A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals

Alugubelli, Yugendar R; Geng, Zhi; Yang, Kun; Shaabani, Namir; Khatua, Kaustav; Ma, Xinyu; Vatansever, Erol C.; Cho, Chia-Chuan; Ma, Yuying; Xiao, Jing; Blankenship, Lauren R.; Yu, Ge; Sankaran, Banumathi; Li, Pingwei; Allen, Robert D.; Ji, Henry; Xu, Shiqing; Liu, Wenshe Ray

doi:10.1016/j.ejmech.2022.114596

Cited by 35 publications

(38 citation statements)

References 46 publications

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“…Our previously works showed that O-t- butyl-L-threonine ( l ) as the P3 residue in tripeptidyl M Pro inhibitors led to high cellular and antiviral potency. 4, 5 We included this residue at the P2 site as well hoping to observe a similar effect. The N -terminal groups were chosen between carboxybenzyl (CBZ, a ), 3-chloro-CBZ ( b ), 3-acetoxy-CBZ ( c ), 4-chloro-2-fluorocinnamoyl ( d ), 1 H -indole-2-carbonyl ( e ), 4-methoxyl-1 H -indole-2-carbonyl ( f ), and trifluoroacetyl ( g ).…”

Section: Resultsmentioning

confidence: 99%

A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease

Geng¹,

Atla²,

Shaabani

et al. 2023

Preprint

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SARS-CoV-2 is the coronavirus pathogen of the currently prevailing COVID-19 pandemic. It relies on its main protease (MPro) for replication and pathogenesis. MPro is a demonstrated target for the development of antivirals for SARS-CoV-2. Past studies have systematically explored tripeptidyl inhibitors such as nirmatrelvir as MPro inhibitors. However, dipeptidyl inhibitors especially those with a spiro residue at their P2 position have not been systematically investigated. In this work, we synthesized about 30 reversibly covalent dipeptidyl MPro inhibitors and characterized them on in vitro enzymatic inhibition potency, structures of their complexes with MPro, cellular MPro inhibition potency, antiviral potency, cytotoxicity, and in vitro metabolic stability. Our results indicated that MPro has a flexible S2 pocket that accommodates dipeptidyl inhibitors with a large P2 residue and revealed that dipeptidyl inhibitors with a large P2 spiro residue such as (S)-2-azaspiro[4,4]nonane-3-carboxylate and (S)-2-azaspiro[4,5]decane-3-carboxylate have optimal characteristics. One compound MPI60 containing a P2 (S)-2-azaspiro[4,4]nonane-3-carboxylate displayed high antiviral potency, low cellular cytotoxicity, and high in vitro metabolic stability and can be potentially advanced to further preclinical tests.

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Section: Resultsmentioning

confidence: 99%

A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease

Geng¹,

Atla²,

Shaabani

et al. 2023

Preprint

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“…This region is part of the M Pro active site, serving as a cap of the protein S2 site to bind the P2 residue in a peptide substrate (Figure 1A). 26,30,31 The electron density of this region was very weak in all of the determined M Pro −inhibitor structures, indicating a highly flexible conformation (Figures 1B and S4). There have been many other M Pro −inhibitor complexes whose crystal structures have been determined and deposited into the Protein Data Bank.…”

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confidence: 83%

“…This is also the approach that we have adopted for the development of M Pro inhibitors . To facilitate a quick determination of M Pro –inhibitor complexes, we have crystallized the apo form of M Pro and then soaked the crystals with different inhibitors for the ensuing X-ray protein crystallographic analysis. − Our obtained apo M Pro crystals belong to space group C 121 or I 121, containing an M Pro dimer or monomer, respectively, in the asymmetric unit. These crystals are different from other reported M Pro crystal forms.…”

