7S6W

Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI29

Summary for 7S6W

• Entry DOI: 10.2210/pdb7s6w/pdb
• Descriptor: 3C-like proteinase, (1R,2S,5S)-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (3 entities in total)
• Functional Keywords: main protease, viral protein, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2, COVID-19 virus)
• Total number of polymer chains: 2
• Total formula weight: 68730.43

Authors

Yang, K.S.,Sankaran, B.,Liu, W.R. (deposition date: 2021-09-15, release date: 2022-07-27, Last modification date: 2024-10-23)

Primary citation

Alugubelli, Y.R.,Geng, Z.Z.,Yang, K.S.,Shaabani, N.,Khatua, K.,Ma, X.R.,Vatansever, E.C.,Cho, C.C.,Ma, Y.,Xiao, J.,Blankenship, L.R.,Yu, G.,Sankaran, B.,Li, P.,Allen, R.,Ji, H.,Xu, S.,Liu, W.R.
A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.
Eur.J.Med.Chem., 240:114596-114596, 2022

PubMed Abstract: Boceprevir is an HCV NSP3 inhibitor that was explored as a repurposed drug for COVID-19. It inhibits the SARS-CoV-2 main protease (M) and contains an α-ketoamide warhead, a P1 β-cyclobutylalanyl moiety, a P2 dimethylcyclopropylproline, a P3 tert-butylglycine, and a P4 N-terminal tert-butylcarbamide. By introducing modifications at all four positions, we synthesized 20 boceprevir-based M inhibitors including PF-07321332 and characterized their M inhibition potency in test tubes (in vitro) and 293T cells (in cellulo). Crystal structures of M bound with 10 inhibitors and cytotoxicity and antiviral potency of 4 inhibitors were characterized as well. Replacing the P1 site with a β-(S-2-oxopyrrolidin-3-yl)-alanyl (Opal) residue and the warhead with an aldehyde leads to high in vitro potency. The original moieties at P2, P3 and the P4 N-terminal cap positions in boceprevir are better than other tested chemical moieties for high in vitro potency. In crystal structures, all inhibitors form a covalent adduct with the M active site cysteine. The P1 Opal residue, P2 dimethylcyclopropylproline and P4 N-terminal tert-butylcarbamide make strong hydrophobic interactions with M, explaining high in vitro potency of inhibitors that contain these moieties. A unique observation was made with an inhibitor that contains a P4 N-terminal isovaleramide. In its M complex structure, the P4 N-terminal isovaleramide is tucked deep in a small pocket of M that originally recognizes a P4 alanine side chain in a substrate. Although all inhibitors show high in vitro potency, they have drastically different in cellulo potency to inhibit ectopically expressed M in human 293T cells. In general, inhibitors with a P4 N-terminal carbamide or amide have low in cellulo potency. This trend is reversed when the P4 N-terminal cap is changed to a carbamate. The installation of a P3 O-tert-butyl-threonine improves in cellulo potency. Three molecules that contain a P4 N-terminal carbamate were advanced to cytotoxicity tests on 293T cells and antiviral potency tests on three SARS-CoV-2 variants. They all have relatively low cytotoxicity and high antiviral potency with EC values around 1 μM. A control compound with a nitrile warhead and a P4 N-terminal amide has undetectable antiviral potency. Based on all observations, we conclude that a P4 N-terminal carbamate in a boceprevir derivative is key for high antiviral potency against SARS-CoV-2.

PubMed: 35839690
DOI: 10.1016/j.ejmech.2022.114596

Experimental method

X-RAY DIFFRACTION (2.29 Å)