( R ) by anomalous dispersion (Flack: −0.06) (Fig.…”