Allosteric inhibitors of the main protease of SARS-CoV-2

Samrat, Subodh Kumar; Xu, Jimin; Xie, Xuping; Gianti, Eleonora; Chen, Haiying; Zou, Jing; Pattis, Jason G.; Elokely, Khaled M.; Lee, Hyun; Li, Zhong; Klein, Michael L.; Shi, Pei–Yong; Zhou, Jia; Li, Hongmin

doi:10.1016/j.antiviral.2022.105381

Cited by 28 publications

(27 citation statements)

References 62 publications

(77 reference statements)

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“…Recently, another study has shown that ebselen can bind not just to the catalytic site of SARS-CoV-2 M pro , but also to between the domains II and III of the protein, where it can act as an allosteric regulator 67 . In fact, allosteric inhibition of M pro is increasingly recognised as a promising treatment modality 68 . This led us to reconsider the in vitro binding results above ( Figure 2(h) ).…”

Section: Resultsmentioning

confidence: 99%

Ligand-based discovery of coronavirus main protease inhibitors using MACAW molecular embeddings

Dong

Varbanov

Philippot

et al. 2022

Journal of Enzyme Inhibition and Medicinal Chemistry

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Ligand-based drug design methods are thought to require large experimental datasets to become useful for virtual screening. In this work, we propose a computational strategy to design novel inhibitors of coronavirus main protease, M pro . The pipeline integrates publicly available screening and binding affinity data in a two-stage machine-learning model using the recent MACAW embeddings. Once trained, the model can be deployed to rapidly screen large libraries of molecules in silico . Several hundred thousand compounds were virtually screened and 10 of them were selected for experimental testing. From these 10 compounds, 8 showed a clear inhibitory effect on recombinant M pro , with half-maximal inhibitory concentration values (IC 50 ) in the range 0.18–18.82 μM. Cellular assays were also conducted to evaluate cytotoxic, haemolytic, and antiviral properties. A promising lead compound against coronavirus M pro was identified with dose-dependent inhibition of virus infectivity and minimal toxicity on human MRC-5 cells.

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Section: Resultsmentioning

confidence: 99%

Ligand-based discovery of coronavirus main protease inhibitors using MACAW molecular embeddings

Dong

Varbanov

Philippot

et al. 2022

Journal of Enzyme Inhibition and Medicinal Chemistry

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“…Importantly, combined treatment with sinefungin and IFN-I had an additive effect, resulting in increased attenuation, likely due to both a loss of viral 2’- O methylation and increased recognition of unmethylated viral RNA by IFIT1/IFIT3. This approach is distinct from those of other CoV therapies targeting the viral polymerase ( 42 ) or the main protease ( 43 ) to arrest virus replication. Targeting NSP16 similarly disrupts a viral enzymatic process, yet here, an effector response is provided by the host via IFIT proteins.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3

Schindewolf

Lokugamage

et al. 2022

Preprint

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Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2′-O methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2′-O MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2′-O methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, a methyltransferase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a possible target for future antiviral therapies.

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“…Desmond software was used to perform the MD simulations with the default energy minimizations and heating algorithm. The top docking pose of A9 and A14 was then solvated in orthorhombic box using TIP3P water model using OPLS3e force-field parameters [ 41 ]. The length of covalent bonds was constrained by the SHAKE algorithm The length of covalent bonds was constrained by the SHAKE algorithm [ 42 ].…”

Section: Methodsmentioning

confidence: 99%

Structurally Modified Bioactive Peptide Inhibits SARS-CoV-2 Lentiviral Particles Expression

et al. 2022

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Coronavirus disease 2019 (COVID-19), the current global pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Various pharmaceuticals are being developed to counter the spread of the virus. The strategy of repurposing known drugs and bioactive molecules is a rational approach. A previously described molecule, Ile-Arg-Trp (IRW), is a bioactive tripeptide that exhibits an ability to boost angiotensin converting enzyme-2 (ACE2) expression in animals and cells. Given the importance of SARS-CoV-2 S receptor binding domain (RBD)-ACE2 interaction in SARS-CoV-2 pathophysiology, we synthesized various IRW analogs intending to mitigate the RBD-ACE-2 interaction. Herein, we describe two analogs of IRW, A9 (Acetyl-Ile-Arg-Trp-Amide) and A14 (Formyl-Ile-Arg-Trp-Amide) which lowered the SARS-CoV-2 S RBD-ACE2 (at 50 µM) in vitro. The free energy of binding suggested that A9 and A14 interacted with the SARS-CoV-2 S RBD more favorably than ACE2. The calculated MMGBSA ΔG of spike binding for A9 was −57.22 kcal/mol, while that of A14 was −52.44 kcal/mol. A14 also inhibited furin enzymatic activity at various tested concentrations (25, 50, and 100 µM). We confirmed the effect of the two potent analogs using SARS-CoV-2 spike protein overexpressing cells. Both peptides lowered the protein expression of SARS-CoV-2 spike protein at the tested concentration (50 µM). Similarly, both peptides, A9 and A14 (50 µM), also inhibited pseudotyped lentiviral particles with SARS-CoV-2 Spike in ACE2 overexpressing cells. Further, the molecular dynamics (MD) calculations showed the interaction of A9 and A14 with multiple residues in spike S1 RBD. In conclusion, novel peptide analogs of ACE2 boosting IRW were prepared and confirmed through in vitro, cellular, and computational evaluations to be potential seed candidates for SARS-CoV-2 host cell binding inhibition.

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Allosteric inhibitors of the main protease of SARS-CoV-2

Cited by 28 publications

References 62 publications

Ligand-based discovery of coronavirus main protease inhibitors using MACAW molecular embeddings

Ligand-based discovery of coronavirus main protease inhibitors using MACAW molecular embeddings

SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3

Structurally Modified Bioactive Peptide Inhibits SARS-CoV-2 Lentiviral Particles Expression

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