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confidence: 97%

“…Therefore, we have soaked these apo M Pro crystals with different inhibitors for the determination of crystal structures of more than 30 M Pro –inhibitor complexes. ,, One unique observation that we have made for almost all of our determined M Pro –inhibitor structures is a poorly defined conformation for the aa46–50 region. This region is part of the M Pro active site, serving as a cap of the protein S2 site to bind the P2 residue in a peptide substrate (Figure A). ,, The electron density of this region was very weak in all of the determined M Pro –inhibitor structures, indicating a highly flexible conformation (Figures B and S4). There have been many other M Pro –inhibitor complexes whose crystal structures have been determined and deposited into the Protein Data Bank. − A lot of them have a clearly defined conformation for aa46–50.…”

mentioning

confidence: 99%

“…Therefore, we have soaked these apo M Pro crystals with different inhibitors for the determination of crystal structures of more than 30 M Pro − inhibitor complexes. 26,30,31 One unique observation that we have made for almost all of our determined M Pro −inhibitor structures is a poorly defined conformation for the aa46−50 region. This region is part of the M Pro active site, serving as a cap of the protein S2 site to bind the P2 residue in a peptide substrate (Figure 1A).…”

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confidence: 99%

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A Novel Y-Shaped, S–O–N–O–S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease

et al. 2023

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As the COVID-19 pathogen, SARS-CoV-2 relies on its main protease (MPro) for pathogenesis and replication. During crystallographic analyses of MPro crystals that were exposed to the air, a uniquely Y-shaped, S–O–N–O–S-bridged post-translational cross-link that connects three residues C22, C44, and K61 at their side chains was frequently observed. As a novel covalent modification, this cross-link serves potentially as a redox switch to regulate the catalytic activity of MPro, a demonstrated drug target of COVID-19. The formation of this linkage leads to a much more open active site that can potentially be targeted for the development of novel SARS-CoV-2 antivirals. The structural rearrangement of MPro by this cross-link indicates that small molecules that lock MPro in the cross-linked form can potentially be used with other active-site-targeting molecules such as paxlovid for synergistic effects in inhibiting SARS-CoV-2 viral replication.

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The S1′–S3′ Pocket of the SARS‐CoV‐2 Main Protease Is Critical for Substrate Selectivity and Can Be Targeted with Covalent Inhibitors

Liu,

Li,

Liu

et al. 2023

Angewandte Chemie

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The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a well‐characterized target for antiviral drug discovery. To date, most antiviral drug discovery efforts have focused on the S4‐S1’ pocket of Mpro; however, it is still unclear whether the S1’‐S3’ pocket per se can serve as a new site for drug discovery. In this study, the S1’‐S3’ pocket of Mpro was found to differentially recognize viral peptidyl substrates; for instance, S3’ in Mpro strongly favors Phe or Trp, and S1’ favors Ala. The peptidyl inhibitor D‐4‐77, which possesses an α‐bromoacetamide warhead, was discovered to be a promising inhibitor of Mpro, with an IC50 of 0.95 µM and an antiviral EC50 of 0.49 µM. The Mpro/inhibitor co‐crystal structure confirmed the binding mode of the inhibitor to the S1’‐S3’ pocket and revealed a covalent mechanism. In addition, D‐4‐77 functions as an immune protectant and suppresses SARS‐CoV‐2 Mpro‐induced antagonism of the host NF‐κB innate immune response. These findings indicate that the S1’‐S3’ pocket of SARS‐CoV‐2 Mpro is druggable, and moreover, inhibiting SARS‐CoV‐2 Mpro can simultaneously protect human innate immunity and inhibit virion assembly.

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A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals

Cited by 35 publications

References 46 publications

A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease

A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease

A Novel Y-Shaped, S–O–N–O–S-Bridged Cross-Link between Three Residues C22, C44, and K61 Is Frequently Observed in the SARS-CoV-2 Main Protease

The S1′–S3′ Pocket of the SARS‐CoV‐2 Main Protease Is Critical for Substrate Selectivity and Can Be Targeted with Covalent Inhibitors

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